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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..0a59cb5 --- /dev/null +++ b/README.md @@ -0,0 +1,116 @@ +# SpecDB: A Relational Database for archiving biomolecular NMR Spectra Data + +SpecDB is a relational database to store and distribute biomoleculae NMR experimental data. SpecDB stores the raw **F**ree **I**nduction **D**ecay (__fid__) from an NMR experiment in a structured way that matches __fid__ records to biomoleculae sample and experimental meta-data. + + +## Repository Organization + +``` +├── LICENSE +├── README.md +├── TUTORIAL.md +├── sample +│   ├── sample.db +│   ├── sample_forms/ +│   └── sample_sessions/ +├── specdb +│   ├── specdb +│   └── specdb.py +└── sql + ├── specdb.sql + └── template.str +``` + +Above is the tree layout for SpecDB's repository structure. + +* `sample/`: location of sample data for the tutorial + - `sample/sample.db`: sample SQLite SpecDB database + - `sample/sample_forms/`: contains example forms for different data types to enter into SpecDB + - `sample/sample_sessions`: contains example Bruker data collection sessions +* `specdb`: location of **specdb** python library and command line interface (__CLI__) + - `specdb/specdb`: the **specdb** CLI + - `specdb/specdb.py`: the **specdb** library. users will typically only interact with the CLI +* `sql/`: directory where the **SpecDB** SQLite schema resides + - `sql/specdb.sql`: the **SpecDB** SQLite schema definitions + - `template.str`: the minimal NMR-STAR file **SpecDB** attempts to write + +## Getting Started + +The goal of SpecDB is to capture and organize time domain data that is generated +from biomolecular NMR experiments. To make the time domain data useful for +downstream applications, the experiment's metadata such as protein sequence, +buffer information, the specific pulse sequence performed, and much more all +should be captured. The idea behind SpecDB is to provide users with a set of tools to enter sample and experiment metadata into a SQLite database. + +This _Getting Started_ guide will cover two common scenarios for users installing SpecDB. (1) on a machine where they have install permissions, and (2) if the user is on a shared cluster where they do not have install permissions. + + +To operate SpecDB on a machine where you do have install permissions, here are the steps we recommend. +1. clone this repository: `git clone https://github.rpi.edu/RPIBioinformatics/SpecDB.git` +2. to make SpecDB operate as a command line tool, the `PATH` environment variable needs to amended. `export PATH=$PATH:{location of SpecDB}/SpecDB/specdb/` + - if a bash profile file is being amended, be sure to `source` the profile after the `PATH` environment variable is edited +3. the required 3rd part modules for SpecDB are `pandas`, `ruamel.yaml`, and `pynmrstar`. do `pip3 install pandas ruamel.yaml pynmrstar` to download the three libraries +4. After the `pip install` SpecDB should be operational. Verify that SpecDB is on the `PATH` and libraries installed with `specdb --help`. The output should be the following: + +``` + +usage: specdb [-h] {create,forms,insert,summary,query,backup,restore} ... + +Command line tool for interfacing with SpecDB + +positional arguments: + {create,forms,insert,summary,query,backup,restore} + command description + create instantiate a new database + forms generate a template form for requested table tables to + generate forms for are: `user`, `project`, `target` + `construct`, `expression`, `batch`, `buffer`, `pst`, + `spectrometer`, and a JSON for a session + insert insert a single json file into SpecDB + summary make a summary report for SpecDB database. if ran with + no table provided, then a summary for every table is + made. + query query records from SpecDB summary table. If no + --output is given then results are simply print to + screen + backup perform incremental backup. specdb configure must be + ran first + restore perform database restoration from a SpecDB backup + +optional arguments: + -h, --help show this help message and exit + +example command lines: + specdb create --db my.db --backup /backups/my.backup.db + specdb query --db my.db --sql "SELECT * FROM table users LIMIT 10" + specdb insert --file specdb.yaml --env my.db --write + specdb backup --db my.db --backup /backups/my.backup.db + specdb forms --table user project --num 3 1 + specdb summary --table user --db my.db + +``` + +To operate SpecDB in a shared cluster without install permissions, it is first recommended to follow whatever standard operating procedures there are for software installation. If virtual environments are an option, the following steps work for SpecDB: +1. make a python virtual environment with `venv`. `python3 -m venv {name of your environment}` +2. to active the environment, `source {name of environment}/bin/activate` +3. perform the `pip install` described above +4. to exit the virtual environment do `deactivate {name of environment}` + +## Acknowledgements + +The functions to perform the incremental backup are taken from the following repository: https://github.com/nokibsarkar/sqlite3-incremental-backup.git. + + + + + + + + + + + + + + + diff --git a/TUTORIAL.md b/TUTORIAL.md new file mode 100644 index 0000000..29fc58c --- /dev/null +++ b/TUTORIAL.md @@ -0,0 +1,498 @@ +# SpecDB Tutorial + +The purpose of the following tutorial is to provide examples of how to use SpecDB. There are six levels to the tutorial. _(1)_ SpecDB subcommands and help menus. _(2)_ how to instantiate a database, _(3)_ how to make forms, _(4)_ how to insert forms, _(5)_ viewing what is in the database, _(6)_ updating records in the database, _(7)_ querying information from the database. + +## 1. SpecDB help menus and subcommands + +The first entry point to look for guidance on SpecDB functions is to use the help menus. If `specdb help` results in the help menu for SpecDB, then it is installed correctly. SpecDB has seven sub commands, each listed below and the command line arguments each take: + +1. `specdb create --db --backup` +2. `specdb forms --table --num` +3. `specdb insert --form --db` +4. `specdb summary --table --db` +5. `specdb query --sql --db --out` +6. `specdb backup --db --backup` +7. `specdb restore --backup --backup` + +The subcommands listed above in the logical order the commands are used in. Each subcommand has a separate help menu from `specdb --help` that can be accessed, (e.g `specdb forms --help`). Users first need to create a SpecDB SQLite database file with `create`. Next, users need to populate the database with information, the `forms` command make the forms for the data fields needed for the SpecDB schema. With a filled form, users use `insert` to insert insert the form into their database. To verify/check what they inserted, users can use `summary` to investigate the contents of any SpecDB table. Users can pull data out of the database with `query`. With `query` users provide a SQL SELECT statement on the SpecDB summary view to pull data out of the database. Commands `backup` and `restore` are for the incremental backup operations. + +## 2. Instantiating a new SpecDB database + +A SpecDB database can be created with `specdb create`. The location of the database .db file needs to be known by the users using the database, or an environment variable can be set. In this tutorial we are going to create a database for the sample data stored in this repository `./sample/`. + +``` +$ specdb create --db sample.db --backup sample.backup.db +``` + +## 3. Making forms + +Now that a database has been made, we can start adding data to the database. To add data we need to populate a text file form to be read into the database. SpecDB uses YAML to build forms. An example can be seen in `/sample/sample_forms/` + +Running `specdb forms --table user` results in the user form being printed to screen. The output should be exactly as seen below. + +``` +user: # provide information about a user, REQUIRED: `user_id` + user_id: '' # no spaces, must be unique, len <= 8, Ex: KJF + given_name: '' # len <= 64, Ex: Keith + family_name: '' # len <= 64, Ex: Fraga + middle_initials: '' # len <= 16, Ex: J + department_and_institution: '' # len <= 128, Ex: MCB UCD + country: '' # len <= 32, Ex: USA + state_province: '' # len <= 32, Ex: NY + city: '' # len <= 32, Ex: Troy + postal_code: '' # len <= 32, Ex: 12180 + role: '' # len <= 64, Ex: postdoc + organization_type: '' # len <= 64, Ex: academic + email_address: '' # no spaces, must have `@`, len <= 64, Ex: user@mail.com +``` + +To fill the form, the output of the `specdb forms` command can be redirected to any file. (Note: the file extension is not strict, tested with `txt`, `yaml`, `yml`. ) + +``` +$ specdb forms --table user > user.yml +``` + +Inspection of the resulting form shows that name of the table this form was created for was created for: `user`. On the same line lists the required items need to be filled into this form for insertion into SpecDB. All items not indicated as required are optional. (Note: optional SpecDB terms may be required for BMRB deposition however). + +In the `sample/sample_forms/` directory is a users yaml form pre filled out with some user information as an example. Each line in the form file has a comment describing the restrictions on allowable values for that data item, as a well as an example of what can be used for that respective field. Viewing the `sample/sample_forms/users.yaml` we see there are actually multiple users filled in. The `specdb forms` command has the `--num` option for specifying the number of forms to make for a requested table. In the case of `sample/sample_forms/users.yaml` we requested 3. To make the template to do something like `users.yaml` is: + +``` +$ specdb forms --table user --num 3 +user: # # provide information about a user, REQUIRED: `user_id` + 0: + user_id: '' # no spaces, must be unique, len <= 8, Ex: KJF + given_name: '' # len <= 64, Ex: Keith + family_name: '' # len <= 64, Ex: Fraga + middle_initials: '' # len <= 16, Ex: J + department_and_institution: '' # len <= 128, Ex: MCB UCD + country: '' # len <= 32, Ex: USA + state_province: '' # len <= 32, Ex: NY + city: '' # len <= 32, Ex: Troy + postal_code: '' # len <= 32, Ex: 12180 + role: '' # len <= 64, Ex: postdoc + organization_type: '' # len <= 64, Ex: academic + email_address: '' # no spaces, must have `@`, len <= 64, Ex: user@mail.com + 1: + user_id: '' # no spaces, must be unique, len <= 8, Ex: KJF + given_name: '' # len <= 64, Ex: Keith + family_name: '' # len <= 64, Ex: Fraga + middle_initials: '' # len <= 16, Ex: J + department_and_institution: '' # len <= 128, Ex: MCB UCD + country: '' # len <= 32, Ex: USA + state_province: '' # len <= 32, Ex: NY + city: '' # len <= 32, Ex: Troy + postal_code: '' # len <= 32, Ex: 12180 + role: '' # len <= 64, Ex: postdoc + organization_type: '' # len <= 64, Ex: academic + email_address: '' # no spaces, must have `@`, len <= 64, Ex: user@mail.com + 2: + user_id: '' # no spaces, must be unique, len <= 8, Ex: KJF + given_name: '' # len <= 64, Ex: Keith + family_name: '' # len <= 64, Ex: Fraga + middle_initials: '' # len <= 16, Ex: J + department_and_institution: '' # len <= 128, Ex: MCB UCD + country: '' # len <= 32, Ex: USA + state_province: '' # len <= 32, Ex: NY + city: '' # len <= 32, Ex: Troy + postal_code: '' # len <= 32, Ex: 12180 + role: '' # len <= 64, Ex: postdoc + organization_type: '' # len <= 64, Ex: academic + email_address: '' # no spaces, must have `@`, len <= 64, Ex: user@mail.com +``` + +This output can be redirected to any file and filled in the with appropriate information. + +Forms can be made for different tables to be in the same form. A very common use for this is inserting a buffer into SpecDB. There are two tables in the SpecDB schema that describe buffers, `buffer` and `buffer_components`. `buffer` provides the name of the buffer, the `buffer_id` and the buffer's pH. The `buffer_components` table allows for variable number of components to be added to the buffer. For example, if a buffer with 3 components needed to be added to SpecDB, the following command would generate the correct form: + +```$ specdb forms --table buffer buffer_components --num 1 3 + buffer components go in the `buffer_components` table + 0: + buffer_id: '' # text identifier for the buffer, must be unique, no spaces, len <= 32, Ex: hn4071 + buffer_ph: 0.0 # pH of buffer, must be a number, Ex: 8.1 + buffer_comment: '' # free text field for any notes about the buffer, len <= 128, Ex: made by KJF 12/04 +buffer_components: # describe the component(s) of a buffer, REQUIRED: `buffer_id`, `buffer_component`, `buffer_component_value`, `buffer_component_unit` + 0: + buffer_id: '' # `buffer_id` this component goes to, must already be in buffer table, Ex: hn4071 + buffer_component: '' # name of the component, len <= 64, Ex: NaCl + buffer_component_value: 0.0 # the numeric concentration value of the component, Ex: 100.0 + buffer_component_unit: '' # unit of concentration, one of (`mM`, `% (v/v)`, `mg/mL`), Ex: mM + 1: + buffer_id: '' # `buffer_id` this component goes to, must already be in buffer table, Ex: hn4071 + buffer_component: '' # name of the component, len <= 64, Ex: NaCl + buffer_component_value: 0.0 # the numeric concentration value of the component, Ex: 100.0 + buffer_component_unit: '' # unit of concentration, one of (`mM`, `% (v/v)`, `mg/mL`), Ex: mM + 2: + buffer_id: '' # `buffer_id` this component goes to, must already be in buffer table, Ex: hn4071 + buffer_component: '' # name of the component, len <= 64, Ex: NaCl + buffer_component_value: 0.0 # the numeric concentration value of the component, Ex: 100.0 + buffer_component_unit: '' # unit of concentration, one of (`mM`, `% (v/v)`, `mg/mL`), Ex: mM + +``` + +It is important to note that if the `--num` option is provided, that the number of iterations to take match the number of tables requested. In the above case, the `buffer` form was created once because of the `1` after the `--num` and three `buffer_components` were made because of the `3` after the `1` in the `--num` options. The number of options in `--table` and `--num` are in a one-to-one correspondence with each other. If no `--num` options are provided it is assumed that all tables are produced just once. + +Inspecting `sample/sample_forms/complete_sample.yaml` will find all the information required to describe a biomolecular NMR sample. It is recommended that users use `specdb forms` to create the forms they when they need because users can define multiple entities at a time, and one general form will not suffice. However, it is instructive to see all the metadata items that are tracked in SpecDB by looking at `complete_sample.yaml`. + +To follow along with the sample forms provided in the repository, perform the following commands: + +``` +$ specdb forms --table user --num 3 > user.yaml +$ specdb forms --table project > project.yaml +$ specdb forms --table buffer buffer_components --num 1 3 > buffer.yaml +$ specdb forms --table target construct expression purification_batch pst batch_components > sample.yaml +$ specdb forms --table spectrometer > spectrometer.yaml +$ specdb forms --table session > session.yaml +``` + +## 4. Inserting forms + +In this section, users can practice with the pre-filled forms in `sample/sample_forms/`. To first insert users in a group, the following insert command will insert the user information provided in `user.yaml`. + +``` +$ specdb insert --db sample.db --form user.yaml +information provided is new +{ + "user_id": "KJF", + "given_name": "Keith", + "family_name": "Fraga", + "middle_initials": "J", + "department_and_institution": "UC MCB", + "country": null, + "state_province": null, + "city": null, + "postal_code": null, + "role": null, + "organization_type": null, + "email_address": "kjfraga@ucdavis.edu" +} +Must set --write to insert provided information to database +Aborting +``` + +`sample.db` is the database created in section (2) of the tutorial. Running the above commnd results in a Aborting error. This means that SpecDB attempted the insert, but found that the requested information was new and could not complete the insertion. This check is in place to ensure users truly want to insert the requested information. Sometimes the provided information may be new, but new and unique because of a typo and the actual information being inserted is already in the database. To overwrite this check, the `--write` flag must be used. + +``` +$ specdb insert --db sample.db --form sample_forms/users.yaml --write +Inserted data from json file at /Users/kfraga/RESEARCH/SpecDB/code/sample/sample_forms/users.yaml +``` + +The last line indicates the data was inserted. Running the `specdb insert` command on the `buffers.yaml` with the `--write` flag results in the following. + +``` +$ specdb insert --db sample.db --form sample_forms/buffers.yaml --write +Inserted data from json file at /Users/kfraga/RESEARCH/SpecDB/code/sample/sample_forms/users.yaml +``` + +Now that the buffer is inserted, we can attempt to insert our information about a sample. To learn more about the relationships and definitions of each of the tables in the SpecDB manuscript refer to the manuscript. Each table, from `target` to `pst` needs to be inserted to fully describe a sample. However, typically for each table there is a subset of required data items, so not every data item is required for insertion. + + +``` +$ specdb insert --db sample.db --form sample_forms/sample.yaml --write +SQLite error on insert on table target +Err Message: +FOREIGN KEY constraint failed +check the template form for instructions and examples +ensure all ids this table relates to (i.e constructs relate to targets) are inserter already +Aborting +``` + +This insertion results in a different error from before. Here, the error was not because the information was new because the `--write` was on. The error is coming from SQLite that foreign key constraint failed. A foreign key is a relationship between two tables. These foreign keys need to be present in the two tables for SpecDB to allow an insert. The error message is not clear on what column the constrain failure came on, but it says the error came from the `target` table and to inspect the form for what is required for a target. Using `forms` we can see what is required for `target`. + +``` +$ specdb forms --table target +target: # molecular target information, REQUIRED: `target_id` + target_id: '' # text identifier for target, must be unique, no spaces, len <= 32, Ex: Db0515 + target_comment: '' # free field comment, anything to note about target, len <= 128, Ex: from UW-Madison + target_sequence: '' # target's molecular seq., any type of code/alphabet, no spaces, len <= 1024, Ex: MGSHHHHILVAM + organism_source: '' # organism name for target source, can indicate if target is synthetic, len <= 128, Ex: synthetic + gene_name: '' # gene name, len <= 64, Ex: SpikeCoV2 + project_id: '' # `project_id` target is a member of, must be in project table, Ex: SpikeFraga + target_preparer: '' # `user_id` that assigned the target, must be in user table, Ex: KJF +``` + +We there are relationships between the `user` table and the `project` table. Inspecting what we tried to add for the target in `sample.yaml` we see: + +``` +target: + target_id: Db0515 + target_comment: '' + target_sequence: MGPLIEVLA + organism_source: synthetic + gene_name: '' + project_id: DBh + target_preparer: GTM +``` + +We inserted the user information for `GTM` but not the project id `DBh` this target is associated with. We can solve this by inserting the project information using the `sample/sample_forms/project.yaml` form. + +``` +$ specdb insert --db sample.db --form project.yaml --write +Inserted data from json file at /Users/kfraga/RESEARCH/SpecDB/code/sample/sample_forms/project.yaml +``` + +Then re-doing the sample insert we get: + +``` +specdb insert --db sample.db --form sample.yaml --write +Inserted data from json file at /Users/kfraga/RESEARCH/SpecDB/code/sample/sample_forms/sample.yaml +``` + +To insert FIDs into SpecDB, we first need to insert the spectrometer information. + +``` +$ specdb insert --db sample.db --form spectrometer.yaml --write +Inserted data from json file at /Users/kfraga/RESEARCH/SpecDB/code/sample/sample_forms/spectrometer.yaml +``` + +Inserting FIDs into SpecDB are typically organized into sessions. When FIDs are recorded from a Bruker instrument, they are recorded into sub-directories of a data collection session directory. We mimiced this situation in `sample/sample_sessions/test00/`. In `test00/`, there are two subdirectories, each with a time domain dataset. There is also a `specdb.session.yaml`. This file can be creatd with `specdb forms --table session`. The session yaml describe thes spectrometer this data collection was at, the user who conducted the session, and the sample tube the data was collected at. Contents of this session is displayed below: + +``` +session: + session_preparer: TAR + spectrometer_id: Hu800 + pst_id: Db0515A.000 +``` + +All three items in this session are required. + +Performing the insert on this session yaml file results in: + +``` +$ specdb insert --db sample.db --form sample_sessions/test00/specdb.session.yaml --write +a ./1/uxnmr.par +a ./1/prosol_History +a ./1/pulseprogram +a ./1/format.temp +a ./1/audita.txt +a ./1/fid +a ./1/scon2 +a ./1/acqu +a ./1/acqus +a ./2/uxnmr.par +a ./2/prosol_History +a ./2/pulseprogram +a ./2/acqu2s +a ./2/format.temp +a ./2/audita.txt +a ./2/acqu2 +a ./2/cpdprg3 +a ./2/ser +a ./2/scon2 +a ./2/acqu +a ./2/acqus +Inserted data from form file at /Users/kfraga/RESEARCH/SpecDB/code/sample/sample_sessions/test00/specdb.session.yaml +``` + +SpecDB is finding what sub directories have time domain data, finding the parameter files, and inserting the time domain data into the database. The session yaml file changes, reflecting all the information the `specdb insert` found: + +``` +session: + session_preparer: TAR + spectrometer_id: Hu800 + pst_id: Db0515A.000 + folder_name: test00 +time_domain_data: + '1': + subdir_name: '1' + pulse_sequence_nickname: + probe_id: + session_id: 1 + md5checksum: f1d80ff78a50d207b4d3b13af239b839 + temperature_from_data: 293.0 + experiment_date: '2010-09-26 21:33:06.812' + pulse_sequence: zgpr + probe_info: 1.7_mm_CPTCI_1H-13C/15N/D_Z-GRD_Z108160/0002 + pst_id: Db0515A.000 + '2': + subdir_name: '2' + pulse_sequence_nickname: + probe_id: + session_id: 1 + md5checksum: e3c4e84d0ae67e8ca1160ebf6d5b6838 + temperature_from_data: 293.0 + experiment_date: '2010-09-26 22:16:43.706' + pulse_sequence: hsqcetf3gpsi + probe_info: 1.7_mm_CPTCI_1H-13C/15N/D_Z-GRD_Z108160/0002 + pst_id: Db0515A.000 +``` + +## 5. View what is in the database + +Each time we inserted a form into the database, we did not check that the provided information actually is stored in the database. If the `Inserted into` message comes up after the `insert` then no errors in the insert arrived. We can view a summary of the current entries in a table in the database by using the `specdb summary` command. With `summary` we need to provide the name of the table we want to summarize and in what database file we want to look into. + + +``` +$ specdb summary --table user --db sample.db + + id user_id given_name family_name middle_initial department_and country state_province city postal_code \ + 3 GTM Gaetano Montelione T None None None None None + 1 KJF Keith Fraga J UC MCB None None None None + 2 TAR Theresa Ramelot A None None None None None + + role organization_t email_address + None None monteg3@rpi.edu + None None kjfraga@ucdavis.edu + None None ramelt2@rpi.edu +``` + +A simple table is printed to screen of the current items in the database. Try it on any other table. + +## 6. Update a record in SpecDB + +It is often the case that information already in the database needs to be amended or added to. Suppose we want to update a user's information. The strategy is to pull out the information already in the database into a yaml form, edit the form, write it back to the database with the write flag. SpecDB detected when in a form, only a table id is provided, like `user_id`, and the rest of the items are blank. In that case, SpecDB understands that what is being requested is the rest of information for that user. We are going to use this functionality to update a record. + +First, make an empty user form. + +``` +$ specdb forms --table user > utest.yml +``` + +Add only the id of the user we want to edit. In this case we are changing `KJF`. Use any text editor you are comfortable. + +``` +cat utest.yml +user: # provide information about a user, REQUIRED: `user_id` + user_id: 'KJF' # no spaces, must be unique, len <= 8, Ex: KJF + given_name: '' # len <= 64, Ex: Keith + family_name: '' # len <= 64, Ex: Fraga + middle_initials: '' # len <= 16, Ex: J + department_and_institution: '' # len <= 128, Ex: MCB UCD + country: '' # len <= 32, Ex: USA + state_province: '' # len <= 32, Ex: NY + city: '' # len <= 32, Ex: Troy + postal_code: '' # len <= 32, Ex: 12180 + role: '' # len <= 64, Ex: postdoc + organization_type: '' # len <= 64, Ex: academic + email_address: '' # no spaces, must have `@`, len <= 64, Ex: user@mail.com +``` + +User `specdb insert` to pull the information for user `KJF` out from the database. + +``` +$ specdb insert --db sample.db --form utest.yml +Inserted data from json file at /Users/kfraga/RESEARCH/SpecDB/code/sample/utest.yml +$ cat utest.yml +user: + user_id: KJF + given_name: Keith + family_name: Fraga + middle_initials: J + department_and_institution: UC MCB + country: '' + state_province: '' + city: '' + postal_code: '' + role: '' + organization_type: '' + email_address: kjfraga@ucdavis.edu +``` + +Edit `utest.yml` to change the first name from Keith to Kevin. (Any example would suffice). Re-insert `utest.yml`. First without `--write`, then with. + +``` +$ specdb insert --db sample.db --form utest.yml +requested data is different than the database +input information: +{ + "user_id": "KJF", + "given_name": "Kevin", + "family_name": "Fraga", + "middle_initials": "J", + "department_and_institution": "UC MCB", + "country": null, + "state_province": null, + "city": null, + "postal_code": null, + "role": null, + "organization_type": null, + "email_address": "kjfraga@ucdavis.edu" +} +database information: +{ + "user_id": "KJF", + "given_name": "Keith", + "family_name": "Fraga", + "middle_initials": "J", + "department_and_institution": "UC MCB", + "country": null, + "state_province": null, + "city": null, + "postal_code": null, + "role": null, + "organization_type": null, + "email_address": "kjfraga@ucdavis.edu" +} +Aborting +$ specdb insert --db sample.db --form utest.yml --write +Inserted data from json file at /Users/kfraga/RESEARCH/SpecDB/code/sample/utest.yml +``` + +Using `summary`, we can see the change. + +``` +$ specdb summary --db sample.db --table user + + id user_id given_name family_name middle_initial department_and country state_province city postal_code \ + 3 GTM Gaetano Montelione T None None None None None + 4 KJF Kevin Fraga J UC MCB None None None None + 2 TAR Theresa Ramelot A None None None None None + + role organization_t email_address + None None monteg3@rpi.edu + None None kjfraga@ucdavis.edu + None None ramelt2@rpi.edu +``` + +## 7. Query information from SpecDB + +To query information from SpecDB, some FID data must be inserted first. The `specdb query` command only accepts queries against the summary view in the database (not to be confused with `specdb summary`). To view the contents of the summary view, we can use `specdb summary`. + +``` +$ specdb summary --db sample.db --table summary + + id experiment_dat pulse_sequence pulse_sequence md5checksum session_id session_prepar \ + 1 2010-09-26 21:33... None zgpr f1d80ff78a50d207... 1 TAR + 2 2010-09-26 22:16... None hsqcetf3gpsi e3c4e84d0ae67e8c... 1 TAR + + temperature buffer_id pst_id pst_preparer batch_id batch_preparer sample_sequenc expression_id \ + 293.0 h7.4n50 Db0515A.000 TAR Db0515A None GPLIEVLA Db0515A + 293.0 h7.4n50 Db0515A.000 TAR Db0515A None GPLIEVLA Db0515A + + expression_pre construct_id construct_prep target_id target_prepare target_sequenc project \ + TAR Db0515A KJF Db0515 GTM MGPLIEVLA DBh + TAR Db0515A KJF Db0515 GTM MGPLIEVLA DBh + + construct_sequ spectrometer_i field probe_id probehd tube_type zipped_dir + MGHHHHHHHSMGPLIEVLA Hu800 800 MHz None 1.7_mm_CPTCI_1H-... NMR tube b'\x1f\x8b\x08\x... + MGHHHHHHHSMGPLIEVLA Hu800 800 MHz None 1.7_mm_CPTCI_1H-... NMR tube b'\x1f\x8b\x08\x... +``` + +In this example we are going to query for FIDs produced from an HSQC. This can be accomplished with the following query: + +``` +specdb query --db sample.db --sql "SELECT * FROM summary WHERE pulse_sequence LIKE '%hsqc%'" --out results +/Users/kfraga/RESEARCH/SpecDB/code/sample/results/TAR_Db0515A.000_20100926 +``` + +The above command made a directory `results/` and put the query results in this folder. The naming of the subdirectories underneath `results` goes `{user_id}_{pst_id}_{date}`. Then underneath this results subdirectory is the FID that was found as a result of the query. Note that the whole directory the `ser` file was in was also saved, keeping the auxillary files that were made in during the `ser` file collection. + +To produce a NMR-STAR file for this result, just use the `--star` command to produce a STAR file in the directory where the `ser` file is. + + + + + + + + + + + + + + + + + + + diff --git a/sample/sample_forms/buffers.yaml b/sample/sample_forms/buffers.yaml new file mode 100644 index 0000000..0e2c5f5 --- /dev/null +++ b/sample/sample_forms/buffers.yaml @@ -0,0 +1,26 @@ +buffer: + '0': + buffer_id: h7.4n50 + buffer_ph: 7.4 + buffer_comment: +buffer_components: + '0': + buffer_id: h7.4n50 + buffer_component: HEPES + buffer_component_value: 20.0 + buffer_component_unit: mM + '1': + buffer_id: h7.4n50 + buffer_component: NaCl + buffer_component_value: 50.0 + buffer_component_unit: mM + '2': + buffer_id: h7.4n50 + buffer_component: NaN3 + buffer_component_value: 0.02 + buffer_component_unit: '% (v/v)' + '3': + buffer_id: h7.4n50 + buffer_component: D20 + buffer_component_value: 10.0 + buffer_component_unit: '% (v/v)' diff --git a/sample/sample_forms/complete_sample.yaml b/sample/sample_forms/complete_sample.yaml new file mode 100644 index 0000000..85b196a --- /dev/null +++ b/sample/sample_forms/complete_sample.yaml @@ -0,0 +1,94 @@ +user: # provide information about a user, REQUIRED: `user_id` + user_id: '' # no spaces, must be unique, len <= 8, Ex: KJF + given_name: '' # len <= 64, Ex: Keith + family_name: '' # len <= 64, Ex: Fraga + middle_initials: '' # len <= 16, Ex: J + department_and_institution: '' # len <= 128, Ex: MCB UCD + country: '' # len <= 32, Ex: USA + state_province: '' # len <= 32, Ex: NY + city: '' # len <= 32, Ex: Troy + postal_code: '' # len <= 32, Ex: 12180 + role: '' # len <= 64, Ex: postdoc + organization_type: '' # len <= 64, Ex: academic + email_address: '' # no spaces, must have `@`, len <= 64, Ex: user@mail.com +project: # provide information describing a project, REQUIRED: `project_id` + structural_genomics: '' # not required, only yes or no + project_id: '' # required, must be unique, no spaces, len <= 32, Ex: SpikeFraga + project_details: '' # not required, short description, len <= 128, Ex: Spike protein project 2022 +target: # molecular target information, REQUIRED: `target_id` + target_id: '' # text identifier for target, must be unique, no spaces, len <= 32, Ex: Db0515 + target_comment: '' # free field comment, anything to note about target, len <= 128, Ex: from UW-Madison + target_sequence: '' # target's molecular seq., any type of code/alphabet, no spaces, len <= 1024, Ex: MGSHHHHILVAM + organism_source: '' # organism name for target source, can indicate if target is synthetic, len <= 128, Ex: synthetic + gene_name: '' # gene name, len <= 64, Ex: SpikeCoV2 + project_id: '' # `project_id` target is a member of, must be in project table, Ex: SpikeFraga + target_preparer: '' # `user_id` that assigned the target, must be in user table, Ex: KJF +construct: # molecular construct from a target, REQUIRED: `construct_id`, `construct_sequence`, `target_id` + construct_id: '' # text identifier for construct, must be unique, no spaces, len <= 32, Ex: Db0515A + construct_sequence: '' # construct sequence, any type of code/alphabet, no spaces, len <= 1024, Ex: MGSHHHINLVAE + target_id: '' # `target id` this construct was made for, must already be in target table, Ex: Db0515 + ext_coefficient_280: 0.0 # extinction coefficient at 280 nm, Ex: 108.7 + expected_mw: 0.0 # expected molecular weight of construct in Da, Ex: 1211.8 + construct_comment: '' # free field comment, anything to note about construct, len <= 128, Ex: with primers RE1A/RE1B + plasmid_id: '' # plasmid construct DNA sequence is cloned in, len <= 64, Ex: pET218(+) + plasmid_id_comment: '' # comments on plasmid, len <= 256, Ex: from Underwood lab + construct_preparer: '' # `user_id` who prepared the construct, must already be in user table, Ex: KJF + construct_company: '' # if the construct was produced by a company, indicate where it came from, len <= 128, Ex: Genscript +expression: # describe a molecular expression experiment/results, REQUIRED: `expression_id`, `construct_id` + expression_id: '' # text identifier for expression, must be unique, no spaces, len <= 32, Ex: Db0515A.X + expression_comment: '' # free field comment, anything of note for expression, len <= 128, Ex: reached 4.5 OD + construct_id: '' # `construct_id` this expression was for, must already be in construct table, Ex: Db0515A + expression_media: '' # growth media expression was in, len <= 32, Ex: MJ9 + strain: '' # cellular strain expression was in, len <= 32, Ex: BL21A (+) + expression_organism: '' # organism expression was in, len <- 32, Ex: E. colli + expression_preparer: '' # `user_id` of person who did the expression, must already be in user table, Ex: KJF +purification_batch: # describe the purification run for an expression product, REQUIRED: `batch_id`, `expression_id`, `sample_sequence` + batch_id: '' # text identifier for batch, must be unique, no spaces, len <= 32, Ex: Db0515.X.batch + expression_id: '' # expression run this purification batch is for, must already be in expression table Ex: Db0515.X + sample_sequence: '' # sequence of molecule after purification (i.e if there was tag cleaving), any type of code/alphabet, no spaces, len <= 1024, Ex: MQNGPILA + purif_comment: '' # free text comment about the purification, len <= 128, Ex: HPLC in RM 204 + production_method: '' # indicate the purification method, len <= 64, Ex: Ni column only + isotopic_labeling_remark: '' # provide the isotopic labeling, preferred method to indicate labeling in the appropriate column below, len <= 64, Ex: NC5 + iso_13c_enrichment: '' # 13C labeling percentage, must contain `% 13C`, len <= 32, Ex: 100% 13C + iso_15n_enrichment: '' # 15N labeling percentage, must contain `% 15N`, len <= 32, Ex: 99% 15N + iso_2h_enrichment: '' # 2H labeling percentage, must contain `% 2H`, len <= 32, Ex: 100% 2H + iso_19f_Trp_enrichment: '' # 19F-Trp labeling percentage, must contain `% 19F-Trp`, len <= 32, Ex: 11% 19F-Trp + iso_19f_Phe_enrichment: '' # 19F-Phe labeling percentage, must contain `% 19F-Phe`, len <= 32, Ex: 9.1% 19F-Phe + iso_1hd1_Leu_methyl_enrichment: '' # 1HD1-Leu stereospecific labeling percentage, must contain `% 1HD1-Leu`, len <= 32, Ex: 13.3% 1HD1-Leu + iso_1hd2_Leu_methyl_enrichment: '' # 1HD2-Leu stereospecific labeling percentage, must contain `% 1HD2-Leu`, len <= 32, Ex: 15% 1HD2-Leu + iso_1hd_Ile_methyl_enrichment: '' # 1HD-Ile labeling percentage, must contain `% 1HD-Ile`, len <= 32, Ex: 50% 1HD-Ile + iso_1hg1_Val_methyl_enrichment: '' # 1HG1-Val stererospecific labeling percentage, must contain `% 1HG1-Val`, len <= 32, Ex: 25% 1HG1-Val + iso_1hg2_Val_methyl_enrichment: '' # 1HG2-Val stereospecific labeling percentage, must contain `% 1HG2-Val`, len <= 32, Ex: 27%% 1HG2-Val + iso_1hb_Ala_methyl_enrichment: '' # 1HB-Ala labeling percentage, must contain `% 1HB-Ala`, len <= 32, Ex: 100% 1HB-Ala + batch_preparer: '' # `user_id` of person who did the purification, must already be in user table, Ex: KJF +buffer: # store all buffers used, their id and their pH, REQUIRED: `buffer_id`, `buffer_pH`, NOTE: the buffer components go in the `buffer_components` table + buffer_id: '' # text identifier for the buffer, must be unique, no spaces, len <= 32, Ex: hn4071 + buffer_ph: 0.0 # pH of buffer, must be a number, Ex: 8.1 + buffer_comment: '' # free text field for any notes about the buffer, len <= 128, Ex: made by KJF 12/04 +buffer_components: # describe the component(s) of a buffer, REQUIRED: `buffer_id`, `buffer_component`, `buffer_component_value`, `buffer_component_unit` + buffer_id: '' # `buffer_id` this component goes to, must already be in buffer table, Ex: hn4071 + buffer_component: '' # name of the component, len <= 64, Ex: NaCl + buffer_component_value: 0.0 # the numeric concentration value of the component, Ex: 100.0 + buffer_component_unit: '' # unit of concentration, one of (`mM`, `% (v/v)`, `mg/mL`), Ex: mM +pst: # description of a protein sample tube, not only proteins, REQUIRED: `pst_id`, `pst_preparer`, `sample_ph`, `total_volume`, `volume_unit`, `tube_type` + pst_id: '' # text identifier for the pst, must be unique, no spaces, len <= 32, Ex: Db0515A.001 + prev_pst_id: '' # if pst derived from another pst, give previous `pst_id`, must already be in pst table, Ex: Db0515A.000 + pst_preparer: '' # `user_id` of user that prepared the sample tube, must be in user table, Ex: KJF + pst_comment: '' # free field comment about pst, len <= 128, Ex: new sample + sample_type: '' # is sample a solution or solid-state sample, one of (`solution`, `solid state`), Ex: solution + solvent_system: '' # solvent system for the sample, len <= 64, Ex: DMSO + sample_ph: 0.0 # pst pH, can be different from buffer ph, Ex: 7.1 + total_volume: 0.0 # numeric volume for total volume in tube, Ex: 2.2 + volume_unit: '' # unit of volume for volume in tube, one of (`nL`, `uL`, `mL`, `L`), Ex: mL + curr_location: '' # current location of tube, len <= 64, Ex: NMR room + prev_location: '' # previous location of tube, len <= 64, Ex: Underwood lab + create_date: '' # date record added to database, format "YYYY-MM-DD", Ex: 2022-01-01 + buffer_id: '' # id of buffer in the tube, must already be in `buffer` table, no spaces, len <= 32, Ex: hn4071 + tube_type: '' # the tube type for sample tube, use `specdb summary --table tubes` to find allowable tube types, Ex: 1-mm Shigemi tube +batch_components: # describe the purification batches in a pst, REQUIRED: `pst_id`, `batch_id`, `volume`, `volume_unit`, `conc`, `conc_unit` + pst_id: '' # text id of sample tube being described, must already be in pst table, Ex: Db0515A.001 + batch_id: '' # text id of batch in the `pst_id` above, must already be in purification_batch table, Ex: Db0515A.X.batch + conc: 0.0 # concentration of sample in the sample tube, numeric, Ex: 10.2 + conc_unit: '' # concentration units, one of (`ug/mL`, `mg/mL`, `nM`, `uM`, `mM`), Ex: mM + mass: 0.0 # mg of protein sample in tube, Ex: 101.1 + diff --git a/sample/sample_forms/project.yaml b/sample/sample_forms/project.yaml new file mode 100644 index 0000000..82efa3d --- /dev/null +++ b/sample/sample_forms/project.yaml @@ -0,0 +1,4 @@ +project: + structural_genomics: no + project_id: DBh + project_details: BakerLab hallunicated protein project diff --git a/sample/sample_forms/sample.yaml b/sample/sample_forms/sample.yaml new file mode 100644 index 0000000..2f004ec --- /dev/null +++ b/sample/sample_forms/sample.yaml @@ -0,0 +1,67 @@ +target: + target_id: Db0515 + target_comment: '' + target_sequence: MGPLIEVLA + organism_source: synthetic + gene_name: '' + project_id: DBh + target_preparer: GTM +construct: + construct_id: Db0515A + construct_sequence: MGHHHHHHHSMGPLIEVLA + target_id: Db0515 + ext_coefficient_280: 0.0 + expected_mw: 0.0 + construct_comment: '' + plasmid_id: '' + plasmid_id_comment: '' + construct_preparer: KJF + construct_company: '' +expression: + expression_id: Db0515A + expression_comment: '' + construct_id: Db0515A + expression_media: MJ9 + strain: '' + expression_organism: '' + expression_preparer: TAR +purification_batch: + batch_id: Db0515A + expression_id: Db0515A + sample_sequence: GPLIEVLA + purif_comment: '' + production_method: Ni column + isotopic_labeling_remark: NC + iso_13c_enrichment: '' + iso_15n_enrichment: '' + iso_2h_enrichment: '' + iso_19f_Trp_enrichment: '' + iso_19f_Phe_enrichment: '' + iso_1hd1_Leu_methyl_enrichment: '' + iso_1hd2_Leu_methyl_enrichment: '' + iso_1hd_Ile_methyl_enrichment: '' + iso_1hg1_Val_methyl_enrichment: '' + iso_1hg2_Val_methyl_enrichment: '' + iso_1hb_Ala_methyl_enrichment: '' + batch_preparer: '' +pst: + pst_id: Db0515A.000 + prev_pst_id: '' + pst_preparer: TAR + pst_comment: '' + sample_type: solution + solvent_system: D20 + sample_ph: 6.1 + total_volume: 2.0 + volume_unit: mL + curr_location: '' + prev_location: '' + create_date: '' + buffer_id: h7.4n50 + tube_type: NMR tube +batch_components: + pst_id: Db0515A.000 + batch_id: Db0515A + conc: 10.0 + conc_unit: mM + mass: 0.0 diff --git a/sample/sample_forms/spectrometer.yaml b/sample/sample_forms/spectrometer.yaml new file mode 100644 index 0000000..b61698c --- /dev/null +++ b/sample/sample_forms/spectrometer.yaml @@ -0,0 +1,7 @@ +spectrometer: + spectrometer_id: Hu800 + manufacturer: Bruker + model: Avance III + serial_number: '' + field_strength: 800 MHz + spectrometer_comment: '' diff --git a/sample/sample_forms/users.yaml b/sample/sample_forms/users.yaml new file mode 100644 index 0000000..3c98728 --- /dev/null +++ b/sample/sample_forms/users.yaml @@ -0,0 +1,40 @@ +user: + '0': + user_id: KJF + given_name: Keith + family_name: Fraga + middle_initials: J + department_and_institution: UC MCB + country: + state_province: + city: + postal_code: + role: + organization_type: + email_address: kjfraga@ucdavis.edu + '1': + user_id: TAR + given_name: Theresa + family_name: Ramelot + middle_initials: A + department_and_institution: + country: + state_province: + city: + postal_code: + role: + organization_type: + email_address: ramelt2@rpi.edu + '2': + user_id: GTM + given_name: Gaetano + family_name: Montelione + middle_initials: T + department_and_institution: + country: + state_province: + city: + postal_code: + role: + organization_type: + email_address: monteg3@rpi.edu diff --git a/sample/sample_sessions/test00/.DS_Store b/sample/sample_sessions/test00/.DS_Store new file mode 100644 index 0000000..011ed9e Binary files /dev/null and b/sample/sample_sessions/test00/.DS_Store differ diff --git a/sample/sample_sessions/test00/1/acqu b/sample/sample_sessions/test00/1/acqu new file mode 100644 index 0000000..6ff6bac --- /dev/null +++ b/sample/sample_sessions/test00/1/acqu @@ -0,0 +1,405 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 22 $$ 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+##$SFO6= 600.132850476506 +##$SFO7= 600.132850476506 +##$SFO8= 600.132850476506 +##$SOLVENT= +##$SP= (0..31) +1 86.27 80.25 6.83 4.69 0 75.92 6.83 120 0 51.32 51.32 0 0 8.31 0 150 150 +12.22 78.21 76.3 79.60999 72.28999 150 150 150 150 150 150 40.1 150 14.33 +##$SP07= 0 +##$SPECTR= 0 +##$SPNAM0= +##$SPNAM1= +##$SPNAM10= +##$SPNAM11= +##$SPNAM12= +##$SPNAM13= +##$SPNAM14= +##$SPNAM15= < > +##$SPNAM16= +##$SPNAM17= +##$SPNAM18= +##$SPNAM19= +##$SPNAM2= +##$SPNAM20= +##$SPNAM21= +##$SPNAM22= +##$SPNAM23= +##$SPNAM24= +##$SPNAM25= +##$SPNAM26= +##$SPNAM27= +##$SPNAM28= +##$SPNAM29= +##$SPNAM3= +##$SPNAM30= +##$SPNAM31= +##$SPNAM4= +##$SPNAM5= +##$SPNAM6= +##$SPNAM7= +##$SPNAM8= < > +##$SPNAM9= +##$SPOAL= (0..31) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$SPOFFS= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$SUBNAM0= <""> +##$SUBNAM1= <""> +##$SUBNAM2= <""> +##$SUBNAM3= 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+##END= diff --git a/sample/sample_sessions/test00/1/audita.txt b/sample/sample_sessions/test00/1/audita.txt new file mode 100644 index 0000000..21d18cf --- /dev/null +++ b/sample/sample_sessions/test00/1/audita.txt @@ -0,0 +1,23 @@ +##TITLE= Audit trail, TOPSPIN Version 2.1 +##JCAMPDX= 5.01 +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/audita.txt +##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT) +( 1,<2010-09-26 22:15:17.520 -0400>,,,,, + ) +( 2,<2010-09-26 22:15:23.238 -0400>,,,,, + ) +##END= + +$$ hash MD5 +$$ 8F 44 24 67 FF 89 A5 C0 B5 C3 70 80 28 EE EA 32 diff --git a/sample/sample_sessions/test00/1/fid b/sample/sample_sessions/test00/1/fid new file mode 100644 index 0000000..56c7f35 Binary files /dev/null and b/sample/sample_sessions/test00/1/fid differ diff --git a/sample/sample_sessions/test00/1/format.temp b/sample/sample_sessions/test00/1/format.temp new file mode 100644 index 0000000..99d85f7 --- /dev/null +++ b/sample/sample_sessions/test00/1/format.temp @@ -0,0 +1,181 @@ +EDIT_PAR COMMAND FILE + +DI_MODE LONG +ED_ENTRY ACQU +ORDER FILE + + +HEADER "F2 - Acquisition Parameters" +T_NAME Date_ + TYPE R64 + CLASS ACQU + SUBRANGE 0.0 50000000 + REL "Date_=itodate(DATE)" + INV_REL "DATE=datetoi(Date_,DATE)" + FORMAT "%14.0f" + TEXT " " +END +T_NAME Time + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000000 + REL "Time=itotime(DATE)" + INV_REL "DATE=timetoi(Time,DATE)" + FORMAT "%14.2f" + TEXT " " +END +NAME INSTRUM + TEXT " " +END +NAME PROBHD + FORMAT "%14.14s" + TEXT " " +END +NAME PULPROG + TEXT " " +END +NAME TD + TEXT " " +END +NAME SOLVENT + TEXT " " +END +NAME NS + TEXT " " +END +NAME DS + TEXT " " +END +T_NAME SWH + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e8 + REL "SWH=SW*SFO1" + INV_REL "SW=SWH/SFO1" + UNIT "Hz" + FORMAT "%14.3f Hz" + TEXT " " +END +T_NAME FIDRES + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 100000 + REL "FIDRES=SW*SFO1/TD" + INV_REL "TD = nextpow(SW*SFO1/FIDRES)" + UNIT "Hz" + FORMAT "%14.6f Hz" + TEXT " " +END +T_NAME AQ + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000 + REL "AQ=aqcalc(SW,SFO1,TD,DIGTYP)" + INV_REL "TD=tdcalc(SW,SFO1,1.0e6*AQ,DIGTYP)" + UNIT "sec" + FORMAT "%14.7f sec" + TEXT " " +END +NAME RG + TEXT " " +END +T_NAME DW + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000000 + REL "DW=1/(2*SW*SFO1)" + INV_REL "SW=1000000/(2*(0.005+DW)*SFO1)" + UNIT "usec" + FORMAT "%14.3lf usec" + TEXT " " +END +NAME DE + FORMAT "%14.2f usec" + TEXT " " +END +NAME TE + FORMAT "%14.1f K" + TEXT " " +END +T_NAME D1 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D1=D[1]" + INV_REL "D[1]=D1" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D12 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D12=D[12]" + INV_REL "D[12]=D12" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +NAME TD0 + TEXT " " +END +HEADER "======== CHANNEL f1 ========" +NAME NUC1 + NONEDIT + TEXT " " +END +T_NAME P1 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P1=P[1]" + INV_REL "P[1]=P1" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END +T_NAME PL1 + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL1=PL[1]" + INV_REL "PL[1]=PL1" + UNIT "dB" + FORMAT "%14.2f dB" + TEXT " " +END +T_NAME PL9 + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL9=PL[9]" + INV_REL "PL[9]=PL9" + UNIT "dB" + FORMAT "%14.2f dB" + TEXT " " +END +T_NAME PL1W + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL1W=63.8*pow(10.0,(-6-PL[1])/10.0)" + INV_REL "PL[1]=-6-4.3425*log(PL1W/63.8)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +T_NAME PL9W + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL9W=63.8*pow(10.0,(-6-PL[9])/10.0)" + INV_REL "PL[9]=-6-4.3425*log(PL9W/63.8)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +NAME SFO1 + FORMAT "%14.7f MHz" + TEXT " " +END diff --git a/sample/sample_sessions/test00/1/pdata/1/1i b/sample/sample_sessions/test00/1/pdata/1/1i new file mode 100644 index 0000000..565511a Binary files /dev/null and b/sample/sample_sessions/test00/1/pdata/1/1i differ diff --git a/sample/sample_sessions/test00/1/pdata/1/1r b/sample/sample_sessions/test00/1/pdata/1/1r new file mode 100644 index 0000000..be37f53 Binary files /dev/null and b/sample/sample_sessions/test00/1/pdata/1/1r differ diff --git a/sample/sample_sessions/test00/1/pdata/1/auditp.txt b/sample/sample_sessions/test00/1/pdata/1/auditp.txt new file mode 100644 index 0000000..fd08300 --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/auditp.txt @@ -0,0 +1,36 @@ +##TITLE= Audit trail, TOPSPIN Version 2.1 +##JCAMPDX= 5.01 +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/pdata/1/auditp.txt +##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT) +( 1,<2010-09-26 22:15:17.520 -0400>,,,,, + ) +( 2,<2010-09-26 22:15:23.238 -0400>,,,,, + ) +( 3,<2010-09-27 14:01:20.501 -0400>,,,,, + ) +( 4,<2010-09-27 14:01:36.356 -0400>,,,,, + ) +( 5,<2010-09-27 14:01:54.938 -0400>,,,,, + ) +##END= + +$$ hash MD5 +$$ 29 B2 63 CE 55 78 52 80 5E D3 65 71 93 69 5A 55 diff --git a/sample/sample_sessions/test00/1/pdata/1/base_info b/sample/sample_sessions/test00/1/pdata/1/base_info new file mode 100644 index 0000000..2d5531f --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/base_info @@ -0,0 +1,8 @@ +0 +982 +30218 +-1.033667E06 +-1.109416E01 +0.000000E00 +0.000000E00 +0.000000E00 diff --git a/sample/sample_sessions/test00/1/pdata/1/intrng b/sample/sample_sessions/test00/1/pdata/1/intrng new file mode 100644 index 0000000..1e58cc4 --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/intrng @@ -0,0 +1,9 @@ +P 0 +8.923863 7.841310 +5.944642 4.705623 +4.705134 3.597644 +3.597155 3.430910 +3.348276 2.511180 +2.469619 2.160108 +2.159619 1.141609 +1.141120 0.440932 diff --git a/sample/sample_sessions/test00/1/pdata/1/outd b/sample/sample_sessions/test00/1/pdata/1/outd new file mode 100644 index 0000000..896b602 --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/outd @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-24 16:07:31.492 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/prog/curdir/changer/inmrchanger/Sep24-2010-1606-micro_screening/11/data/nmr/HR4762D.007_1D_1H/1/pdata/1/outd +$$ process /opt/topspin2.1/prog/mod/xwish3 +##$CURPLOT= +##$CURPRIN= <$hp-laserjet-1300-1> +##$DFORMAT= +##$LAYOUT= +##$LFORMAT= +##$PFORMAT= +##$SURQMSG= 1 +##END= diff --git a/sample/sample_sessions/test00/1/pdata/1/parm.txt b/sample/sample_sessions/test00/1/pdata/1/parm.txt new file mode 100644 index 0000000..e81a2d8 --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/parm.txt @@ -0,0 +1,38 @@ +NAME HR4762D.007_1D_1H +EXPNO 1 +PROCNO 1 +Date_ 20100926 +Time 22.15 +INSTRUM spect +PROBHD 1.7 mm CPTCI 1 +PULPROG zgpr +TD 8192 +SOLVENT H2O+D2O +NS 1024 +DS 2 +SWH 9615.385 Hz +FIDRES 1.173753 Hz +AQ 0.4260860 sec +RG 181 +DW 52.000 usec +DE 6.50 usec +TE 293.0 K +D1 2.00000000 sec +D12 0.00002000 sec +TD0 1 + +======== CHANNEL f1 ======== +NUC1 1H +P1 12.00 usec +PL1 17.50 dB +PL9 69.90 dB +PL1W 0.28498414 W +PL9W 0.00000164 W +SFO1 600.1328182 MHz +SI 32768 +SF 600.1299044 MHz +WDW EM +SSB 0 +LB 2.00 Hz +GB 0 +PC 1.00 diff --git a/sample/sample_sessions/test00/1/pdata/1/peaklist.xml b/sample/sample_sessions/test00/1/pdata/1/peaklist.xml new file mode 100644 index 0000000..7929c94 --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/peaklist.xml @@ -0,0 +1,474 @@ + + + + + F1=12.866ppm, F2=-3.156ppm, MI=0.00cm, MAXI=10000.00cm, PC=1.000 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/sample/sample_sessions/test00/1/pdata/1/peaks b/sample/sample_sessions/test00/1/pdata/1/peaks new file mode 100644 index 0000000..1bdd480 Binary files /dev/null and b/sample/sample_sessions/test00/1/pdata/1/peaks differ diff --git a/sample/sample_sessions/test00/1/pdata/1/proc b/sample/sample_sessions/test00/1/pdata/1/proc new file mode 100644 index 0000000..b6a78b5 --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/proc @@ -0,0 +1,110 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 14 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 14:01:36.143 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/pdata/1/proc +$$ process /opt/topspin2.1/prog/mod/dataserver +##$ABSF1= 10 +##$ABSF2= 0 +##$ABSG= 0 +##$ABSL= 3 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= +##$AXLEFT= 0 +##$AXNAME= <> +##$AXNUC= +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.1 +##$BCFW= 1 +##$BC_mod= 2 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 2 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 32768 +##$FT_mod= 4 +##$GAMMA= 1 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 2 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 0 +##$MEAN= 0 +##$ME_mod= 0 +##$MI= 0 +##$NCOEF= 0 +##$NC_proc= 0 +##$NLEV= 6 +##$NOISF1= 8.174992 +##$NOISF2= 6.675002 +##$NSP= 1 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 12.86633 +##$PC= 1 +##$PHC0= -41.2 +##$PHC1= 0 +##$PH_mod= 0 +##$PKNL= yes +##$PPARMOD= 0 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 4 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 600.129904433336 +##$SI= 32768 +##$SIGF1= 5.6 +##$SIGF2= 5.2 +##$SINO= 400 +##$SIOLD= 32768 +##$SPECTYP= <> +##$SREGLST= <1H.H2O+D2O> +##$SSB= 2 +##$STSI= 0 +##$STSR= 0 +##$SW_p= 9615.38461538459 +##$SYMM= 0 +##$S_DEV= 0 +##$TDeff= 16384 +##$TDoff= 0 +##$TI= +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 1 +##$XDIM= 8192 +##$YMAX_p= 0 +##$YMIN_p= 0 +##END= diff --git a/sample/sample_sessions/test00/1/pdata/1/procs b/sample/sample_sessions/test00/1/pdata/1/procs new file mode 100644 index 0000000..7afc3a7 --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/procs @@ -0,0 +1,112 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 13 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 14:01:54.938 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/pdata/1/procs +$$ process /opt/topspin2.1/prog/mod/proc1d +##$ABSF1= 0 +##$ABSF2= 0 +##$ABSG= 0 +##$ABSL= 0 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= +##$AXLEFT= 0 +##$AXNAME= <> +##$AXNUC= <1H> +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.1 +##$BCFW= 0 +##$BC_mod= 0 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 0 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 32768 +##$FT_mod= 6 +##$GAMMA= 0 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 2 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 0 +##$MEAN= 0 +##$ME_mod= 0 +##$MI= 0 +##$NCOEF= 0 +##$NC_proc= 2 +##$NLEV= 6 +##$NOISF1= 8.174992 +##$NOISF2= 6.675002 +##$NSP= 0 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 12.86633 +##$PC= 1 +##$PHC0= -41.2 +##$PHC1= 0 +##$PH_mod= 1 +##$PKNL= yes +##$PPARMOD= 0 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 4 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 600.129904433336 +##$SI= 32768 +##$SIGF1= 5.6 +##$SIGF2= 5.2 +##$SINO= 400 +##$SIOLD= 32768 +##$SPECTYP= <> +##$SREGLST= <1H.H2O+D2O> +##$SSB= 0 +##$STSI= 32768 +##$STSR= 0 +##$SW_p= 9615.38461538459 +##$SYMM= 0 +##$S_DEV= 0 +##$TDeff= 8192 +##$TDoff= 0 +##$TI= +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 1 +##$XDIM= 8192 +##$YMAX_p= 450832046 +##$YMIN_p= -1384636 +##END= diff --git a/sample/sample_sessions/test00/1/pdata/1/title b/sample/sample_sessions/test00/1/pdata/1/title new file mode 100644 index 0000000..e0608a5 --- /dev/null +++ b/sample/sample_sessions/test00/1/pdata/1/title @@ -0,0 +1,3 @@ +HR4762D.007 1D proton +ZGPRMS H2O+D2O /opt/topspin2.1 micro_screening 11 +Clear \ No newline at end of file diff --git a/sample/sample_sessions/test00/1/prosol_History b/sample/sample_sessions/test00/1/prosol_History new file mode 100644 index 0000000..b1d9b9f --- /dev/null +++ b/sample/sample_sessions/test00/1/prosol_History @@ -0,0 +1,173 @@ +#******************************************************************* +# +# $Source: /sc/CvsTree/sc/gen/src/prg/scripts/tix/prosol/lib/lists/default,v $ +# +# Copyright (c) 1999 +# BRUKER ANALYTIK GMBH +# D-76287 Rheinstetten, Germany +# +# All Rights Reserved +# +# +# $Id: default,v 1.15.2.2 2007/12/14 16:22:31 ber Exp $ +# +#******************************************************************* +#../conf/instr/spect/prosol/relations/default +#avance-version (07/12/14) +# +#pulses +# +P[0]=P90[F1]; # 90 deg pulse F1 +P[1]=P90[F1]; # 90 deg pulse F1 +P[2]=P90[F1]*2; # 180 deg pulse F1 +P[3]=P90[F2]; # 90 deg pulse F2 +P[4]=P90[F2]*2; # 180 deg pulse F2 +P[5]=PTOC[F1]*0.66; # 60 deg pulse F1, TOCSY +P[6]=PTOC[F1]; # 90 deg pulse F1, TOCSY +P[7]=PTOC[F1]*2; # 180 deg pulse F1, TOCSY +P[8]=PSH3[F1]; # 90 deg selective F1, WET +P[9]=PTOC[F2]; # 90 deg pulse F2, TOCSY +P[10]=PTOC[F2]*2; # 180 deg pulse F2, TOCSY +P[11]=PSH1[F1]; # 90 deg selective F1 +P[12]=PSH2[F1]; # 180 deg selective F1 +# +P[14]=PSH3[F2]; # 180 deg inversion, adiabatic +P[15]=TROE[F1]; # cw pulse F1, ROESY +P[18]=PSH7[F1]; # off-resonance presat F1 +P[21]=P90[F3]; # 90 deg pulse F3 +P[22]=P90[F3]*2; # 180 deg pulse F3 +P[23]=P90[F4]; # 90 deg pulse F4 +P[24]=PSH2[F2]; # 180 deg refocussing, adiabatic +P[25]=PROE[F1]*2; # 180 deg pulse, Shaka ROESY +P[26]=PSH12[F1]; # 180 deg inversion F1, adiabatic +P[27]=P90[F1]; # 90 deg pulse F1, WATERGATE +# +P[29]=PSH8[F1]; # flip back pulse +P[31]=PSH15[F2]; # 180 deg adiabatic, F2, 13C x-filter +P[32]=PSH16[F1]; # 180 deg adiabatic, F1, z-spoil +#P[33]=PSH[F1]; # 90 deg, F1, hadamard +#P[34]=PSH[F1]; # 180 deg, F1, hadamard +#P[35]=PSH[F2]; # 90 deg, F2, hadamard +#P[36]=PSH[F2]; # 180 deg, F2, hadamard +#P[37]=PSH[F3]; # 90 deg, F3, hadamard +#P[38]=PSH[F3]; # 180 deg, F3, hadamard +P[39]=PSH21[F2]; # 180 deg, F2, Bip +P[40]=PSH8[F1]*2; # 180 deg sel. F1, 1H (exc. scul) +# +P[63]=PSH11[F2]; # 180 deg adiabatic decoupling, F2, 13C +# +#decoupling pulses +# +PCPD[1]=PCPDP[F1]; # 90 deg pulse F1, dec. +PCPD[2]=PCPDP[F2]; # 90 deg pulse F2, dec. +PCPD[3]=PCPDP[F3]; # 90 deg pulse F3, dec. +# +#power levels +# +PL[1]=PL90[F1]; # high power, F1 +PL[2]=PL90[F2]; # high power, F2 +PL[3]=PL90[F3]; # high power, F3 +PL[4]=PL90[F4]; # high power, F4 +PL[9]=PLCW[F1]; # presat power, F1 +PL[10]=PLTOC[F1]; # TOCSY power, F1 +PL[11]=PLROE[F1]; # ROESY power, F1 +PL[12]=PLCPDP[F2]; # dec. power, F2 +PL[13]=PLCPD2[F2]; # dec. power 2, F2 +PL[14]=PLNOE[F2]; # low power cw, F2 +PL[15]=PLTOC[F2]; # TOCSY power, F2 +PL[16]=PLCPDP[F3]; # dec. power, F3 +PL[18]=PL90[F1]; # WATERGATE power, F1 +PL[19]=PLCPDP[F1]; # dec. power, F1 +PL[21]=PLCW[F2]; # +PL[23]=PLTOC[F3]; # TOCSY power, F3 +PL[24]=PLHD[F2]; # HD decoupling, F2 +PL[25]=PLSH8U[F2]; # Eretic, F2 +PL[27]=PLROE[F1]; # Shaka Spinlock +PL[30]=PLCPDP[F2]; # dec. power, F2, 13C (=pl12) +PL[31]=PLUSER2[F2]; # dec. power, F2, 13C, cw bilev +# +#shapes +# +SP[1]=PLSH1[F1]; # 90 deg selective F1 +SP[2]=PLSH2[F1]; # 180 deg selective F1 +SP[3]=PLSH3[F2]; # adiabatic 180 deg, F2, inversion +SP[4]=PLSH21[F2]; # 180 deg Bip, F2, inversion +SP[6]=PLSH7[F1]; # off-resonance presat F1 +SP[7]=PLSH2[F2]; # adiabatic 180 deg, F2, refocussing +SP[8]=PLSH12[F1]; # adiabatic 180 deg, F1, inversion +SP[10]=PLSH8[F1]; # flip-back pulse, F1, 1H +SP[11]=PLSH8[F1]; # flip-back pulse, F1, H +SP[14]=PLSH12[F2]; # adiab. bilev dec., F2, 13C +SP[18]=PLSH15[F2]; # adiabatic 180 deg, F2, 13C, x-filter +SP[19]=PLSH3[F1] +0.87; # 90 deg, F1, wet +SP[20]=PLSH3[F1] -1.04; # 90 deg, F1, wet +SP[21]=PLSH3[F1] +2.27; # 90 deg, F1, wet +SP[22]=PLSH3[F1] -5.05; # 90 deg, F1, wet +#SP[23]=PLSH[F1]; # 90 deg, F1, hadamard +#SP[24]=PLSH[F1]; # 180 deg, F1, hadamard +#SP[25]=PLSH[F2]; # 90 deg, F2, hadamard +#SP[26]=PLSH[F2]; # 180 deg, F2, hadamard +#SP[27]=PLSH[F3]; # 90 deg, F3, hadamard +#SP[28]=PLSH[F3]; # 180 deg, F3, hadamard +SP[29]=PLSH16[F1]; # adiabatic 180 deg, F1, z-spoil +SP[31]=PLSH11[F2]; # adiab. dec., F2, 13C +# +SPNAM1=PNSH1[F1]; # +SPNAM2=PNSH2[F1]; # +SPNAM3=PNSH3[F2]; # +SPNAM4=PNSH21[F2]; # +SPNAM6=PNSH7[F1]; # +SPNAM7=PNSH2[F2]; # +SPNAM8=PNSH12[F1]; # +SPNAM10=PNSH8[F1]; # +SPNAM11=PNSH8[F1]; # +SPNAM14=PNSH12[F2]; # +SPNAM15=PNSH8U[F2]; # Eretic, F2 +SPNAM18=PNSH15[F2]; # +SPNAM19=PNSH3[F1]; # +SPNAM20=PNSH3[F1]; # +SPNAM21=PNSH3[F1]; # +SPNAM22=PNSH3[F1]; # +#SPNAM23=PNSH[]; # +#SPNAM24=PNSH[]; # +#SPNAM25=PNSH[]; # +#SPNAM26=PNSH[]; # +#SPNAM27=PNSH[]; # +#SPNAM28=PNSH[]; # +SPNAM29=PNSH16[F1]; # +SPNAM31=PNSH11[F2]; # +# +SPOAL[1]=PASH1[F1]; # +SPOAL[2]=PASH2[F1]; # +SPOAL[3]=PASH3[F2]; # +SPOAL[4]=PASH21[F2]; # +SPOAL[6]=PASH7[F1]; # +SPOAL[7]=PASH2[F2]; # +SPOAL[8]=PASH12[F1]; # +SPOAL[10]=PASH8[F1]; +SPOAL[11]=PASH8[F1]; +SPOAL[14]=PASH12[F2]; # +SPOAL[18]=PASH15[F2]; # +SPOAL[19]=PASH3[F1]; # +SPOAL[20]=PASH3[F1]; # +SPOAL[21]=PASH3[F1]; # +SPOAL[22]=PASH3[F1]; # +#SPOAL[23]=PASH[]; # +#SPOAL[24]=PASH[]; # +#SPOAL[25]=PASH[]; # +#SPOAL[26]=PASH[]; # +#SPOAL[27]=PASH[]; # +#SPOAL[28]=PASH[]; # +SPOAL[29]=PASH16[F1]; # +SPOAL[31]=PASH11[F2]; # +# +#global +# +D[9]=TTOC[F1]; # +D[16]=D_grad; # +P[16]=P_grad1; # +P[17]=P_mlev; # +P[19]=P_grad2; # +P[20]=P_mlev; # +P[28]=P_hsqc; # +# diff --git a/sample/sample_sessions/test00/1/pulseprogram b/sample/sample_sessions/test00/1/pulseprogram new file mode 100644 index 0000000..d826ebf --- /dev/null +++ b/sample/sample_sessions/test00/1/pulseprogram @@ -0,0 +1,210 @@ +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" +;zgpr +;avance-version (06/11/09) +;1D sequence with f1 presaturation +; +;$CLASS=HighRes +;$DIM=1D +;$TYPE= +;$SUBTYPE= +;$COMMENT= + + +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/Avance.incl" 1 +;Avance2.incl +; for 1 +; +;avance-version (07/08/21) +; +;$CLASS=HighRes Incl +;$COMMENT= + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +;$Id: Avance2.incl,v 1.17.2.1 2007/09/14 16:17:35 ber Exp $ +# 12 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" 2 + + + +"d12=20u" + + +"acqt0=-p1*2/3.1416" + + +# 1 "mc_line 21 file /opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr expanding definition part of mc command before ze" +define delay MCWRK +define delay MCREST +"MCWRK = 0.333333*30m" +"MCREST = 30m - 30m" + dccorr +# 21 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" +1 ze +# 1 "mc_line 21 file /opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr expanding definition of mc command after ze" +# 22 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" +# 1 "mc_line 22 file /opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr expanding start label for mc command" +2 MCWRK * 2 +LBLF0, MCWRK + MCREST +# 23 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" + d12 pl9:f1 + d1 cw:f1 ph29 + 4u do:f1 + d12 pl1:f1 + p1 ph1 + go=2 ph31 +# 1 "mc_line 29 file /opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr expanding mc command in line" + MCWRK wr #0 + MCWRK zd + lo to LBLF0 times td0 + + MCWRK +# 30 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" +exit + + +ph1=0 2 2 0 1 3 3 1 +ph29=0 +ph31=0 2 2 0 1 3 3 1 + + +;pl1 : f1 channel - power level for pulse (default) +;pl9 : f1 channel - power level for presaturation +;p1 : f1 channel - 90 degree high power pulse +;d1 : relaxation delay; 1-5 * T1 +;d12: delay for power switching [20 usec] +;NS: 1 * n, total number of scans: NS * TD0 + + + +;$Id: zgpr,v 1.9 2006/11/10 10:56:44 ber Exp $ diff --git a/sample/sample_sessions/test00/1/scon2 b/sample/sample_sessions/test00/1/scon2 new file mode 100644 index 0000000..8bc66ef --- /dev/null +++ b/sample/sample_sessions/test00/1/scon2 @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-26 21:33:06.757 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/scon2 +$$ process /opt/topspin2.1/prog/mod/go +##$BLKTR= (0..15) +3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 +##$DE1= 4.5 +##$DEADC= 0.5 +##$DEPA= 4.5 +##$DERX= 1.5 +##$FILCOR= 0.2 +##END= diff --git a/sample/sample_sessions/test00/1/uxnmr.par b/sample/sample_sessions/test00/1/uxnmr.par new file mode 100644 index 0000000..c90a4f2 --- /dev/null +++ b/sample/sample_sessions/test00/1/uxnmr.par @@ -0,0 +1,527 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 104 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2009-12-15 16:47:14.463 -0500 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/conf/instr/spect/uxnmr.par +$$ process /opt/topspin2.1/prog/mod/hconfserver +##$ACB= 1 +##$ACBTAT= (0..15) +0 88 72 88 0 0 88 0 0 0 0 0 0 0 0 0 +##$ACBTBA= (0..15) +0 30 60 90 0 0 180 0 0 0 0 0 0 0 0 0 +##$ACBTBLK= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTCTL= (0..15) +0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 +##$ACBTDI= (0..15) +0 70 71 72 0 0 75 0 0 0 0 0 0 0 0 0 +##$ACBTDM= (0..15) +0 6 25 10 0 0 10 0 0 0 0 0 0 0 0 0 +##$ACBTFHI= (0..15) +0 365 600 365 0 0 365 0 0 0 0 0 0 0 0 0 +##$ACBTFL= (0..15) +0 249 249 249 0 0 249 0 0 0 0 0 0 0 0 0 +##$ACBTFLO= (0..15) +0 6 188 6 0 0 6 0 0 0 0 0 0 0 0 0 +##$ACBTINP= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTOUT= (0..15) +0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 +##$ACBTPO= (0..15) +0 500000 100000 300000 0 0 300000 0 0 0 0 0 0 0 0 0 +##$ACBTPW= (0..15) +0 600 1000 1000 0 0 1000 0 0 0 0 0 0 0 0 0 +##$ACBTSB= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTY= +##$AQSBDCH= (0..95) +0 0 0 0 0 0 0 0 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDHW= (0..95) +1 4 4 4 0 1 4 4 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDID= (0..95) +88 83 83 83 89 88 83 83 89 80 80 66 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSBDNO= (0..95) +1 1 2 3 1 2 4 5 2 1 2 1 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDSL= (0..95) +4 5 6 7 8 10 11 12 15 17 18 19 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 +##$AQSBDTY= (0..95) +194 16 24 16 4 194 24 16 4 10 10 7 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSBUAD= (0..95) +52 36 37 38 60 53 39 40 61 33 34 32 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSECL= (0..95) +0 1 1 1 1 0 1 1 1 1 1 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSECLS= (0..95) +3 1 1 1 0 3 1 1 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSSPLT= no +##$ATT19F= (0..1) +0 0 +##$ATT1H= (0..1) +0 0 +##$ATT3H= (0..1) +0 0 +##$ATTX= (0..1) +0 0 +##$ATTY= (0..1) +0 0 +##$ATTZ= (0..1) +0 0 +##$BACSAIR= yes +##$BACSCAP= 60 +##$BACSDEL= 10 +##$BACSFCM= no +##$BACSOPT= +##$BACSTY= +##$BARPTY= +##$BFREQ= 600.13 +##$BGAETH1= +##$BGAETH2= +##$BGAETH3= +##$BGAETH4= +##$BGAETH5= +##$BGAETH6= +##$BGAETH7= +##$BGAETH8= +##$BIRDS= yes +##$BMPC= 0 +##$BMPCTY= +##$BPSUTY= +##$BSMS= 1 +##$BSMSETH= +##$BSMSTY= +##$CFASMOD= (0..7) +1 1 1 1 1 1 1 1 +##$CFASMUL= (0..7) +1 1 1 1 1 1 1 1 +##$CNFTXDR= (0..7) +6 6 6 6 6 0 0 0 +##$COMDIG2= 0 +##$CPDBTY= +##$CRCOTY= +##$CSW1= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$CSW2= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$CSWNUM= (0..7) +0 0 0 0 0 0 0 0 +##$DATSTAT= no +##$DIGI140= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIB12= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIB16= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIFA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIHA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIHAF= (0..7) +1 0 0 0 0 0 0 0 +##$DIGIHRD= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIIA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIO16= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISAF= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISL= (0..7) +0 0 0 0 0 0 0 0 +##$DIGITYI= (0..7) +0 0 0 0 0 0 0 0 +##$DIGITYP= (0..7) +2 0 0 0 0 0 0 0 +##$DIGITZ= 0 +##$DRU= no +##$DRUETH01= +##$DRUETH02= +##$DRUETH03= +##$DRUETH04= +##$DRUETH05= +##$DRUETH06= +##$DRUETH07= +##$DRUETH08= +##$DRUETH09= +##$DRUETH10= +##$DRUETH11= +##$DRUETH12= +##$DRUETH13= +##$DRUETH14= +##$DRUETH15= +##$DRUETH16= +##$DRUETH17= +##$DRUETH18= +##$DRUETH19= +##$DRUETH20= +##$DRUETH21= +##$DRUETH22= +##$DRUETH23= +##$DRUETH24= +##$DRUETH25= 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0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$DATE= 0 +##$DBL= (0..7) +120 120 120 120 120 120 120 120 +##$DBP= (0..7) +150 150 150 150 150 150 150 150 +##$DBP07= 0 +##$DBPNAM0= <> +##$DBPNAM1= <> +##$DBPNAM2= <> +##$DBPNAM3= <> +##$DBPNAM4= <> +##$DBPNAM5= <> +##$DBPNAM6= <> +##$DBPNAM7= <> +##$DBPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DBPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DE= 6.5 +##$DECBNUC= +##$DECIM= 16 +##$DECNUC= +##$DECSTAT= 4 +##$DIGMOD= 1 +##$DIGTYP= 8 +##$DL= (0..7) +0 120 120 120 120 120 120 120 +##$DP= (0..7) +150 150 150 150 150 150 150 150 +##$DP07= 0 +##$DPNAME0= <> +##$DPNAME1= <> +##$DPNAME2= <> +##$DPNAME3= <> +##$DPNAME4= <> +##$DPNAME5= <> +##$DPNAME6= <> +##$DPNAME7= <> +##$DPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DQDMODE= 0 +##$DR= 18 +##$DS= 8 +##$DSLIST= +##$DSPFIRM= 0 +##$DSPFVS= 0 +##$DTYPA= 0 +##$EXP= +##$F1LIST= <111111111111111> +##$F2LIST= <222222222222222> +##$F3LIST= <333333333333333> +##$FCUCHAN= (0..9) +0 2 1 3 0 0 0 0 0 0 +##$FL1= 90 +##$FL2= 90 +##$FL3= 90 +##$FL4= 90 +##$FOV= 20 +##$FQ1LIST= +##$FQ2LIST= +##$FQ3LIST= +##$FQ4LIST= +##$FQ5LIST= +##$FQ6LIST= +##$FQ7LIST= +##$FQ8LIST= +##$FRQLO3= 0 +##$FRQLO3N= 0 +##$FS= (0..7) +83 83 83 83 83 83 83 83 +##$FTLPGN= 0 +##$FW= 125000 +##$FnMODE= 0 +##$FnTYPE= 0 +##$GP031= 0 +##$GPNAM0= +##$GPNAM1= +##$GPNAM10= +##$GPNAM11= +##$GPNAM12= +##$GPNAM13= +##$GPNAM14= +##$GPNAM15= +##$GPNAM16= +##$GPNAM17= +##$GPNAM18= +##$GPNAM19= +##$GPNAM2= +##$GPNAM20= +##$GPNAM21= +##$GPNAM22= +##$GPNAM23= +##$GPNAM24= +##$GPNAM25= +##$GPNAM26= +##$GPNAM27= +##$GPNAM28= +##$GPNAM29= +##$GPNAM3= +##$GPNAM30= +##$GPNAM31= +##$GPNAM4= +##$GPNAM5= +##$GPNAM6= +##$GPNAM7= +##$GPNAM8= +##$GPNAM9= +##$GPX= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GPY= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GPZ= (0..31) +0 50 80 8.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GRDPROG= <> +##$GRPDLY= -1 +##$HDDUTY= 20 +##$HDRATE= 20 +##$HGAIN= (0..3) +0 0 0 0 +##$HL1= 256 +##$HL2= 35 +##$HL3= 16 +##$HL4= 17 +##$HOLDER= 11 +##$HPMOD= (0..7) +0 0 0 0 0 0 0 0 +##$HPPRGN= 0 +##$IN= (0..63) +0.000310000003082678 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 +##$INF= (0..7) +0 0 0 0 0 0 0 0 +##$INP= (0..63) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$INSTRUM= <> +##$L= (0..31) +1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +##$LFILTER= 10 +##$LGAIN= -10 +##$LINPSTP= 0 +##$LOCKED= no +##$LOCKFLD= 0 +##$LOCKGN= 0 +##$LOCKPOW= -20 +##$LOCKPPM= 0 +##$LOCNUC= <2H> +##$LOCPHAS= 0 +##$LOCSHFT= yes +##$LOCSW= 0 +##$LTIME= 0.1 +##$MASR= 4200 +##$MASRLST= +##$NBL= 1 +##$NC= 0 +##$NLOGCH= 1 +##$NS= 64 +##$NUC1= <1H> +##$NUC2= <13C> +##$NUC3= <15N> +##$NUC4= +##$NUC5= +##$NUC6= +##$NUC7= +##$NUC8= +##$NUCLEI= 0 +##$NUCLEUS= +##$O1= 2818.21048 +##$O2= 7469.21502263831 +##$O3= 7175.65611 +##$O4= 2850.47650618253 +##$O5= 2850.47650618253 +##$O6= 2850.47650618253 +##$O7= 2850.47650618253 +##$O8= 2850.47650618253 +##$OBSCHAN= (0..9) +0 0 0 0 0 0 0 0 0 0 +##$OVERFLW= 0 +##$P= (0..63) +12 12 24 11 22 18.48 28 56 20000 25 50 80000 80000 0 500 250000 1000 2500 +10000 600 2500 32 64 0 2000 250 0 12 1000 1000 0 1730 20000 0 0 0 0 0 0 +160 2000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1500 +##$PACOIL= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAPS= 2 +##$PARMODE= 1 +##$PCPD= (0..9) +100 60 60 200 100 100 100 100 100 100 +##$PHCOR= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PHLIST= <> +##$PHP= 1 +##$PH_ref= 0 +##$PL= (0..63) +120 17.5 -0.5 -2 120 120 120 120 120 69.9 24.86 37.85 14.24 120 120 6.63 +13.92 120 17.5 31.48 120 120 120 1.88 120 120 120 37.85 120 120 14.24 8.21 +120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 +120 120 120 120 120 120 120 120 120 120 120 120 120 120 +##$PLSTEP= 0.1 +##$PLSTRT= -6 +##$POWMOD= 0 +##$PQPHASE= 0 +##$PQSCALE= 0 +##$PR= 1 +##$PRECHAN= (0..15) +-1 3 0 4 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$PRGAIN= 0 +##$PROBHD= <05> +##$PROSOL= no +##$PULPROG= +##$PW= 0 +##$PYNM= +##$QNP= 1 +##$RD= 0 +##$RECCHAN= (0..15) +0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$RECPH= 0 +##$RECPRE= (0..15) +-1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$RECPRFX= (0..15) +-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$RECSEL= (0..15) +0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$RG= 512 +##$RO= 0 +##$ROUTWD1= (0..23) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 +##$ROUTWD2= (0..23) +0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 +##$RSEL= (0..9) +0 1 2 3 0 0 0 0 0 0 +##$S= (0..7) +83 4 83 83 83 83 83 83 +##$SEOUT= 0 +##$SFO1= 600.13281821048 +##$SFO2= 150.910278215023 +##$SFO3= 60.81782065611 +##$SFO4= 600.132850476506 +##$SFO5= 600.132850476506 +##$SFO6= 600.132850476506 +##$SFO7= 600.132850476506 +##$SFO8= 600.132850476506 +##$SOLVENT= +##$SP= (0..31) +1 86.27 80.25 6.83 4.69 0 75.92 6.83 120 0 51.32 51.32 0 0 8.31 0 150 150 +12.22 78.21 76.3 79.60999 72.28999 150 150 150 150 150 150 40.1 150 14.33 +##$SP07= 0 +##$SPECTR= 0 +##$SPNAM0= +##$SPNAM1= +##$SPNAM10= +##$SPNAM11= +##$SPNAM12= +##$SPNAM13= +##$SPNAM14= +##$SPNAM15= < > +##$SPNAM16= +##$SPNAM17= +##$SPNAM18= +##$SPNAM19= +##$SPNAM2= +##$SPNAM20= +##$SPNAM21= +##$SPNAM22= +##$SPNAM23= +##$SPNAM24= +##$SPNAM25= +##$SPNAM26= +##$SPNAM27= +##$SPNAM28= +##$SPNAM29= +##$SPNAM3= +##$SPNAM30= +##$SPNAM31= +##$SPNAM4= +##$SPNAM5= +##$SPNAM6= +##$SPNAM7= +##$SPNAM8= < > +##$SPNAM9= +##$SPOAL= (0..31) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$SPOFFS= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$SUBNAM0= <""> +##$SUBNAM1= <""> +##$SUBNAM2= <""> +##$SUBNAM3= <""> +##$SUBNAM4= <""> +##$SUBNAM5= <""> +##$SUBNAM6= <""> +##$SUBNAM7= <""> +##$SUBNAM8= <""> +##$SUBNAM9= <""> +##$SW= 13.9790084634634 +##$SWIBOX= (0..15) +0 1 2 3 0 0 6 0 0 0 0 0 0 0 0 0 +##$SW_h= 8389.26174496644 +##$SWfinal= 0 +##$TD= 1024 +##$TD0= 1 +##$TE= 300 +##$TE2= 300 +##$TE3= 300 +##$TEG= 300 +##$TL= (0..7) +0 120 120 120 120 120 120 120 +##$TP= (0..7) +150 150 150 150 150 150 150 150 +##$TP07= 0 +##$TPNAME0= <> +##$TPNAME1= <> +##$TPNAME2= <> +##$TPNAME3= <> +##$TPNAME4= <> +##$TPNAME5= <> +##$TPNAME6= <> +##$TPNAME7= <> +##$TPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$TPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$TUNHIN= 0 +##$TUNHOUT= 0 +##$TUNXOUT= 0 +##$USERA1= +##$USERA2= +##$USERA3= +##$USERA4= +##$USERA5= +##$V9= 5 +##$VALIST= +##$VCLIST= +##$VD= 0 +##$VDLIST= +##$VPLIST= +##$VTLIST= +##$WBST= 1024 +##$WBSW= 20 +##$XGAIN= (0..3) +0 0 0 0 +##$XL= 0 +##$YL= 0 +##$YMAX_a= 0 +##$YMIN_a= 0 +##$ZGOPTNS= <> +##$ZL1= 120 +##$ZL2= 120 +##$ZL3= 120 +##$ZL4= 120 +##END= diff --git a/sample/sample_sessions/test00/2/acqu2 b/sample/sample_sessions/test00/2/acqu2 new file mode 100644 index 0000000..af9b147 --- /dev/null +++ b/sample/sample_sessions/test00/2/acqu2 @@ -0,0 +1,21 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 3 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-24 16:07:31.567 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/prog/curdir/changer/inmrchanger/Sep24-2010-1606-micro_screening/11/data/./nmr/HR4762D.007_N_HSQC/1/acqu2 +$$ process /opt/topspin2.1/prog/mod/xwish3 +##$BF1= 60.810645 +##$DECIM= 32 +##$DR= 18 +##$FW= 90000 +##$FnMODE= 6 +##$NUC1= <15N> +##$O1= 5827.94102 +##$SFO1= 60.8176380097503 +##$SW= 34.9545034911622 +##$SW_h= 2125.85034013605 +##$TD= 120 +##END= diff --git a/sample/sample_sessions/test00/2/acqu2s b/sample/sample_sessions/test00/2/acqu2s new file mode 100644 index 0000000..c4d228d --- /dev/null +++ b/sample/sample_sessions/test00/2/acqu2s @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 121 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 00:37:56.542 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/acqu2s +$$ process /opt/topspin2.1/prog/mod/go +##$BF1= 60.810645 +##$FnMODE= 6 +##$NUC1= <15N> +##$O1= 5827.94102 +##$SFO1= 60.8176380097503 +##$SW= 34.9545034911622 +##$TD= 120 +##END= diff --git a/sample/sample_sessions/test00/2/acqus b/sample/sample_sessions/test00/2/acqus new file mode 100644 index 0000000..dbb4da3 --- /dev/null +++ b/sample/sample_sessions/test00/2/acqus @@ -0,0 +1,407 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 12 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 00:38:07.009 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/acqus +$$ process /opt/topspin2.1/prog/mod/shimcntl +##$ACQT0= 1000000 +##$AMP= (0..31) +100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 +100 100 100 100 100 100 100 100 100 100 100 100 100 100 +##$ANAVPT= -1 +##$AQSEQ= 0 +##$AQ_mod= 3 +##$AUNM= +##$AUTOPOS= <11 > +##$BF1= 600.13 +##$BF2= 150.902809 +##$BF3= 60.810645 +##$BF4= 600.13 +##$BF5= 600.13 +##$BF6= 600.13 +##$BF7= 600.13 +##$BF8= 600.13 +##$BYTORDA= 1 +##$CFDGTYP= 2 +##$CFRGTYP= 5 +##$CHEMSTR= +##$CNST= (0..63) +1 1 145 1 90 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +##$CPDPRG= <> +##$CPDPRG1= <> +##$CPDPRG2= <> +##$CPDPRG3= +##$CPDPRG4= +##$CPDPRG5= +##$CPDPRG6= +##$CPDPRG7= +##$CPDPRG8= +##$CPDPRGB= <> +##$CPDPRGT= <> +##$D= (0..63) +3e-06 1 0 0 0 0 0 0 0 0.06 0 0.03 0 4e-06 0 0 0.0002 0 0 0 0 0 0 0 0.00225 +0 0.002777778 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 +##$DATE= 1285553889 +##$DBL= (0..7) +120 120 120 120 120 120 120 120 +##$DBP= (0..7) +150 150 150 150 150 150 150 150 +##$DBP07= 0 +##$DBPNAM0= <> +##$DBPNAM1= <> +##$DBPNAM2= <> +##$DBPNAM3= <> +##$DBPNAM4= <> +##$DBPNAM5= <> +##$DBPNAM6= <> +##$DBPNAM7= <> +##$DBPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DBPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DE= 6.5 +##$DECBNUC= +##$DECIM= 16 +##$DECNUC= +##$DECSTAT= 4 +##$DIGMOD= 1 +##$DIGTYP= 8 +##$DL= (0..7) +0 120 120 120 120 120 120 120 +##$DP= (0..7) +150 150 150 150 150 150 150 150 +##$DP07= 0 +##$DPNAME0= <> +##$DPNAME1= <> +##$DPNAME2= <> +##$DPNAME3= <> +##$DPNAME4= <> +##$DPNAME5= <> +##$DPNAME6= <> +##$DPNAME7= <> +##$DPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DQDMODE= 0 +##$DR= 18 +##$DS= 8 +##$DSLIST= +##$DSPFIRM= 0 +##$DSPFVS= 12 +##$DTYPA= 0 +##$EXP= +##$F1LIST= <111111111111111> +##$F2LIST= <222222222222222> +##$F3LIST= <333333333333333> +##$FCUCHAN= (0..9) +0 2 1 3 0 0 0 0 0 0 +##$FL1= 90 +##$FL2= 90 +##$FL3= 90 +##$FL4= 90 +##$FOV= 20 +##$FQ1LIST= +##$FQ2LIST= +##$FQ3LIST= +##$FQ4LIST= +##$FQ5LIST= +##$FQ6LIST= +##$FQ7LIST= +##$FQ8LIST= +##$FRQLO3= 1891778.52348993 +##$FRQLO3N= 0 +##$FS= (0..7) +83 83 83 83 83 83 83 83 +##$FTLPGN= 0 +##$FW= 125000 +##$FnMODE= 0 +##$FnTYPE= 0 +##$GP031= 0 +##$GPNAM0= +##$GPNAM1= +##$GPNAM10= +##$GPNAM11= +##$GPNAM12= +##$GPNAM13= +##$GPNAM14= +##$GPNAM15= +##$GPNAM16= +##$GPNAM17= +##$GPNAM18= +##$GPNAM19= +##$GPNAM2= +##$GPNAM20= +##$GPNAM21= +##$GPNAM22= +##$GPNAM23= +##$GPNAM24= +##$GPNAM25= +##$GPNAM26= +##$GPNAM27= +##$GPNAM28= +##$GPNAM29= +##$GPNAM3= +##$GPNAM30= +##$GPNAM31= +##$GPNAM4= +##$GPNAM5= +##$GPNAM6= +##$GPNAM7= +##$GPNAM8= 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<> +##$TPNAME2= <> +##$TPNAME3= <> +##$TPNAME4= <> +##$TPNAME5= <> +##$TPNAME6= <> +##$TPNAME7= <> +##$TPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$TPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$TUNHIN= 0 +##$TUNHOUT= 0 +##$TUNXOUT= 0 +##$USERA1= +##$USERA2= +##$USERA3= +##$USERA4= +##$USERA5= +##$V9= 5 +##$VALIST= +##$VCLIST= +##$VD= 0 +##$VDLIST= +##$VPLIST= +##$VTLIST= +##$WBST= 1024 +##$WBSW= 20 +##$XGAIN= (0..3) +0 0 0 0 +##$XL= 0 +##$YL= 0 +##$YMAX_a= 115504 +##$YMIN_a= -133374 +##$ZGOPTNS= <> +##$ZL1= 120 +##$ZL2= 120 +##$ZL3= 120 +##$ZL4= 120 +##END= diff --git a/sample/sample_sessions/test00/2/audita.txt b/sample/sample_sessions/test00/2/audita.txt new file mode 100644 index 0000000..749cb0c --- /dev/null +++ b/sample/sample_sessions/test00/2/audita.txt @@ -0,0 +1,23 @@ +##TITLE= Audit trail, TOPSPIN Version 2.1 +##JCAMPDX= 5.01 +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/audita.txt +##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT) +( 1,<2010-09-27 00:37:57.695 -0400>,,,,, + ) +( 2,<2010-09-27 00:38:07.366 -0400>,,,,, + ) +##END= + +$$ hash MD5 +$$ 52 B5 1D CD E1 CF C1 15 EA 29 FD D9 BB FE AC 2E diff --git a/sample/sample_sessions/test00/2/cpdprg3 b/sample/sample_sessions/test00/2/cpdprg3 new file mode 100644 index 0000000..c6eb071 --- /dev/null +++ b/sample/sample_sessions/test00/2/cpdprg3 @@ -0,0 +1,101 @@ +1 pcpd*0.339:0 + pcpd*0.613:180 + pcpd*2.864:0 + pcpd*2.981:180 + pcpd*0.770:0 + pcpd*0.691:180 + pcpd*0.944:0 + pcpd*1.020:180 + pcpd*1.494:0 + pcpd*2.846:180 + pcpd*0.738:0 + pcpd*0.510:180 + pcpd*0.283:0 + pcpd*0.808:180 + pcpd*1.328:0 + pcpd*1.536:180 + pcpd*2.871:0 + pcpd*0.721:180 + pcpd*0.788 :0 + pcpd*0.858:180 + pcpd*1.091:0 + pcpd*1.484:180 + pcpd*2.843:0 + pcpd*0.729:180 + pcpd*0.593:0 + pcpd*0.339:0 + pcpd*0.613:180 + pcpd*2.864:0 + pcpd*2.981:180 + pcpd*0.770:0 + pcpd*0.691:180 + pcpd*0.944:0 + pcpd*1.020:180 + pcpd*1.494:0 + pcpd*2.846:180 + pcpd*0.738:0 + pcpd*0.510:180 + pcpd*0.283:0 + pcpd*0.808:180 + pcpd*1.328:0 + pcpd*1.536:180 + pcpd*2.871:0 + pcpd*0.721:180 + pcpd*0.788 :0 + pcpd*0.858:180 + pcpd*1.091:0 + pcpd*1.484:180 + pcpd*2.843:0 + pcpd*0.729:180 + pcpd*0.593:0 + pcpd*0.339:180 + pcpd*0.613:0 + pcpd*2.864:180 + pcpd*2.981:0 + pcpd*0.770:180 + pcpd*0.691:0 + pcpd*0.944:180 + pcpd*1.020:0 + pcpd*1.494:180 + pcpd*2.846:0 + pcpd*0.738:180 + pcpd*0.510:0 + pcpd*0.283:180 + pcpd*0.808:0 + pcpd*1.328:180 + pcpd*1.536:0 + pcpd*2.871:180 + pcpd*0.721:0 + pcpd*0.788:180 + pcpd*0.858:0 + pcpd*1.091:180 + pcpd*1.484:0 + pcpd*2.843:180 + pcpd*0.729:0 + pcpd*0.593:180 + pcpd*0.339:180 + pcpd*0.613:0 + pcpd*2.864:180 + pcpd*2.981:0 + pcpd*0.770:180 + pcpd*0.691:0 + pcpd*0.944:180 + pcpd*1.020:0 + pcpd*1.494:180 + pcpd*2.846:0 + pcpd*0.738:180 + pcpd*0.510:0 + pcpd*0.283:180 + pcpd*0.808:0 + pcpd*1.328:180 + pcpd*1.536:0 + pcpd*2.871:180 + pcpd*0.721:0 + pcpd*0.788:180 + pcpd*0.858:0 + pcpd*1.091:180 + pcpd*1.484:0 + pcpd*2.843:180 + pcpd*0.729:0 + pcpd*0.593:180 + jump to 1 diff --git a/sample/sample_sessions/test00/2/format.temp b/sample/sample_sessions/test00/2/format.temp new file mode 100644 index 0000000..0bcc8cc --- /dev/null +++ b/sample/sample_sessions/test00/2/format.temp @@ -0,0 +1,382 @@ +EDIT_PAR COMMAND FILE + +DI_MODE LONG +ED_ENTRY ACQU +ORDER FILE + + +HEADER "F2 - Acquisition Parameters" +T_NAME Date_ + TYPE R64 + CLASS ACQU + SUBRANGE 0.0 50000000 + REL "Date_=itodate(DATE)" + INV_REL "DATE=datetoi(Date_,DATE)" + FORMAT "%14.0f" + TEXT " " +END +T_NAME Time + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000000 + REL "Time=itotime(DATE)" + INV_REL "DATE=timetoi(Time,DATE)" + FORMAT "%14.2f" + TEXT " " +END +NAME INSTRUM + TEXT " " +END +NAME PROBHD + FORMAT "%14.14s" + TEXT " " +END +NAME PULPROG + TEXT " " +END +NAME TD + TEXT " " +END +NAME SOLVENT + TEXT " " +END +NAME NS + TEXT " " +END +NAME DS + TEXT " " +END +T_NAME SWH + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e8 + REL 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FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D1 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D1=D[1]" + INV_REL "D[1]=D1" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D11 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D11=D[11]" + INV_REL "D[11]=D11" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D13 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D13=D[13]" + INV_REL "D[13]=D13" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D16 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D16=D[16]" + INV_REL "D[16]=D16" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D24 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D24=D[24]" + INV_REL "D[24]=D24" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D26 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D26=D[26]" + INV_REL "D[26]=D26" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME IN0 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "IN0=IN[0]" + INV_REL 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"PL[3]=-6-4.3425*log(PL3W/288)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +T_NAME PL16W + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL16W=288*pow(10.0,(-6-PL[16])/10.0)" + INV_REL "PL[16]=-6-4.3425*log(PL16W/288)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +NAME SFO3 + FORMAT "%14.7f MHz" + TEXT " " +END +HEADER "====== GRADIENT CHANNEL =====" +NAME GPNAM1 + TEXT " " +END +NAME GPNAM2 + TEXT " " +END +NAME GPNAM3 + TEXT " " +END +T_NAME GPZ1 + TYPE R32 + CLASS ACQU + SUBRANGE -100.0 100.0 + REL "GPZ1=GPZ[1]" + INV_REL "GPZ[1]=GPZ1" + UNIT "%" + FORMAT "%14.2f %" + TEXT " " +END +T_NAME GPZ2 + TYPE R32 + CLASS ACQU + SUBRANGE -100.0 100.0 + REL "GPZ2=GPZ[2]" + INV_REL "GPZ[2]=GPZ2" + UNIT "%" + FORMAT "%14.2f %" + TEXT " " +END +T_NAME GPZ3 + TYPE R32 + CLASS ACQU + SUBRANGE -100.0 100.0 + REL "GPZ3=GPZ[3]" + INV_REL "GPZ[3]=GPZ3" + UNIT "%" + FORMAT "%14.2f %" + TEXT " " +END +T_NAME P16 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P16=P[16]" + INV_REL "P[16]=P16" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END diff --git a/sample/sample_sessions/test00/2/pdata/1/2ii b/sample/sample_sessions/test00/2/pdata/1/2ii new file mode 100644 index 0000000..cf54eac Binary files /dev/null and b/sample/sample_sessions/test00/2/pdata/1/2ii differ diff --git a/sample/sample_sessions/test00/2/pdata/1/2ir b/sample/sample_sessions/test00/2/pdata/1/2ir new file mode 100644 index 0000000..deac384 Binary files /dev/null and b/sample/sample_sessions/test00/2/pdata/1/2ir differ diff --git a/sample/sample_sessions/test00/2/pdata/1/2ri b/sample/sample_sessions/test00/2/pdata/1/2ri new file mode 100644 index 0000000..b532e42 Binary files /dev/null and b/sample/sample_sessions/test00/2/pdata/1/2ri differ diff --git a/sample/sample_sessions/test00/2/pdata/1/2rr b/sample/sample_sessions/test00/2/pdata/1/2rr new file mode 100644 index 0000000..26bfd23 Binary files /dev/null and b/sample/sample_sessions/test00/2/pdata/1/2rr differ diff --git a/sample/sample_sessions/test00/2/pdata/1/auditp.txt b/sample/sample_sessions/test00/2/pdata/1/auditp.txt new file mode 100644 index 0000000..a88517d --- /dev/null +++ b/sample/sample_sessions/test00/2/pdata/1/auditp.txt @@ -0,0 +1,32 @@ +##TITLE= Audit trail, TOPSPIN Version 2.1 +##JCAMPDX= 5.01 +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/auditp.txt +##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT) +( 1,<2010-09-27 00:37:57.695 -0400>,,,,, + ) +( 2,<2010-09-27 00:38:07.366 -0400>,,,,, + ) +( 3,<2010-09-27 10:54:28.898 -0400>,,,,, + ) +( 4,<2010-09-27 15:02:16.968 -0400>,,,,, + ) +##END= + +$$ hash MD5 +$$ 5C BB 6C F7 27 6D B5 92 11 DE A2 17 D4 05 70 C8 diff --git a/sample/sample_sessions/test00/2/pdata/1/clevels b/sample/sample_sessions/test00/2/pdata/1/clevels new file mode 100644 index 0000000..fe79542 --- /dev/null +++ b/sample/sample_sessions/test00/2/pdata/1/clevels @@ -0,0 +1,33 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 16 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 15:02:27.405 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/clevels +$$ process /opt/topspin2.1/prog/mod/dataserver +##$LEVELS= (0..255) +-5800829716762.1 -3222683175979 -1790379542210.5 -994655301228.1 -552586278460 +-306992376922.2 -170551320512.4 -94750733618 -52639296454.4 -29244053585.8 +-16246696436.6 -9025942464.8 -5014412480.4 -2785784711.3 -1547658173 -859810096.1 +-477672275.6 -265373486.4 -147429714.7 -81905397.1 -45502998.4 -25279443.5 +-14044135.3 -7802297.4 -4334609.7 -2408116.5 -1337842.5 -743245.8 -412914.3 +-229396.9 -127442.7 -70801.5 70801.5 81421.7 93635 107680.2 123832.3 142407.1 +163768.2 188333.4 216583.4 249070.9 286431.6 329396.3 378805.7 435626.6 +500970.6 576116.2 662533.6 761913.6 876200.7 1007630.8 1158775.4 1332591.7 +1532480.5 1762352.5 2026705.4 2330711.2 2680317.9 3082365.6 3544720.4 4076428.5 +4687892.8 5391076.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$LEVSIGN= 3 +##$MAXLEV= 60 +##$METHOD= 0 +##$NEGBASE= -70801.5 +##$NEGINCR= 1.8 +##$POSBASE= 70801.5 +##$POSINCR= 1.15 +##END= diff --git a/sample/sample_sessions/test00/2/pdata/1/outd b/sample/sample_sessions/test00/2/pdata/1/outd new file mode 100644 index 0000000..55c6d6d --- /dev/null +++ b/sample/sample_sessions/test00/2/pdata/1/outd @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-24 16:07:31.541 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/prog/curdir/changer/inmrchanger/Sep24-2010-1606-micro_screening/11/data/nmr/HR4762D.007_N_HSQC/1/pdata/1/outd +$$ process /opt/topspin2.1/prog/mod/xwish3 +##$CURPLOT= +##$CURPRIN= <$hp-laserjet-1300-1> +##$DFORMAT= +##$LAYOUT= <+/2D_inv.xwp> +##$LFORMAT= +##$PFORMAT= +##$SURQMSG= 1 +##END= diff --git a/sample/sample_sessions/test00/2/pdata/1/proc b/sample/sample_sessions/test00/2/pdata/1/proc new file mode 100644 index 0000000..b7d6205 --- /dev/null +++ b/sample/sample_sessions/test00/2/pdata/1/proc @@ -0,0 +1,110 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 7 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 15:02:16.968 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/proc +$$ process /opt/topspin2.1/prog/mod/proc2d +##$ABSF1= 4.6 +##$ABSF2= -100 +##$ABSG= 5 +##$ABSL= 3 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= +##$AXLEFT= 0 +##$AXNAME= <> +##$AXNUC= +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.1 +##$BCFW= 1 +##$BC_mod= 4 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 2 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 0 +##$FT_mod= 4 +##$GAMMA= 1 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 0.3 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 0 +##$MEAN= 0 +##$ME_mod= 0 +##$MI= 0 +##$NCOEF= 0 +##$NC_proc= 0 +##$NLEV= 6 +##$NOISF1= 8.174992 +##$NOISF2= 6.675002 +##$NSP= 1 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 11.68554 +##$PC= 1 +##$PHC0= 37.5853 +##$PHC1= -6.6 +##$PH_mod= 1 +##$PKNL= yes +##$PPARMOD= 1 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 4 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 600.13 +##$SI= 2048 +##$SIGF1= 5.6 +##$SIGF2= 5.2 +##$SINO= 400 +##$SIOLD= 2048 +##$SPECTYP= <> +##$SREGLST= <1H.H2O+D2O> +##$SSB= 2 +##$STSI= 0 +##$STSR= 0 +##$SW_p= 8389.26174496644 +##$SYMM= 0 +##$S_DEV= 0 +##$TDeff= 16384 +##$TDoff= 0 +##$TI= +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 4 +##$XDIM= 8192 +##$YMAX_p= 0 +##$YMIN_p= 0 +##END= diff --git a/sample/sample_sessions/test00/2/pdata/1/proc2 b/sample/sample_sessions/test00/2/pdata/1/proc2 new file mode 100644 index 0000000..f676dde --- /dev/null +++ b/sample/sample_sessions/test00/2/pdata/1/proc2 @@ -0,0 +1,109 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-24 16:07:31.541 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/prog/curdir/changer/inmrchanger/Sep24-2010-1606-micro_screening/11/data/nmr/HR4762D.007_N_HSQC/1/pdata/1/proc2 +$$ process /opt/topspin2.1/prog/mod/xwish3 +##$ABSF1= 1000 +##$ABSF2= -1000 +##$ABSG= 5 +##$ABSL= 3 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= < > +##$AXLEFT= 0 +##$AXNAME= <> +##$AXNUC= +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.5 +##$BCFW= 1 +##$BC_mod= 0 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 1 +##$DFILT= < > +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 0 +##$FT_mod= 0 +##$GAMMA= 1 +##$GB= 0.1 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 0.3 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 5 +##$MEAN= 0 +##$ME_mod= 2 +##$MI= 1 +##$NCOEF= 32 +##$NC_proc= 0 +##$NLEV= 6 +##$NOISF1= 0 +##$NOISF2= 0 +##$NSP= 1 +##$NTH_PI= 0 +##$NZP= 1 +##$OFFSET= 132.4757 +##$PC= 4 +##$PHC0= 0 +##$PHC1= 0 +##$PH_mod= 1 +##$PKNL= yes +##$PPARMOD= 1 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 1 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 60.810645 +##$SI= 256 +##$SIGF1= 0 +##$SIGF2= 0 +##$SINO= 16 +##$SIOLD= 256 +##$SPECTYP= <> +##$SREGLST= <.MeOH> +##$SSB= 2 +##$STSI= 0 +##$STSR= 0 +##$SW_p= 2125.85034013606 +##$SYMM= 0 +##$S_DEV= 0 +##$TDeff= 0 +##$TDoff= 0 +##$TI= < > +##$TILT= no +##$TM1= 0.1 +##$TM2= 0.9 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 4 +##$XDIM= 64 +##$YMAX_p= 0 +##$YMIN_p= 0 +##END= diff --git a/sample/sample_sessions/test00/2/pdata/1/proc2s b/sample/sample_sessions/test00/2/pdata/1/proc2s new file mode 100644 index 0000000..d7ae2a1 --- /dev/null +++ b/sample/sample_sessions/test00/2/pdata/1/proc2s @@ -0,0 +1,109 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 3 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 15:02:16.968 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/proc2s +$$ process /opt/topspin2.1/prog/mod/proc2d +##$ABSF1= 0 +##$ABSF2= 0 +##$ABSG= 0 +##$ABSL= 0 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= < > +##$AXLEFT= 0 +##$AXNAME= +##$AXNUC= <15N> +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.5 +##$BCFW= 0 +##$BC_mod= 0 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 0 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 256 +##$FT_mod= 6 +##$GAMMA= 0 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 0 +##$LEV0= 0 +##$LPBIN= 240 +##$MAXI= 10000 +##$MC2= 5 +##$MEAN= 0 +##$ME_mod= 2 +##$MI= 1 +##$NCOEF= 32 +##$NC_proc= -7 +##$NLEV= 6 +##$NOISF1= 0 +##$NOISF2= 0 +##$NSP= 0 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 132.4757 +##$PC= 4 +##$PHC0= 0 +##$PHC1= 0 +##$PH_mod= 1 +##$PKNL= no +##$PPARMOD= 1 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 1 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 60.810645 +##$SI= 256 +##$SIGF1= 0 +##$SIGF2= 0 +##$SINO= 16 +##$SIOLD= 256 +##$SPECTYP= <> +##$SREGLST= <.MeOH> +##$SSB= 2 +##$STSI= 256 +##$STSR= 0 +##$SW_p= 2125.85034013606 +##$SYMM= 0 +##$S_DEV= 3.127548e+07 +##$TDeff= 240 +##$TDoff= 0 +##$TI= < > +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 4 +##$XDIM= 128 +##$YMAX_p= 225681412 +##$YMIN_p= -132028372 +##END= diff --git a/sample/sample_sessions/test00/2/pdata/1/procs b/sample/sample_sessions/test00/2/pdata/1/procs new file mode 100644 index 0000000..60cb5fb --- /dev/null +++ b/sample/sample_sessions/test00/2/pdata/1/procs @@ -0,0 +1,110 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 5 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 15:02:16.967 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/procs +$$ process /opt/topspin2.1/prog/mod/proc2d +##$ABSF1= 0 +##$ABSF2= 0 +##$ABSG= 0 +##$ABSL= 0 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= +##$AXLEFT= 0 +##$AXNAME= +##$AXNUC= <1H> +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.1 +##$BCFW= 0 +##$BC_mod= 4 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 0 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 2048 +##$FT_mod= 6 +##$GAMMA= 0 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 0 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 0 +##$MEAN= 0 +##$ME_mod= 0 +##$MI= 0 +##$NCOEF= 0 +##$NC_proc= -7 +##$NLEV= 6 +##$NOISF1= 8.174992 +##$NOISF2= 6.675002 +##$NSP= 0 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 11.68554 +##$PC= 1 +##$PHC0= 37.5853 +##$PHC1= -6.6 +##$PH_mod= 1 +##$PKNL= yes +##$PPARMOD= 1 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 4 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 600.13 +##$SI= 2048 +##$SIGF1= 0 +##$SIGF2= 0 +##$SINO= 400 +##$SIOLD= 2048 +##$SPECTYP= <> +##$SREGLST= <1H.H2O+D2O> +##$SSB= 2 +##$STSI= 2048 +##$STSR= 0 +##$SW_p= 8389.26174496644 +##$SYMM= 0 +##$S_DEV= 3.127548e+07 +##$TDeff= 4096 +##$TDoff= 0 +##$TI= +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 4 +##$XDIM= 2048 +##$YMAX_p= 225681412 +##$YMIN_p= -132028372 +##END= diff --git a/sample/sample_sessions/test00/2/pdata/1/title b/sample/sample_sessions/test00/2/pdata/1/title new file mode 100644 index 0000000..439f677 --- /dev/null +++ b/sample/sample_sessions/test00/2/pdata/1/title @@ -0,0 +1,3 @@ +HR4762D.007 2D NH HSQC +HSQCETF3GPSIMS H2O+D2O /opt/topspin2.1 micro_screening 11 +Clear \ No newline at end of file diff --git a/sample/sample_sessions/test00/2/prosol_History b/sample/sample_sessions/test00/2/prosol_History new file mode 100644 index 0000000..b1d9b9f --- /dev/null +++ b/sample/sample_sessions/test00/2/prosol_History @@ -0,0 +1,173 @@ +#******************************************************************* +# +# $Source: /sc/CvsTree/sc/gen/src/prg/scripts/tix/prosol/lib/lists/default,v $ +# +# Copyright (c) 1999 +# BRUKER ANALYTIK GMBH +# D-76287 Rheinstetten, Germany +# +# All Rights Reserved +# +# +# $Id: default,v 1.15.2.2 2007/12/14 16:22:31 ber Exp $ +# +#******************************************************************* +#../conf/instr/spect/prosol/relations/default +#avance-version (07/12/14) +# +#pulses +# +P[0]=P90[F1]; # 90 deg pulse F1 +P[1]=P90[F1]; # 90 deg pulse F1 +P[2]=P90[F1]*2; # 180 deg pulse F1 +P[3]=P90[F2]; # 90 deg pulse F2 +P[4]=P90[F2]*2; # 180 deg pulse F2 +P[5]=PTOC[F1]*0.66; # 60 deg pulse F1, TOCSY +P[6]=PTOC[F1]; # 90 deg pulse F1, TOCSY +P[7]=PTOC[F1]*2; # 180 deg pulse F1, TOCSY +P[8]=PSH3[F1]; # 90 deg selective F1, WET +P[9]=PTOC[F2]; # 90 deg pulse F2, TOCSY +P[10]=PTOC[F2]*2; # 180 deg pulse F2, TOCSY +P[11]=PSH1[F1]; # 90 deg selective F1 +P[12]=PSH2[F1]; # 180 deg selective F1 +# +P[14]=PSH3[F2]; # 180 deg inversion, adiabatic +P[15]=TROE[F1]; # cw pulse F1, ROESY +P[18]=PSH7[F1]; # off-resonance presat F1 +P[21]=P90[F3]; # 90 deg pulse F3 +P[22]=P90[F3]*2; # 180 deg pulse F3 +P[23]=P90[F4]; # 90 deg pulse F4 +P[24]=PSH2[F2]; # 180 deg refocussing, adiabatic +P[25]=PROE[F1]*2; # 180 deg pulse, Shaka ROESY +P[26]=PSH12[F1]; # 180 deg inversion F1, adiabatic +P[27]=P90[F1]; # 90 deg pulse F1, WATERGATE +# +P[29]=PSH8[F1]; # flip back pulse +P[31]=PSH15[F2]; # 180 deg adiabatic, F2, 13C x-filter +P[32]=PSH16[F1]; # 180 deg adiabatic, F1, z-spoil +#P[33]=PSH[F1]; # 90 deg, F1, hadamard +#P[34]=PSH[F1]; # 180 deg, F1, hadamard +#P[35]=PSH[F2]; # 90 deg, F2, hadamard +#P[36]=PSH[F2]; # 180 deg, F2, hadamard +#P[37]=PSH[F3]; # 90 deg, F3, hadamard +#P[38]=PSH[F3]; # 180 deg, F3, hadamard +P[39]=PSH21[F2]; # 180 deg, F2, Bip +P[40]=PSH8[F1]*2; # 180 deg sel. F1, 1H (exc. scul) +# +P[63]=PSH11[F2]; # 180 deg adiabatic decoupling, F2, 13C +# +#decoupling pulses +# +PCPD[1]=PCPDP[F1]; # 90 deg pulse F1, dec. +PCPD[2]=PCPDP[F2]; # 90 deg pulse F2, dec. +PCPD[3]=PCPDP[F3]; # 90 deg pulse F3, dec. +# +#power levels +# +PL[1]=PL90[F1]; # high power, F1 +PL[2]=PL90[F2]; # high power, F2 +PL[3]=PL90[F3]; # high power, F3 +PL[4]=PL90[F4]; # high power, F4 +PL[9]=PLCW[F1]; # presat power, F1 +PL[10]=PLTOC[F1]; # TOCSY power, F1 +PL[11]=PLROE[F1]; # ROESY power, F1 +PL[12]=PLCPDP[F2]; # dec. power, F2 +PL[13]=PLCPD2[F2]; # dec. power 2, F2 +PL[14]=PLNOE[F2]; # low power cw, F2 +PL[15]=PLTOC[F2]; # TOCSY power, F2 +PL[16]=PLCPDP[F3]; # dec. power, F3 +PL[18]=PL90[F1]; # WATERGATE power, F1 +PL[19]=PLCPDP[F1]; # dec. power, F1 +PL[21]=PLCW[F2]; # +PL[23]=PLTOC[F3]; # TOCSY power, F3 +PL[24]=PLHD[F2]; # HD decoupling, F2 +PL[25]=PLSH8U[F2]; # Eretic, F2 +PL[27]=PLROE[F1]; # Shaka Spinlock +PL[30]=PLCPDP[F2]; # dec. power, F2, 13C (=pl12) +PL[31]=PLUSER2[F2]; # dec. power, F2, 13C, cw bilev +# +#shapes +# +SP[1]=PLSH1[F1]; # 90 deg selective F1 +SP[2]=PLSH2[F1]; # 180 deg selective F1 +SP[3]=PLSH3[F2]; # adiabatic 180 deg, F2, inversion +SP[4]=PLSH21[F2]; # 180 deg Bip, F2, inversion +SP[6]=PLSH7[F1]; # off-resonance presat F1 +SP[7]=PLSH2[F2]; # adiabatic 180 deg, F2, refocussing +SP[8]=PLSH12[F1]; # adiabatic 180 deg, F1, inversion +SP[10]=PLSH8[F1]; # flip-back pulse, F1, 1H +SP[11]=PLSH8[F1]; # flip-back pulse, F1, H +SP[14]=PLSH12[F2]; # adiab. bilev dec., F2, 13C +SP[18]=PLSH15[F2]; # adiabatic 180 deg, F2, 13C, x-filter +SP[19]=PLSH3[F1] +0.87; # 90 deg, F1, wet +SP[20]=PLSH3[F1] -1.04; # 90 deg, F1, wet +SP[21]=PLSH3[F1] +2.27; # 90 deg, F1, wet +SP[22]=PLSH3[F1] -5.05; # 90 deg, F1, wet +#SP[23]=PLSH[F1]; # 90 deg, F1, hadamard +#SP[24]=PLSH[F1]; # 180 deg, F1, hadamard +#SP[25]=PLSH[F2]; # 90 deg, F2, hadamard +#SP[26]=PLSH[F2]; # 180 deg, F2, hadamard +#SP[27]=PLSH[F3]; # 90 deg, F3, hadamard +#SP[28]=PLSH[F3]; # 180 deg, F3, hadamard +SP[29]=PLSH16[F1]; # adiabatic 180 deg, F1, z-spoil +SP[31]=PLSH11[F2]; # adiab. dec., F2, 13C +# +SPNAM1=PNSH1[F1]; # +SPNAM2=PNSH2[F1]; # +SPNAM3=PNSH3[F2]; # +SPNAM4=PNSH21[F2]; # +SPNAM6=PNSH7[F1]; # +SPNAM7=PNSH2[F2]; # +SPNAM8=PNSH12[F1]; # +SPNAM10=PNSH8[F1]; # +SPNAM11=PNSH8[F1]; # +SPNAM14=PNSH12[F2]; # +SPNAM15=PNSH8U[F2]; # Eretic, F2 +SPNAM18=PNSH15[F2]; # +SPNAM19=PNSH3[F1]; # +SPNAM20=PNSH3[F1]; # +SPNAM21=PNSH3[F1]; # +SPNAM22=PNSH3[F1]; # +#SPNAM23=PNSH[]; # +#SPNAM24=PNSH[]; # +#SPNAM25=PNSH[]; # +#SPNAM26=PNSH[]; # +#SPNAM27=PNSH[]; # +#SPNAM28=PNSH[]; # +SPNAM29=PNSH16[F1]; # +SPNAM31=PNSH11[F2]; # +# +SPOAL[1]=PASH1[F1]; # +SPOAL[2]=PASH2[F1]; # +SPOAL[3]=PASH3[F2]; # +SPOAL[4]=PASH21[F2]; # +SPOAL[6]=PASH7[F1]; # +SPOAL[7]=PASH2[F2]; # +SPOAL[8]=PASH12[F1]; # +SPOAL[10]=PASH8[F1]; +SPOAL[11]=PASH8[F1]; +SPOAL[14]=PASH12[F2]; # +SPOAL[18]=PASH15[F2]; # +SPOAL[19]=PASH3[F1]; # +SPOAL[20]=PASH3[F1]; # +SPOAL[21]=PASH3[F1]; # +SPOAL[22]=PASH3[F1]; # +#SPOAL[23]=PASH[]; # +#SPOAL[24]=PASH[]; # +#SPOAL[25]=PASH[]; # +#SPOAL[26]=PASH[]; # +#SPOAL[27]=PASH[]; # +#SPOAL[28]=PASH[]; # +SPOAL[29]=PASH16[F1]; # +SPOAL[31]=PASH11[F2]; # +# +#global +# +D[9]=TTOC[F1]; # +D[16]=D_grad; # +P[16]=P_grad1; # +P[17]=P_mlev; # +P[19]=P_grad2; # +P[20]=P_mlev; # +P[28]=P_hsqc; # +# diff --git a/sample/sample_sessions/test00/2/pulseprogram b/sample/sample_sessions/test00/2/pulseprogram new file mode 100644 index 0000000..1cfe5ac --- /dev/null +++ b/sample/sample_sessions/test00/2/pulseprogram @@ -0,0 +1,422 @@ +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" +;hsqcetf3gpsi +;avance-version (07/04/04) +;HSQC +;2D H-1/X correlation via double inept transfer +; using sensitivity improvement +;phase sensitive using Echo/Antiecho-TPPI gradient selection +;with decoupling during acquisition +;using trim pulses in inept transfer +;using f3 - channel +; +;A.G. Palmer III, J. Cavanagh, P.E. Wright & M. Rance, J. Magn. +; Reson. 93, 151-170 (1991) +;L.E. Kay, P. Keifer & T. Saarinen, J. Am. Chem. Soc. 114, +; 10663-5 (1992) +;J. Schleucher, M. Schwendinger, M. Sattler, P. Schmidt, O. Schedletzky, +; S.J. Glaser, O.W. Sorensen & C. Griesinger, J. Biomol. NMR 4, +; 301-306 (1994) +; +;$CLASS=HighRes +;$DIM=2D +;$TYPE= +;$SUBTYPE= +;$COMMENT= + + + +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/Avance.incl" 1 +;Avance2.incl +; for 1 +; +;avance-version (07/08/21) +; +;$CLASS=HighRes Incl +;$COMMENT= + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +;$Id: Avance2.incl,v 1.17.2.1 2007/09/14 16:17:35 ber Exp $ +# 27 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" 2 + +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/Grad.incl" 1 +;Grad2.incl - include file for Gradient Spectroscopy +; for 1 +; +;avance-version (07/01/17) +; +;$CLASS=HighRes Incl +;$COMMENT= + + + + + + + + + + + + + + + + + + + +define list EA= + + + +;$Id: Grad2.incl,v 1.12 2007/01/22 14:22:35 ber Exp $ +# 28 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" 2 + +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/Delay.incl" 1 +;Delay.incl - include file for commonly used delays +; +;version 00/02/07 +; +;$CLASS=HighRes Incl +;$COMMENT= + + +;general delays + +define delay DELTA +define delay DELTA1 +define delay DELTA2 +define delay DELTA3 +define delay DELTA4 +define delay DELTA5 +define delay DELTA6 +define delay DELTA7 +define delay DELTA8 + +define delay TAU +define delay TAU1 +define delay TAU2 +define delay TAU3 +define delay TAU4 +define delay TAU5 + + +;delays for centering pulses + +define delay CEN_HN1 +define delay CEN_HN2 +define delay CEN_HN3 +define delay CEN_HC1 +define delay CEN_HC2 +define delay CEN_HC3 +define delay CEN_HC4 +define delay CEN_HP1 +define delay CEN_HP2 +define delay CEN_CN1 +define delay CEN_CN2 +define delay CEN_CN3 +define delay CEN_CN4 +define delay CEN_CP1 +define delay CEN_CP2 + + +;loop counters + +define loopcounter COUNTER +define loopcounter SCALEF +define loopcounter FACTOR1 +define loopcounter FACTOR2 +define loopcounter FACTOR3 + + + +;$Id: Delay.incl,v 1.12 2005/11/10 12:16:58 ber Exp $ +# 29 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" 2 + + + +"p2=p1*2" +"p22=p21*2" +"d11=30m" +"d13=4u" +"d26=1s/(cnst4*4)" + + +"d0=3u" + +"in0=inf1/2" + + +"DELTA1=d13+p16+d16+4u" + + + + +"DELTA=p16+d16+p2+d0*2" + + + +# 1 "mc_line 53 file /opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi expanding definition part of mc command before ze" +define delay MCWRK +define delay MCREST +define loopcounter ST1CNT +"ST1CNT = td1 / (2)" +"MCWRK = 0.142857*d1" +"MCREST = d1 - d1" + dccorr +# 53 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" +1 ze +# 1 "mc_line 53 file /opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi expanding definition of mc command after ze" +# 54 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" + d11 pl16:f3 +# 1 "mc_line 55 file /opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi expanding start label for mc command" +2 MCWRK * 2 do:f3 +LBLSTS1, MCWRK * 4 +LBLF1, MCWRK + MCREST +# 56 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" +3 (p1 ph1) + d26 pl3:f3 + (center (p2 ph1) (p22 ph6):f3 ) + d26 setnmr3|0 setnmr0|34|32|33 ctrlgrad 0 + p28 ph1 + d13 + (p1 ph2) + 3u + p16:gp1 + d16 + (p21 ph3):f3 + d0 + + + + + (p2 ph7) + + + d0 + p16:gp2*EA + d16 + (p22 ph4):f3 + DELTA + (center (p1 ph1) (p21 ph4):f3 ) + d24 + (center (p2 ph1) (p22 ph1):f3 ) + d24 + (center (p1 ph2) (p21 ph5):f3 ) + d26 + (center (p2 ph1) (p22 ph1):f3 ) + d26 + (p1 ph1) + DELTA1 + (p2 ph1) + d13 + p16:gp3 + d16 pl16:f3 + 4u setnmr3^0 setnmr0^34^32^33 ctrlgrad 7 + go=2 ph31 cpd3:f3 +# 1 "mc_line 96 file /opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi expanding mc command in line" + MCWRK do:f3 wr #0 if #0 zd igrad EA MCWRK ip5*2 + lo to LBLSTS1 times 2 + MCWRK id0 MCWRK ip3*2 MCWRK ip6*2 MCWRK ip31*2 + lo to LBLF1 times ST1CNT + MCWRK +# 98 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" +exit + + +ph1=0 +ph2=1 +ph3=0 2 +ph4=0 0 2 2 +ph5=1 1 3 3 +ph6=0 +ph7=0 0 2 2 +ph31=0 2 2 0 + + +;pl1 : f1 channel - power level for pulse (default) +;pl3 : f3 channel - power level for pulse (default) +;pl16: f3 channel - power level for CPD/BB decoupling +;sp3: f2 channel - shaped pulse 180 degree (adiabatic) +;p1 : f1 channel - 90 degree high power pulse +;p2 : f1 channel - 180 degree high power pulse +;p14: f2 channel - 180 degree shaped pulse for inversion (adiabatic) +;p16: homospoil/gradient pulse [1 msec] +;p21: f3 channel - 90 degree high power pulse +;p22: f3 channel - 180 degree high power pulse +;p28: f1 channel - trim pulse [1 msec] +;d0 : incremented delay (2D) [3 usec] +;d1 : relaxation delay; 1-5 * T1 +;d11: delay for disk I/O [30 msec] +;d13: short delay [4 usec] +;d16: delay for homospoil/gradient recovery +;d24: 1/(4J)YH for YH +; 1/(8J)YH for all multiplicities +;d26: 1/(4J(YH)) +;cnst4: = J(YH) +;inf1: 1/SW(X) = 2 * DW(X) +;in0: 1/(2 * SW(X)) = DW(X) +;nd0: 2 +;NS: 1 * n +;DS: >= 16 +;td1: number of experiments +;FnMODE: echo-antiecho +;cpd3: decoupling according to sequence defined by cpdprg3 +;pcpd3: f3 channel - 90 degree pulse for decoupling sequence + + +;use gradient ratio: gp 1 : gp 2 : gp 3 +; 50 : 80 : 20.1 for C-13 +; 50 : 80 : 8.1 for N-15 + +;for z-only gradients: +;gpz1: 50% +;gpz2: 80% +;gpz3: 20.1% for C-13, 8.1% for N-15 + +;use gradient files: +;gpnam1: SINE.100 +;gpnam2: SINE.100 +;gpnam3: SINE.100 + + + ;preprocessor-flags-start +;LABEL_CN: for C-13 and N-15 labeled samples start experiment with +; option -DLABEL_CN (eda: ZGOPTNS) + ;preprocessor-flags-end + + + +;$Id: hsqcetf3gpsi,v 1.4 2007/04/11 13:34:30 ber Exp $ diff --git a/sample/sample_sessions/test00/2/scon2 b/sample/sample_sessions/test00/2/scon2 new file mode 100644 index 0000000..867251b --- /dev/null +++ b/sample/sample_sessions/test00/2/scon2 @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-26 22:16:43.586 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/scon2 +$$ process /opt/topspin2.1/prog/mod/go +##$BLKTR= (0..15) +3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 +##$DE1= 4.5 +##$DEADC= 0.5 +##$DEPA= 4.5 +##$DERX= 1.5 +##$FILCOR= 0.2 +##END= diff --git a/sample/sample_sessions/test00/2/ser b/sample/sample_sessions/test00/2/ser new file mode 100644 index 0000000..09b1825 Binary files /dev/null and b/sample/sample_sessions/test00/2/ser differ diff --git a/sample/sample_sessions/test00/2/uxnmr.par b/sample/sample_sessions/test00/2/uxnmr.par new file mode 100644 index 0000000..c90a4f2 --- /dev/null +++ b/sample/sample_sessions/test00/2/uxnmr.par @@ -0,0 +1,527 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 104 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2009-12-15 16:47:14.463 -0500 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/conf/instr/spect/uxnmr.par +$$ process /opt/topspin2.1/prog/mod/hconfserver +##$ACB= 1 +##$ACBTAT= (0..15) +0 88 72 88 0 0 88 0 0 0 0 0 0 0 0 0 +##$ACBTBA= (0..15) +0 30 60 90 0 0 180 0 0 0 0 0 0 0 0 0 +##$ACBTBLK= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTCTL= (0..15) +0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 +##$ACBTDI= (0..15) +0 70 71 72 0 0 75 0 0 0 0 0 0 0 0 0 +##$ACBTDM= (0..15) +0 6 25 10 0 0 10 0 0 0 0 0 0 0 0 0 +##$ACBTFHI= (0..15) +0 365 600 365 0 0 365 0 0 0 0 0 0 0 0 0 +##$ACBTFL= (0..15) +0 249 249 249 0 0 249 0 0 0 0 0 0 0 0 0 +##$ACBTFLO= (0..15) +0 6 188 6 0 0 6 0 0 0 0 0 0 0 0 0 +##$ACBTINP= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTOUT= (0..15) +0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 +##$ACBTPO= (0..15) +0 500000 100000 300000 0 0 300000 0 0 0 0 0 0 0 0 0 +##$ACBTPW= (0..15) +0 600 1000 1000 0 0 1000 0 0 0 0 0 0 0 0 0 +##$ACBTSB= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTY= +##$AQSBDCH= (0..95) +0 0 0 0 0 0 0 0 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDHW= (0..95) +1 4 4 4 0 1 4 4 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDID= (0..95) +88 83 83 83 89 88 83 83 89 80 80 66 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSBDNO= (0..95) +1 1 2 3 1 2 4 5 2 1 2 1 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDSL= (0..95) +4 5 6 7 8 10 11 12 15 17 18 19 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 +##$AQSBDTY= (0..95) +194 16 24 16 4 194 24 16 4 10 10 7 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSBUAD= (0..95) +52 36 37 38 60 53 39 40 61 33 34 32 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSECL= (0..95) +0 1 1 1 1 0 1 1 1 1 1 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 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-1 -1 -1 +-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$ROUT14= (0..7) +0 0 0 0 0 0 0 0 +##$ROUTER= 2 +##$RX22TY= +##$RXFMAX= (0..7) +-1 -1 -1 -1 -1 -1 -1 -1 +##$RXFMIN= (0..7) +-1 -1 -1 -1 -1 -1 -1 -1 +##$RXINTLV= (0..7) +0 0 0 0 0 0 0 0 +##$RXMSTY= +##$SCMTY= +##$SGUC1= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$SGUC2= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$SPECTR= 5 +##$SY2FLAG= 0 +##$TFXNUM= 0 +##$TRIPLO2= 0 +##$VTUTY= +##$WBREFAM= (0..15) +100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 +##$WBREFPH= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$XFAC= 2 +##END= diff --git a/sample/sample_sessions/test00/specdb.session.yaml b/sample/sample_sessions/test00/specdb.session.yaml new file mode 100644 index 0000000..0e5de84 --- /dev/null +++ b/sample/sample_sessions/test00/specdb.session.yaml @@ -0,0 +1,28 @@ +session: + session_preparer: TAR + spectrometer_id: Hu800 + pst_id: Db0515A.000 + folder_name: test00 +time_domain_data: + '1': + subdir_name: '1' + pulse_sequence_nickname: + probe_id: + session_id: 1 + md5checksum: f1d80ff78a50d207b4d3b13af239b839 + temperature_from_data: 293.0 + experiment_date: '2010-09-26 21:33:06.812' + pulse_sequence: zgpr + probe_info: 1.7_mm_CPTCI_1H-13C/15N/D_Z-GRD_Z108160/0002 + pst_id: Db0515A.000 + '2': + subdir_name: '2' + pulse_sequence_nickname: + probe_id: + session_id: 1 + md5checksum: e3c4e84d0ae67e8ca1160ebf6d5b6838 + temperature_from_data: 293.0 + experiment_date: '2010-09-26 22:16:43.706' + pulse_sequence: hsqcetf3gpsi + probe_info: 1.7_mm_CPTCI_1H-13C/15N/D_Z-GRD_Z108160/0002 + pst_id: Db0515A.000 diff --git a/sample/sample_sessions/test01/.DS_Store b/sample/sample_sessions/test01/.DS_Store new file mode 100644 index 0000000..3b13d6d Binary files /dev/null and b/sample/sample_sessions/test01/.DS_Store differ diff --git a/sample/sample_sessions/test01/1/.DS_Store b/sample/sample_sessions/test01/1/.DS_Store new file mode 100644 index 0000000..835f63a Binary files /dev/null and b/sample/sample_sessions/test01/1/.DS_Store differ diff --git a/sample/sample_sessions/test01/1/acqu b/sample/sample_sessions/test01/1/acqu new file mode 100644 index 0000000..6ff6bac --- /dev/null +++ b/sample/sample_sessions/test01/1/acqu @@ -0,0 +1,405 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 22 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-26 21:32:08.427 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/acqu +$$ process /opt/topspin2.1/prog/mod/sipar +##$ACQT0= 0 +##$AMP= (0..31) +100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 +100 100 100 100 100 100 100 100 100 100 100 100 100 100 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0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DBPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DE= 6.5 +##$DECBNUC= +##$DECIM= 16 +##$DECNUC= +##$DECSTAT= 4 +##$DIGMOD= 1 +##$DIGTYP= 8 +##$DL= (0..7) +0 120 120 120 120 120 120 120 +##$DP= (0..7) +150 150 150 150 150 150 150 150 +##$DP07= 0 +##$DPNAME0= <> +##$DPNAME1= <> +##$DPNAME2= <> +##$DPNAME3= <> +##$DPNAME4= <> +##$DPNAME5= <> +##$DPNAME6= <> +##$DPNAME7= <> +##$DPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DQDMODE= 0 +##$DR= 18 +##$DS= 2 +##$DSLIST= +##$DSPFIRM= 0 +##$DSPFVS= 0 +##$DTYPA= 0 +##$EXP= +##$F1LIST= <111111111111111> +##$F2LIST= <222222222222222> +##$F3LIST= <333333333333333> +##$FCUCHAN= (0..9) +0 2 1 0 0 0 0 0 0 0 +##$FL1= 90 +##$FL2= 90 +##$FL3= 90 +##$FL4= 90 +##$FOV= 20 +##$FQ1LIST= +##$FQ2LIST= +##$FQ3LIST= +##$FQ4LIST= +##$FQ5LIST= +##$FQ6LIST= +##$FQ7LIST= +##$FQ8LIST= +##$FRQLO3= 0 +##$FRQLO3N= 0 +##$FS= (0..7) +83 83 83 83 83 83 83 83 +##$FTLPGN= 0 +##$FW= 125000 +##$FnMODE= 0 +##$FnTYPE= 0 +##$GP031= 0 +##$GPNAM0= +##$GPNAM1= +##$GPNAM10= +##$GPNAM11= +##$GPNAM12= +##$GPNAM13= +##$GPNAM14= +##$GPNAM15= +##$GPNAM16= +##$GPNAM17= +##$GPNAM18= +##$GPNAM19= +##$GPNAM2= +##$GPNAM20= +##$GPNAM21= +##$GPNAM22= +##$GPNAM23= +##$GPNAM24= +##$GPNAM25= +##$GPNAM26= +##$GPNAM27= +##$GPNAM28= +##$GPNAM29= +##$GPNAM3= +##$GPNAM30= +##$GPNAM31= +##$GPNAM4= +##$GPNAM5= +##$GPNAM6= +##$GPNAM7= +##$GPNAM8= +##$GPNAM9= +##$GPX= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GPY= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GPZ= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GRDPROG= <> +##$GRPDLY= -1 +##$HDDUTY= 20 +##$HDRATE= 20 +##$HGAIN= (0..3) +0 0 0 0 +##$HL1= 1 +##$HL2= 35 +##$HL3= 16 +##$HL4= 17 +##$HOLDER= 11 +##$HPMOD= (0..7) +0 0 0 0 0 0 0 0 +##$HPPRGN= 0 +##$IN= (0..63) +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 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75.92 6.83 120 0 51.32 51.32 0 0 8.31 0 150 150 +12.22 78.21 76.3 79.60999 72.28999 150 150 150 150 150 150 40.1 150 14.33 +##$SP07= 0 +##$SPECTR= 0 +##$SPNAM0= +##$SPNAM1= +##$SPNAM10= +##$SPNAM11= +##$SPNAM12= +##$SPNAM13= +##$SPNAM14= +##$SPNAM15= < > +##$SPNAM16= +##$SPNAM17= +##$SPNAM18= +##$SPNAM19= +##$SPNAM2= +##$SPNAM20= +##$SPNAM21= +##$SPNAM22= +##$SPNAM23= +##$SPNAM24= +##$SPNAM25= +##$SPNAM26= +##$SPNAM27= +##$SPNAM28= +##$SPNAM29= +##$SPNAM3= +##$SPNAM30= +##$SPNAM31= +##$SPNAM4= +##$SPNAM5= +##$SPNAM6= +##$SPNAM7= +##$SPNAM8= < > +##$SPNAM9= +##$SPOAL= (0..31) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$SPOFFS= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$SUBNAM0= <""> +##$SUBNAM1= <""> +##$SUBNAM2= <""> +##$SUBNAM3= <""> +##$SUBNAM4= <""> +##$SUBNAM5= <""> +##$SUBNAM6= <""> +##$SUBNAM7= <""> +##$SUBNAM8= <""> +##$SUBNAM9= <""> +##$SW= 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0000000..f07b868 --- /dev/null +++ b/sample/sample_sessions/test01/1/acqus @@ -0,0 +1,406 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 11 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-26 22:15:22.481 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/acqus +$$ process /opt/topspin2.1/prog/mod/shimcntl +##$ACQT0= -7.63941940412529 +##$AMP= (0..31) +100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 +100 100 100 100 100 100 100 100 100 100 100 100 100 100 +##$ANAVPT= -1 +##$AQSEQ= 0 +##$AQ_mod= 3 +##$AUNM= +##$AUTOPOS= <11 > +##$BF1= 600.13 +##$BF2= 150.902809 +##$BF3= 600.13 +##$BF4= 600.13 +##$BF5= 600.13 +##$BF6= 600.13 +##$BF7= 600.13 +##$BF8= 600.13 +##$BYTORDA= 1 +##$CFDGTYP= 2 +##$CFRGTYP= 5 +##$CHEMSTR= +##$CNST= (0..63) +1 1 145 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +##$CPDPRG= <> +##$CPDPRG1= <> +##$CPDPRG2= <> +##$CPDPRG3= <> +##$CPDPRG4= +##$CPDPRG5= +##$CPDPRG6= +##$CPDPRG7= +##$CPDPRG8= +##$CPDPRGB= <> +##$CPDPRGT= <> +##$D= (0..63) +0 2 0 0 0 0 0 0 0 0.06 0 0 2e-05 0 0 0 0.0002 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$DATE= 1285553717 +##$DBL= (0..7) +120 120 120 120 120 120 120 120 +##$DBP= (0..7) +150 150 150 150 150 150 150 150 +##$DBP07= 0 +##$DBPNAM0= <> +##$DBPNAM1= <> +##$DBPNAM2= <> +##$DBPNAM3= <> +##$DBPNAM4= <> +##$DBPNAM5= <> +##$DBPNAM6= <> +##$DBPNAM7= <> +##$DBPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DBPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DE= 6.5 +##$DECBNUC= +##$DECIM= 16 +##$DECNUC= +##$DECSTAT= 4 +##$DIGMOD= 1 +##$DIGTYP= 8 +##$DL= (0..7) +0 120 120 120 120 120 120 120 +##$DP= (0..7) +150 150 150 150 150 150 150 150 +##$DP07= 0 +##$DPNAME0= <> +##$DPNAME1= <> +##$DPNAME2= <> +##$DPNAME3= <> +##$DPNAME4= <> +##$DPNAME5= <> +##$DPNAME6= <> +##$DPNAME7= <> +##$DPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DQDMODE= 0 +##$DR= 18 +##$DS= 2 +##$DSLIST= +##$DSPFIRM= 0 +##$DSPFVS= 12 +##$DTYPA= 0 +##$EXP= +##$F1LIST= <111111111111111> +##$F2LIST= <222222222222222> +##$F3LIST= <333333333333333> +##$FCUCHAN= (0..9) +0 2 1 0 0 0 0 0 0 0 +##$FL1= 90 +##$FL2= 90 +##$FL3= 90 +##$FL4= 90 +##$FOV= 20 +##$FQ1LIST= +##$FQ2LIST= +##$FQ3LIST= +##$FQ4LIST= +##$FQ5LIST= +##$FQ6LIST= +##$FQ7LIST= +##$FQ8LIST= +##$FRQLO3= 1894230.76923077 +##$FRQLO3N= 0 +##$FS= (0..7) +83 83 83 83 83 83 83 83 +##$FTLPGN= 0 +##$FW= 125000 +##$FnMODE= 0 +##$FnTYPE= 0 +##$GP031= 0 +##$GPNAM0= +##$GPNAM1= +##$GPNAM10= +##$GPNAM11= +##$GPNAM12= +##$GPNAM13= +##$GPNAM14= +##$GPNAM15= +##$GPNAM16= +##$GPNAM17= +##$GPNAM18= +##$GPNAM19= +##$GPNAM2= +##$GPNAM20= +##$GPNAM21= +##$GPNAM22= +##$GPNAM23= +##$GPNAM24= +##$GPNAM25= +##$GPNAM26= +##$GPNAM27= +##$GPNAM28= +##$GPNAM29= +##$GPNAM3= +##$GPNAM30= +##$GPNAM31= +##$GPNAM4= +##$GPNAM5= +##$GPNAM6= +##$GPNAM7= +##$GPNAM8= +##$GPNAM9= +##$GPX= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GPY= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GPZ= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GRDPROG= <> +##$GRPDLY= -1 +##$HDDUTY= 20 +##$HDRATE= 20 +##$HGAIN= (0..3) +0 0 0 0 +##$HL1= 1 +##$HL2= 35 +##$HL3= 16 +##$HL4= 17 +##$HOLDER= 0 +##$HPMOD= (0..7) +0 0 0 0 0 0 0 0 +##$HPPRGN= 0 +##$IN= (0..63) +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 +##$INF= (0..7) +0 0 0 0 0 0 0 0 +##$INP= (0..63) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$INSTRUM= +##$L= (0..31) +1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +##$LFILTER= 100 +##$LGAIN= -15 +##$LINPSTP= 10 +##$LOCKED= yes +##$LOCKFLD= 4675 +##$LOCKGN= 131.399993896484 +##$LOCKPOW= -10 +##$LOCKPPM= 4.69999980926514 +##$LOCNUC= <2H> +##$LOCPHAS= 269.6 +##$LOCSHFT= yes +##$LOCSW= 0 +##$LTIME= 0.200000002980232 +##$MASR= 4200 +##$MASRLST= +##$NBL= 1 +##$NC= -2 +##$NLOGCH= 1 +##$NS= 1024 +##$NUC1= <1H> +##$NUC2= <13C> +##$NUC3= +##$NUC4= +##$NUC5= +##$NUC6= +##$NUC7= +##$NUC8= +##$NUCLEI= 0 +##$NUCLEUS= +##$O1= 2818.21048 +##$O2= 7469.21502263831 +##$O3= 2850.6175 +##$O4= 2850.47650618253 +##$O5= 2850.47650618253 +##$O6= 2850.47650618253 +##$O7= 2850.47650618253 +##$O8= 2850.47650618253 +##$OBSCHAN= (0..9) +0 0 0 0 0 0 0 0 0 0 +##$OVERFLW= 0 +##$P= (0..63) +12 12 24 11 22 18.48 28 56 20000 25 50 80000 80000 0 500 250000 1000 2500 +10000 600 2500 0 0 0 2000 250 0 12 1000 1000 0 1730 20000 0 0 0 0 0 0 160 +2000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1500 +##$PACOIL= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAPS= 2 +##$PARMODE= 0 +##$PCPD= (0..9) +100 60 60 100 100 100 100 100 100 100 +##$PHCOR= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PHLIST= <> +##$PHP= 1 +##$PH_ref= 0 +##$PL= (0..63) +120 17.5 -0.5 120 120 120 120 120 120 69.9 24.86 37.85 14.24 120 120 6.63 +120 120 17.5 31.48 120 120 120 120 120 120 120 37.85 120 120 14.24 8.21 +120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 +120 120 120 120 120 120 120 120 120 120 120 120 120 120 +##$PLSTEP= 0.1 +##$PLSTRT= -6 +##$POWMOD= 0 +##$PQPHASE= 0 +##$PQSCALE= 0 +##$PR= 1 +##$PRECHAN= (0..15) +-1 3 0 4 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$PRGAIN= 0 +##$PROBHD= <1.7 mm CPTCI 1H-13C/15N/D Z-GRD Z108160/0002 +> +##$PROSOL= no +##$PULPROG= +##$PW= 0 +##$PYNM= +##$QNP= 1 +##$RD= 0 +##$RECCHAN= (0..15) +0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$RECPH= 0 +##$RECPRE= (0..15) +-1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$RECPRFX= (0..15) +-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$RECSEL= (0..15) +0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$RG= 181 +##$RO= 0 +##$ROUTWD1= (0..23) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 +##$ROUTWD2= (0..23) +0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 +##$RSEL= (0..9) +0 1 2 0 0 0 0 0 0 0 +##$S= (0..7) +83 4 83 83 83 83 83 83 +##$SEOUT= 0 +##$SFO1= 600.13281821048 +##$SFO2= 150.910278215023 +##$SFO3= 600.1328506175 +##$SFO4= 600.132850476506 +##$SFO5= 600.132850476506 +##$SFO6= 600.132850476506 +##$SFO7= 600.132850476506 +##$SFO8= 600.132850476506 +##$SOLVENT= +##$SP= (0..31) +1 86.27 80.25 6.83 4.69 0 75.92 6.83 120 0 51.32 51.32 0 0 8.31 0 150 150 +12.22 78.21 76.3 79.60999 72.28999 150 150 150 150 150 150 40.1 150 14.33 +##$SP07= 0 +##$SPECTR= 0 +##$SPNAM0= +##$SPNAM1= +##$SPNAM10= +##$SPNAM11= +##$SPNAM12= +##$SPNAM13= +##$SPNAM14= +##$SPNAM15= < > +##$SPNAM16= +##$SPNAM17= +##$SPNAM18= +##$SPNAM19= +##$SPNAM2= +##$SPNAM20= +##$SPNAM21= +##$SPNAM22= +##$SPNAM23= +##$SPNAM24= +##$SPNAM25= +##$SPNAM26= +##$SPNAM27= +##$SPNAM28= +##$SPNAM29= +##$SPNAM3= +##$SPNAM30= +##$SPNAM31= +##$SPNAM4= +##$SPNAM5= +##$SPNAM6= +##$SPNAM7= +##$SPNAM8= < > +##$SPNAM9= +##$SPOAL= (0..31) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$SPOFFS= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$SUBNAM0= <""> +##$SUBNAM1= <""> +##$SUBNAM2= <""> +##$SUBNAM3= <""> +##$SUBNAM4= <""> +##$SUBNAM5= <""> +##$SUBNAM6= <""> +##$SUBNAM7= <""> +##$SUBNAM8= <""> +##$SUBNAM9= <""> +##$SW= 16.0220943158157 +##$SWIBOX= (0..15) +0 1 2 3 0 0 6 0 0 0 0 0 0 0 0 0 +##$SW_h= 9615.38461538462 +##$SWfinal= 0 +##$TD= 8192 +##$TD0= 1 +##$TE= 293 +##$TE2= 300 +##$TE3= 300 +##$TEG= 300 +##$TL= (0..7) +0 120 120 120 120 120 120 120 +##$TP= (0..7) +150 150 150 150 150 150 150 150 +##$TP07= 0 +##$TPNAME0= <> +##$TPNAME1= <> +##$TPNAME2= <> +##$TPNAME3= <> +##$TPNAME4= <> +##$TPNAME5= <> +##$TPNAME6= <> +##$TPNAME7= <> +##$TPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$TPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$TUNHIN= 0 +##$TUNHOUT= 0 +##$TUNXOUT= 0 +##$USERA1= +##$USERA2= +##$USERA3= +##$USERA4= +##$USERA5= +##$V9= 5 +##$VALIST= +##$VCLIST= +##$VD= 0 +##$VDLIST= +##$VPLIST= +##$VTLIST= +##$WBST= 1024 +##$WBSW= 20 +##$XGAIN= (0..3) +0 0 0 0 +##$XL= 0 +##$YL= 0 +##$YMAX_a= 38758765 +##$YMIN_a= -62247272 +##$ZGOPTNS= <> +##$ZL1= 120 +##$ZL2= 120 +##$ZL3= 120 +##$ZL4= 120 +##END= diff --git a/sample/sample_sessions/test01/1/audita.txt b/sample/sample_sessions/test01/1/audita.txt new file mode 100644 index 0000000..21d18cf --- /dev/null +++ b/sample/sample_sessions/test01/1/audita.txt @@ -0,0 +1,23 @@ +##TITLE= Audit trail, TOPSPIN Version 2.1 +##JCAMPDX= 5.01 +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/audita.txt +##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT) +( 1,<2010-09-26 22:15:17.520 -0400>,,,,, + ) +( 2,<2010-09-26 22:15:23.238 -0400>,,,,, + ) +##END= + +$$ hash MD5 +$$ 8F 44 24 67 FF 89 A5 C0 B5 C3 70 80 28 EE EA 32 diff --git a/sample/sample_sessions/test01/1/fid b/sample/sample_sessions/test01/1/fid new file mode 100644 index 0000000..56c7f35 Binary files /dev/null and b/sample/sample_sessions/test01/1/fid differ diff --git a/sample/sample_sessions/test01/1/format.temp b/sample/sample_sessions/test01/1/format.temp new file mode 100644 index 0000000..99d85f7 --- /dev/null +++ b/sample/sample_sessions/test01/1/format.temp @@ -0,0 +1,181 @@ +EDIT_PAR COMMAND FILE + +DI_MODE LONG +ED_ENTRY ACQU +ORDER FILE + + +HEADER "F2 - Acquisition Parameters" +T_NAME Date_ + TYPE R64 + CLASS ACQU + SUBRANGE 0.0 50000000 + REL "Date_=itodate(DATE)" + INV_REL "DATE=datetoi(Date_,DATE)" + FORMAT "%14.0f" + TEXT " " +END +T_NAME Time + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000000 + REL "Time=itotime(DATE)" + INV_REL "DATE=timetoi(Time,DATE)" + FORMAT "%14.2f" + TEXT " " +END +NAME INSTRUM + TEXT " " +END +NAME PROBHD + FORMAT "%14.14s" + TEXT " " +END +NAME PULPROG + TEXT " " +END +NAME TD + TEXT " " +END +NAME SOLVENT + TEXT " " +END +NAME NS + TEXT " " +END +NAME DS + TEXT " " +END +T_NAME SWH + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e8 + REL "SWH=SW*SFO1" + INV_REL "SW=SWH/SFO1" + UNIT "Hz" + FORMAT "%14.3f Hz" + TEXT " " +END +T_NAME FIDRES + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 100000 + REL "FIDRES=SW*SFO1/TD" + INV_REL "TD = nextpow(SW*SFO1/FIDRES)" + UNIT "Hz" + FORMAT "%14.6f Hz" + TEXT " " +END +T_NAME AQ + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000 + REL "AQ=aqcalc(SW,SFO1,TD,DIGTYP)" + INV_REL "TD=tdcalc(SW,SFO1,1.0e6*AQ,DIGTYP)" + UNIT "sec" + FORMAT "%14.7f sec" + TEXT " " +END +NAME RG + TEXT " " +END +T_NAME DW + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000000 + REL "DW=1/(2*SW*SFO1)" + INV_REL "SW=1000000/(2*(0.005+DW)*SFO1)" + UNIT "usec" + FORMAT "%14.3lf usec" + TEXT " " +END +NAME DE + FORMAT "%14.2f usec" + TEXT " " +END +NAME TE + FORMAT "%14.1f K" + TEXT " " +END +T_NAME D1 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D1=D[1]" + INV_REL "D[1]=D1" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D12 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D12=D[12]" + INV_REL "D[12]=D12" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +NAME TD0 + TEXT " " +END +HEADER "======== CHANNEL f1 ========" +NAME NUC1 + NONEDIT + TEXT " " +END +T_NAME P1 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P1=P[1]" + INV_REL "P[1]=P1" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END +T_NAME PL1 + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL1=PL[1]" + INV_REL "PL[1]=PL1" + UNIT "dB" + FORMAT "%14.2f dB" + TEXT " " +END +T_NAME PL9 + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL9=PL[9]" + INV_REL "PL[9]=PL9" + UNIT "dB" + FORMAT "%14.2f dB" + TEXT " " +END +T_NAME PL1W + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL1W=63.8*pow(10.0,(-6-PL[1])/10.0)" + INV_REL "PL[1]=-6-4.3425*log(PL1W/63.8)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +T_NAME PL9W + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL9W=63.8*pow(10.0,(-6-PL[9])/10.0)" + INV_REL "PL[9]=-6-4.3425*log(PL9W/63.8)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +NAME SFO1 + FORMAT "%14.7f MHz" + TEXT " " +END diff --git a/sample/sample_sessions/test01/1/pdata/1/1i b/sample/sample_sessions/test01/1/pdata/1/1i new file mode 100644 index 0000000..565511a Binary files /dev/null and b/sample/sample_sessions/test01/1/pdata/1/1i differ diff --git a/sample/sample_sessions/test01/1/pdata/1/1r b/sample/sample_sessions/test01/1/pdata/1/1r new file mode 100644 index 0000000..be37f53 Binary files /dev/null and b/sample/sample_sessions/test01/1/pdata/1/1r differ diff --git a/sample/sample_sessions/test01/1/pdata/1/auditp.txt b/sample/sample_sessions/test01/1/pdata/1/auditp.txt new file mode 100644 index 0000000..fd08300 --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/auditp.txt @@ -0,0 +1,36 @@ +##TITLE= Audit trail, TOPSPIN Version 2.1 +##JCAMPDX= 5.01 +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/pdata/1/auditp.txt +##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT) +( 1,<2010-09-26 22:15:17.520 -0400>,,,,, + ) +( 2,<2010-09-26 22:15:23.238 -0400>,,,,, + ) +( 3,<2010-09-27 14:01:20.501 -0400>,,,,, + ) +( 4,<2010-09-27 14:01:36.356 -0400>,,,,, + ) +( 5,<2010-09-27 14:01:54.938 -0400>,,,,, + ) +##END= + +$$ hash MD5 +$$ 29 B2 63 CE 55 78 52 80 5E D3 65 71 93 69 5A 55 diff --git a/sample/sample_sessions/test01/1/pdata/1/base_info b/sample/sample_sessions/test01/1/pdata/1/base_info new file mode 100644 index 0000000..2d5531f --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/base_info @@ -0,0 +1,8 @@ +0 +982 +30218 +-1.033667E06 +-1.109416E01 +0.000000E00 +0.000000E00 +0.000000E00 diff --git a/sample/sample_sessions/test01/1/pdata/1/intrng b/sample/sample_sessions/test01/1/pdata/1/intrng new file mode 100644 index 0000000..1e58cc4 --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/intrng @@ -0,0 +1,9 @@ +P 0 +8.923863 7.841310 +5.944642 4.705623 +4.705134 3.597644 +3.597155 3.430910 +3.348276 2.511180 +2.469619 2.160108 +2.159619 1.141609 +1.141120 0.440932 diff --git a/sample/sample_sessions/test01/1/pdata/1/outd b/sample/sample_sessions/test01/1/pdata/1/outd new file mode 100644 index 0000000..896b602 --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/outd @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-24 16:07:31.492 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/prog/curdir/changer/inmrchanger/Sep24-2010-1606-micro_screening/11/data/nmr/HR4762D.007_1D_1H/1/pdata/1/outd +$$ process /opt/topspin2.1/prog/mod/xwish3 +##$CURPLOT= +##$CURPRIN= <$hp-laserjet-1300-1> +##$DFORMAT= +##$LAYOUT= +##$LFORMAT= +##$PFORMAT= +##$SURQMSG= 1 +##END= diff --git a/sample/sample_sessions/test01/1/pdata/1/parm.txt b/sample/sample_sessions/test01/1/pdata/1/parm.txt new file mode 100644 index 0000000..e81a2d8 --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/parm.txt @@ -0,0 +1,38 @@ +NAME HR4762D.007_1D_1H +EXPNO 1 +PROCNO 1 +Date_ 20100926 +Time 22.15 +INSTRUM spect +PROBHD 1.7 mm CPTCI 1 +PULPROG zgpr +TD 8192 +SOLVENT H2O+D2O +NS 1024 +DS 2 +SWH 9615.385 Hz +FIDRES 1.173753 Hz +AQ 0.4260860 sec +RG 181 +DW 52.000 usec +DE 6.50 usec +TE 293.0 K +D1 2.00000000 sec +D12 0.00002000 sec +TD0 1 + +======== CHANNEL f1 ======== +NUC1 1H +P1 12.00 usec +PL1 17.50 dB +PL9 69.90 dB +PL1W 0.28498414 W +PL9W 0.00000164 W +SFO1 600.1328182 MHz +SI 32768 +SF 600.1299044 MHz +WDW EM +SSB 0 +LB 2.00 Hz +GB 0 +PC 1.00 diff --git a/sample/sample_sessions/test01/1/pdata/1/peaklist.xml b/sample/sample_sessions/test01/1/pdata/1/peaklist.xml new file mode 100644 index 0000000..7929c94 --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/peaklist.xml @@ -0,0 +1,474 @@ + + + + + F1=12.866ppm, F2=-3.156ppm, MI=0.00cm, MAXI=10000.00cm, PC=1.000 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/sample/sample_sessions/test01/1/pdata/1/peaks b/sample/sample_sessions/test01/1/pdata/1/peaks new file mode 100644 index 0000000..1bdd480 Binary files /dev/null and b/sample/sample_sessions/test01/1/pdata/1/peaks differ diff --git a/sample/sample_sessions/test01/1/pdata/1/proc b/sample/sample_sessions/test01/1/pdata/1/proc new file mode 100644 index 0000000..b6a78b5 --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/proc @@ -0,0 +1,110 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 14 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 14:01:36.143 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/pdata/1/proc +$$ process /opt/topspin2.1/prog/mod/dataserver +##$ABSF1= 10 +##$ABSF2= 0 +##$ABSG= 0 +##$ABSL= 3 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= +##$AXLEFT= 0 +##$AXNAME= <> +##$AXNUC= +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.1 +##$BCFW= 1 +##$BC_mod= 2 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 2 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 32768 +##$FT_mod= 4 +##$GAMMA= 1 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 2 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 0 +##$MEAN= 0 +##$ME_mod= 0 +##$MI= 0 +##$NCOEF= 0 +##$NC_proc= 0 +##$NLEV= 6 +##$NOISF1= 8.174992 +##$NOISF2= 6.675002 +##$NSP= 1 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 12.86633 +##$PC= 1 +##$PHC0= -41.2 +##$PHC1= 0 +##$PH_mod= 0 +##$PKNL= yes +##$PPARMOD= 0 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 4 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 600.129904433336 +##$SI= 32768 +##$SIGF1= 5.6 +##$SIGF2= 5.2 +##$SINO= 400 +##$SIOLD= 32768 +##$SPECTYP= <> +##$SREGLST= <1H.H2O+D2O> +##$SSB= 2 +##$STSI= 0 +##$STSR= 0 +##$SW_p= 9615.38461538459 +##$SYMM= 0 +##$S_DEV= 0 +##$TDeff= 16384 +##$TDoff= 0 +##$TI= +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 1 +##$XDIM= 8192 +##$YMAX_p= 0 +##$YMIN_p= 0 +##END= diff --git a/sample/sample_sessions/test01/1/pdata/1/procs b/sample/sample_sessions/test01/1/pdata/1/procs new file mode 100644 index 0000000..7afc3a7 --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/procs @@ -0,0 +1,112 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 13 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 14:01:54.938 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/pdata/1/procs +$$ process /opt/topspin2.1/prog/mod/proc1d +##$ABSF1= 0 +##$ABSF2= 0 +##$ABSG= 0 +##$ABSL= 0 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= +##$AXLEFT= 0 +##$AXNAME= <> +##$AXNUC= <1H> +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.1 +##$BCFW= 0 +##$BC_mod= 0 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 0 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 32768 +##$FT_mod= 6 +##$GAMMA= 0 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 2 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 0 +##$MEAN= 0 +##$ME_mod= 0 +##$MI= 0 +##$NCOEF= 0 +##$NC_proc= 2 +##$NLEV= 6 +##$NOISF1= 8.174992 +##$NOISF2= 6.675002 +##$NSP= 0 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 12.86633 +##$PC= 1 +##$PHC0= -41.2 +##$PHC1= 0 +##$PH_mod= 1 +##$PKNL= yes +##$PPARMOD= 0 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 4 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 600.129904433336 +##$SI= 32768 +##$SIGF1= 5.6 +##$SIGF2= 5.2 +##$SINO= 400 +##$SIOLD= 32768 +##$SPECTYP= <> +##$SREGLST= <1H.H2O+D2O> +##$SSB= 0 +##$STSI= 32768 +##$STSR= 0 +##$SW_p= 9615.38461538459 +##$SYMM= 0 +##$S_DEV= 0 +##$TDeff= 8192 +##$TDoff= 0 +##$TI= +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 1 +##$XDIM= 8192 +##$YMAX_p= 450832046 +##$YMIN_p= -1384636 +##END= diff --git a/sample/sample_sessions/test01/1/pdata/1/title b/sample/sample_sessions/test01/1/pdata/1/title new file mode 100644 index 0000000..e0608a5 --- /dev/null +++ b/sample/sample_sessions/test01/1/pdata/1/title @@ -0,0 +1,3 @@ +HR4762D.007 1D proton +ZGPRMS H2O+D2O /opt/topspin2.1 micro_screening 11 +Clear \ No newline at end of file diff --git a/sample/sample_sessions/test01/1/prosol_History b/sample/sample_sessions/test01/1/prosol_History new file mode 100644 index 0000000..b1d9b9f --- /dev/null +++ b/sample/sample_sessions/test01/1/prosol_History @@ -0,0 +1,173 @@ +#******************************************************************* +# +# $Source: /sc/CvsTree/sc/gen/src/prg/scripts/tix/prosol/lib/lists/default,v $ +# +# Copyright (c) 1999 +# BRUKER ANALYTIK GMBH +# D-76287 Rheinstetten, Germany +# +# All Rights Reserved +# +# +# $Id: default,v 1.15.2.2 2007/12/14 16:22:31 ber Exp $ +# +#******************************************************************* +#../conf/instr/spect/prosol/relations/default +#avance-version (07/12/14) +# +#pulses +# +P[0]=P90[F1]; # 90 deg pulse F1 +P[1]=P90[F1]; # 90 deg pulse F1 +P[2]=P90[F1]*2; # 180 deg pulse F1 +P[3]=P90[F2]; # 90 deg pulse F2 +P[4]=P90[F2]*2; # 180 deg pulse F2 +P[5]=PTOC[F1]*0.66; # 60 deg pulse F1, TOCSY +P[6]=PTOC[F1]; # 90 deg pulse F1, TOCSY +P[7]=PTOC[F1]*2; # 180 deg pulse F1, TOCSY +P[8]=PSH3[F1]; # 90 deg selective F1, WET +P[9]=PTOC[F2]; # 90 deg pulse F2, TOCSY +P[10]=PTOC[F2]*2; # 180 deg pulse F2, TOCSY +P[11]=PSH1[F1]; # 90 deg selective F1 +P[12]=PSH2[F1]; # 180 deg selective F1 +# +P[14]=PSH3[F2]; # 180 deg inversion, adiabatic +P[15]=TROE[F1]; # cw pulse F1, ROESY +P[18]=PSH7[F1]; # off-resonance presat F1 +P[21]=P90[F3]; # 90 deg pulse F3 +P[22]=P90[F3]*2; # 180 deg pulse F3 +P[23]=P90[F4]; # 90 deg pulse F4 +P[24]=PSH2[F2]; # 180 deg refocussing, adiabatic +P[25]=PROE[F1]*2; # 180 deg pulse, Shaka ROESY +P[26]=PSH12[F1]; # 180 deg inversion F1, adiabatic +P[27]=P90[F1]; # 90 deg pulse F1, WATERGATE +# +P[29]=PSH8[F1]; # flip back pulse +P[31]=PSH15[F2]; # 180 deg adiabatic, F2, 13C x-filter +P[32]=PSH16[F1]; # 180 deg adiabatic, F1, z-spoil +#P[33]=PSH[F1]; # 90 deg, F1, hadamard +#P[34]=PSH[F1]; # 180 deg, F1, hadamard +#P[35]=PSH[F2]; # 90 deg, F2, hadamard +#P[36]=PSH[F2]; # 180 deg, F2, hadamard +#P[37]=PSH[F3]; # 90 deg, F3, hadamard +#P[38]=PSH[F3]; # 180 deg, F3, hadamard +P[39]=PSH21[F2]; # 180 deg, F2, Bip +P[40]=PSH8[F1]*2; # 180 deg sel. F1, 1H (exc. scul) +# +P[63]=PSH11[F2]; # 180 deg adiabatic decoupling, F2, 13C +# +#decoupling pulses +# +PCPD[1]=PCPDP[F1]; # 90 deg pulse F1, dec. +PCPD[2]=PCPDP[F2]; # 90 deg pulse F2, dec. +PCPD[3]=PCPDP[F3]; # 90 deg pulse F3, dec. +# +#power levels +# +PL[1]=PL90[F1]; # high power, F1 +PL[2]=PL90[F2]; # high power, F2 +PL[3]=PL90[F3]; # high power, F3 +PL[4]=PL90[F4]; # high power, F4 +PL[9]=PLCW[F1]; # presat power, F1 +PL[10]=PLTOC[F1]; # TOCSY power, F1 +PL[11]=PLROE[F1]; # ROESY power, F1 +PL[12]=PLCPDP[F2]; # dec. power, F2 +PL[13]=PLCPD2[F2]; # dec. power 2, F2 +PL[14]=PLNOE[F2]; # low power cw, F2 +PL[15]=PLTOC[F2]; # TOCSY power, F2 +PL[16]=PLCPDP[F3]; # dec. power, F3 +PL[18]=PL90[F1]; # WATERGATE power, F1 +PL[19]=PLCPDP[F1]; # dec. power, F1 +PL[21]=PLCW[F2]; # +PL[23]=PLTOC[F3]; # TOCSY power, F3 +PL[24]=PLHD[F2]; # HD decoupling, F2 +PL[25]=PLSH8U[F2]; # Eretic, F2 +PL[27]=PLROE[F1]; # Shaka Spinlock +PL[30]=PLCPDP[F2]; # dec. power, F2, 13C (=pl12) +PL[31]=PLUSER2[F2]; # dec. power, F2, 13C, cw bilev +# +#shapes +# +SP[1]=PLSH1[F1]; # 90 deg selective F1 +SP[2]=PLSH2[F1]; # 180 deg selective F1 +SP[3]=PLSH3[F2]; # adiabatic 180 deg, F2, inversion +SP[4]=PLSH21[F2]; # 180 deg Bip, F2, inversion +SP[6]=PLSH7[F1]; # off-resonance presat F1 +SP[7]=PLSH2[F2]; # adiabatic 180 deg, F2, refocussing +SP[8]=PLSH12[F1]; # adiabatic 180 deg, F1, inversion +SP[10]=PLSH8[F1]; # flip-back pulse, F1, 1H +SP[11]=PLSH8[F1]; # flip-back pulse, F1, H +SP[14]=PLSH12[F2]; # adiab. bilev dec., F2, 13C +SP[18]=PLSH15[F2]; # adiabatic 180 deg, F2, 13C, x-filter +SP[19]=PLSH3[F1] +0.87; # 90 deg, F1, wet +SP[20]=PLSH3[F1] -1.04; # 90 deg, F1, wet +SP[21]=PLSH3[F1] +2.27; # 90 deg, F1, wet +SP[22]=PLSH3[F1] -5.05; # 90 deg, F1, wet +#SP[23]=PLSH[F1]; # 90 deg, F1, hadamard +#SP[24]=PLSH[F1]; # 180 deg, F1, hadamard +#SP[25]=PLSH[F2]; # 90 deg, F2, hadamard +#SP[26]=PLSH[F2]; # 180 deg, F2, hadamard +#SP[27]=PLSH[F3]; # 90 deg, F3, hadamard +#SP[28]=PLSH[F3]; # 180 deg, F3, hadamard +SP[29]=PLSH16[F1]; # adiabatic 180 deg, F1, z-spoil +SP[31]=PLSH11[F2]; # adiab. dec., F2, 13C +# +SPNAM1=PNSH1[F1]; # +SPNAM2=PNSH2[F1]; # +SPNAM3=PNSH3[F2]; # +SPNAM4=PNSH21[F2]; # +SPNAM6=PNSH7[F1]; # +SPNAM7=PNSH2[F2]; # +SPNAM8=PNSH12[F1]; # +SPNAM10=PNSH8[F1]; # +SPNAM11=PNSH8[F1]; # +SPNAM14=PNSH12[F2]; # +SPNAM15=PNSH8U[F2]; # Eretic, F2 +SPNAM18=PNSH15[F2]; # +SPNAM19=PNSH3[F1]; # +SPNAM20=PNSH3[F1]; # +SPNAM21=PNSH3[F1]; # +SPNAM22=PNSH3[F1]; # +#SPNAM23=PNSH[]; # +#SPNAM24=PNSH[]; # +#SPNAM25=PNSH[]; # +#SPNAM26=PNSH[]; # +#SPNAM27=PNSH[]; # +#SPNAM28=PNSH[]; # +SPNAM29=PNSH16[F1]; # +SPNAM31=PNSH11[F2]; # +# +SPOAL[1]=PASH1[F1]; # +SPOAL[2]=PASH2[F1]; # +SPOAL[3]=PASH3[F2]; # +SPOAL[4]=PASH21[F2]; # +SPOAL[6]=PASH7[F1]; # +SPOAL[7]=PASH2[F2]; # +SPOAL[8]=PASH12[F1]; # +SPOAL[10]=PASH8[F1]; +SPOAL[11]=PASH8[F1]; +SPOAL[14]=PASH12[F2]; # +SPOAL[18]=PASH15[F2]; # +SPOAL[19]=PASH3[F1]; # +SPOAL[20]=PASH3[F1]; # +SPOAL[21]=PASH3[F1]; # +SPOAL[22]=PASH3[F1]; # +#SPOAL[23]=PASH[]; # +#SPOAL[24]=PASH[]; # +#SPOAL[25]=PASH[]; # +#SPOAL[26]=PASH[]; # +#SPOAL[27]=PASH[]; # +#SPOAL[28]=PASH[]; # +SPOAL[29]=PASH16[F1]; # +SPOAL[31]=PASH11[F2]; # +# +#global +# +D[9]=TTOC[F1]; # +D[16]=D_grad; # +P[16]=P_grad1; # +P[17]=P_mlev; # +P[19]=P_grad2; # +P[20]=P_mlev; # +P[28]=P_hsqc; # +# diff --git a/sample/sample_sessions/test01/1/pulseprogram b/sample/sample_sessions/test01/1/pulseprogram new file mode 100644 index 0000000..d826ebf --- /dev/null +++ b/sample/sample_sessions/test01/1/pulseprogram @@ -0,0 +1,210 @@ +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" +;zgpr +;avance-version (06/11/09) +;1D sequence with f1 presaturation +; +;$CLASS=HighRes +;$DIM=1D +;$TYPE= +;$SUBTYPE= +;$COMMENT= + + +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/Avance.incl" 1 +;Avance2.incl +; for 1 +; +;avance-version (07/08/21) +; +;$CLASS=HighRes Incl +;$COMMENT= + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +;$Id: Avance2.incl,v 1.17.2.1 2007/09/14 16:17:35 ber Exp $ +# 12 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" 2 + + + +"d12=20u" + + +"acqt0=-p1*2/3.1416" + + +# 1 "mc_line 21 file /opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr expanding definition part of mc command before ze" +define delay MCWRK +define delay MCREST +"MCWRK = 0.333333*30m" +"MCREST = 30m - 30m" + dccorr +# 21 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" +1 ze +# 1 "mc_line 21 file /opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr expanding definition of mc command after ze" +# 22 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" +# 1 "mc_line 22 file /opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr expanding start label for mc command" +2 MCWRK * 2 +LBLF0, MCWRK + MCREST +# 23 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" + d12 pl9:f1 + d1 cw:f1 ph29 + 4u do:f1 + d12 pl1:f1 + p1 ph1 + go=2 ph31 +# 1 "mc_line 29 file /opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr expanding mc command in line" + MCWRK wr #0 + MCWRK zd + lo to LBLF0 times td0 + + MCWRK +# 30 "/opt/topspin2.1/exp/stan/nmr/lists/pp/zgpr" +exit + + +ph1=0 2 2 0 1 3 3 1 +ph29=0 +ph31=0 2 2 0 1 3 3 1 + + +;pl1 : f1 channel - power level for pulse (default) +;pl9 : f1 channel - power level for presaturation +;p1 : f1 channel - 90 degree high power pulse +;d1 : relaxation delay; 1-5 * T1 +;d12: delay for power switching [20 usec] +;NS: 1 * n, total number of scans: NS * TD0 + + + +;$Id: zgpr,v 1.9 2006/11/10 10:56:44 ber Exp $ diff --git a/sample/sample_sessions/test01/1/scon2 b/sample/sample_sessions/test01/1/scon2 new file mode 100644 index 0000000..8bc66ef --- /dev/null +++ b/sample/sample_sessions/test01/1/scon2 @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-26 21:33:06.757 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_1D_1H/1/scon2 +$$ process /opt/topspin2.1/prog/mod/go +##$BLKTR= (0..15) +3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 +##$DE1= 4.5 +##$DEADC= 0.5 +##$DEPA= 4.5 +##$DERX= 1.5 +##$FILCOR= 0.2 +##END= diff --git a/sample/sample_sessions/test01/1/uxnmr.par b/sample/sample_sessions/test01/1/uxnmr.par new file mode 100644 index 0000000..c90a4f2 --- /dev/null +++ b/sample/sample_sessions/test01/1/uxnmr.par @@ -0,0 +1,527 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 104 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2009-12-15 16:47:14.463 -0500 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/conf/instr/spect/uxnmr.par +$$ process /opt/topspin2.1/prog/mod/hconfserver +##$ACB= 1 +##$ACBTAT= (0..15) +0 88 72 88 0 0 88 0 0 0 0 0 0 0 0 0 +##$ACBTBA= (0..15) +0 30 60 90 0 0 180 0 0 0 0 0 0 0 0 0 +##$ACBTBLK= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTCTL= (0..15) +0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 +##$ACBTDI= (0..15) +0 70 71 72 0 0 75 0 0 0 0 0 0 0 0 0 +##$ACBTDM= (0..15) +0 6 25 10 0 0 10 0 0 0 0 0 0 0 0 0 +##$ACBTFHI= (0..15) +0 365 600 365 0 0 365 0 0 0 0 0 0 0 0 0 +##$ACBTFL= (0..15) +0 249 249 249 0 0 249 0 0 0 0 0 0 0 0 0 +##$ACBTFLO= (0..15) +0 6 188 6 0 0 6 0 0 0 0 0 0 0 0 0 +##$ACBTINP= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTOUT= (0..15) +0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 +##$ACBTPO= (0..15) +0 500000 100000 300000 0 0 300000 0 0 0 0 0 0 0 0 0 +##$ACBTPW= (0..15) +0 600 1000 1000 0 0 1000 0 0 0 0 0 0 0 0 0 +##$ACBTSB= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTY= +##$AQSBDCH= (0..95) +0 0 0 0 0 0 0 0 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDHW= (0..95) +1 4 4 4 0 1 4 4 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDID= (0..95) +88 83 83 83 89 88 83 83 89 80 80 66 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSBDNO= (0..95) +1 1 2 3 1 2 4 5 2 1 2 1 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDSL= (0..95) +4 5 6 7 8 10 11 12 15 17 18 19 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 +##$AQSBDTY= (0..95) +194 16 24 16 4 194 24 16 4 10 10 7 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSBUAD= (0..95) +52 36 37 38 60 53 39 40 61 33 34 32 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSECL= (0..95) +0 1 1 1 1 0 1 1 1 1 1 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSECLS= (0..95) +3 1 1 1 0 3 1 1 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSSPLT= no +##$ATT19F= (0..1) +0 0 +##$ATT1H= (0..1) +0 0 +##$ATT3H= (0..1) +0 0 +##$ATTX= (0..1) +0 0 +##$ATTY= (0..1) +0 0 +##$ATTZ= (0..1) +0 0 +##$BACSAIR= yes +##$BACSCAP= 60 +##$BACSDEL= 10 +##$BACSFCM= no +##$BACSOPT= +##$BACSTY= +##$BARPTY= +##$BFREQ= 600.13 +##$BGAETH1= +##$BGAETH2= +##$BGAETH3= +##$BGAETH4= +##$BGAETH5= +##$BGAETH6= +##$BGAETH7= +##$BGAETH8= +##$BIRDS= yes +##$BMPC= 0 +##$BMPCTY= +##$BPSUTY= +##$BSMS= 1 +##$BSMSETH= +##$BSMSTY= +##$CFASMOD= (0..7) +1 1 1 1 1 1 1 1 +##$CFASMUL= (0..7) +1 1 1 1 1 1 1 1 +##$CNFTXDR= (0..7) +6 6 6 6 6 0 0 0 +##$COMDIG2= 0 +##$CPDBTY= +##$CRCOTY= +##$CSW1= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$CSW2= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$CSWNUM= (0..7) +0 0 0 0 0 0 0 0 +##$DATSTAT= no +##$DIGI140= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIB12= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIB16= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIFA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIHA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIHAF= (0..7) +1 0 0 0 0 0 0 0 +##$DIGIHRD= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIIA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIO16= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISAF= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISL= (0..7) +0 0 0 0 0 0 0 0 +##$DIGITYI= (0..7) +0 0 0 0 0 0 0 0 +##$DIGITYP= (0..7) +2 0 0 0 0 0 0 0 +##$DIGITZ= 0 +##$DRU= no +##$DRUETH01= +##$DRUETH02= +##$DRUETH03= +##$DRUETH04= +##$DRUETH05= +##$DRUETH06= +##$DRUETH07= +##$DRUETH08= +##$DRUETH09= +##$DRUETH10= +##$DRUETH11= +##$DRUETH12= +##$DRUETH13= +##$DRUETH14= +##$DRUETH15= +##$DRUETH16= +##$DRUETH17= +##$DRUETH18= +##$DRUETH19= +##$DRUETH20= +##$DRUETH21= +##$DRUETH22= +##$DRUETH23= +##$DRUETH24= +##$DRUETH25= +##$DRUETH26= +##$DRUETH27= +##$DRUETH28= +##$DRUETH29= +##$DRUETH30= +##$DRUETH31= +##$DRUETH32= +##$FCUMEM= (0..7) +2093056 2093056 2093056 2093056 2093056 2093056 0 0 +##$FCUPAL= (0..7) +260 260 260 260 260 260 0 0 +##$FGSVTY= +##$FQMIX= 0 +##$FUNCMOD= <> +##$GCUTYPE= 2 +##$GPREDEL= 0 +##$GPSCUTY= +##$GRADRES= 5 +##$GTUTY= +##$HFAC= 3 +##$HPCU= 0 +##$HPCUTY= +##$HPTXLP= (0..3) +-1 -1 -1 -1 +##$HPTXPI= (0..3) +0 0 0 0 +##$HPTXPO= (0..3) +0 0 0 0 +##$HPTXTY= (0..3) +0 0 0 0 +##$IF451= 0 +##$IFREQ= 1 +##$INTFPR= 0 +##$IPSOETH= <> +##$LOCKTY= +##$LOCSWID= 6 +##$LOCSWIF= 0 +##$M2FAC= 0 +##$MAS= 0 +##$MASETIME= 10 +##$MASITIME= 10 +##$MASTY= +##$MAS_CT= 0 +##$MAS_SG= 0 +##$MAS_TO= 0 +##$MEMPRM= 0 +##$MHFAC= 0 +##$MXFAC= 0 +##$NAMPD1= <1H LNA> +##$NAMPD10= <> +##$NAMPD11= <> +##$NAMPD12= <> +##$NAMPD13= <> +##$NAMPD14= <> +##$NAMPD15= <> +##$NAMPD16= <> +##$NAMPD2= +##$NAMPD3= <2H> +##$NAMPD4= <13C> +##$NAMPD5= <15N> +##$NAMPD6= <> +##$NAMPD7= <> +##$NAMPD8= <> +##$NAMPD9= <> +##$NFCU= 5 +##$NMRCH= 0 +##$NMRMEM= 0 +##$NRCU= 1 +##$NROUT= 2 +##$NSGU= 5 +##$PAMPF1= (0..15) +75 24 64 96 88 88 0 0 0 0 0 0 0 0 0 0 +##$PAMPF2= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF3= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF4= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF5= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF6= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF7= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF8= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PH4= 0 +##$PHF4TY= +##$POWCHK= yes +##$PRAMD1= (0..7) +2 0 0 536870912 0 0 0 0 +##$PRAMD10= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD11= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD12= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD13= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD14= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD15= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD16= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD17= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD18= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD19= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD2= (0..7) +2147483644 2131230719 2147483647 671088639 0 0 0 0 +##$PRAMD20= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD21= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD3= (0..7) +0 1048576 0 536870912 0 1048576 0 536870912 +##$PRAMD4= (0..7) +16777216 0 0 536870912 0 0 0 0 +##$PRAMD5= (0..7) +0 0 4 536870912 0 0 0 0 +##$PRAMD6= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD7= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD8= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD9= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMLED= (0..1) +15 15 +##$PRAMP1= +##$PRAMP2= +##$PRAMP3= +##$PRAMP4= +##$PRAMP5= +##$PRAMP6= +##$PRAMP7= +##$PRAMP8= +##$PRAMPTP= 1 +##$PREPTY= +##$PRESHLD= 0 +##$PTS160= -1 +##$PTSA2X= (0..7) +0 0 0 0 0 0 0 0 +##$PTSF2X= (0..7) +0 0 0 0 0 0 0 0 +##$PTSFMX= (0..7) +429.9 643.52499 429.9 643.52499 429.9 0 0 0 +##$PULCHK= no +##$RCUCDS= (0..7) +8388608 0 0 0 0 0 0 0 +##$RCUCFS= (0..7) +4096 0 0 0 0 0 0 0 +##$RCUCSS= (0..7) +1048576 0 0 0 0 0 0 0 +##$RCUI2C1= (0..7) +78 0 0 0 0 0 0 0 +##$RCUI2C2= (0..7) +0 0 0 0 0 0 0 0 +##$RCUI2C3= (0..7) +0 0 0 0 0 0 0 0 +##$RCUI2C4= (0..7) +0 0 0 0 0 0 0 0 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0.5 0.5 0.5 0.5 0.5 0.5 0.5 +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$SPOFFS= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$SUBNAM0= <""> +##$SUBNAM1= <""> +##$SUBNAM2= <""> +##$SUBNAM3= <""> +##$SUBNAM4= <""> +##$SUBNAM5= <""> +##$SUBNAM6= <""> +##$SUBNAM7= <""> +##$SUBNAM8= <""> +##$SUBNAM9= <""> +##$SW= 13.9790084634634 +##$SWIBOX= (0..15) +0 1 2 3 0 0 6 0 0 0 0 0 0 0 0 0 +##$SW_h= 8389.26174496644 +##$SWfinal= 0 +##$TD= 1024 +##$TD0= 1 +##$TE= 300 +##$TE2= 300 +##$TE3= 300 +##$TEG= 300 +##$TL= (0..7) +0 120 120 120 120 120 120 120 +##$TP= (0..7) +150 150 150 150 150 150 150 150 +##$TP07= 0 +##$TPNAME0= <> +##$TPNAME1= <> +##$TPNAME2= <> +##$TPNAME3= <> +##$TPNAME4= <> +##$TPNAME5= <> +##$TPNAME6= <> +##$TPNAME7= <> +##$TPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$TPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$TUNHIN= 0 +##$TUNHOUT= 0 +##$TUNXOUT= 0 +##$USERA1= +##$USERA2= +##$USERA3= +##$USERA4= +##$USERA5= +##$V9= 5 +##$VALIST= +##$VCLIST= +##$VD= 0 +##$VDLIST= +##$VPLIST= +##$VTLIST= +##$WBST= 1024 +##$WBSW= 20 +##$XGAIN= (0..3) +0 0 0 0 +##$XL= 0 +##$YL= 0 +##$YMAX_a= 0 +##$YMIN_a= 0 +##$ZGOPTNS= <> +##$ZL1= 120 +##$ZL2= 120 +##$ZL3= 120 +##$ZL4= 120 +##END= diff --git a/sample/sample_sessions/test01/2/acqu2 b/sample/sample_sessions/test01/2/acqu2 new file mode 100644 index 0000000..af9b147 --- /dev/null +++ b/sample/sample_sessions/test01/2/acqu2 @@ -0,0 +1,21 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 3 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-24 16:07:31.567 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/prog/curdir/changer/inmrchanger/Sep24-2010-1606-micro_screening/11/data/./nmr/HR4762D.007_N_HSQC/1/acqu2 +$$ process /opt/topspin2.1/prog/mod/xwish3 +##$BF1= 60.810645 +##$DECIM= 32 +##$DR= 18 +##$FW= 90000 +##$FnMODE= 6 +##$NUC1= <15N> +##$O1= 5827.94102 +##$SFO1= 60.8176380097503 +##$SW= 34.9545034911622 +##$SW_h= 2125.85034013605 +##$TD= 120 +##END= diff --git a/sample/sample_sessions/test01/2/acqu2s b/sample/sample_sessions/test01/2/acqu2s new file mode 100644 index 0000000..c4d228d --- /dev/null +++ b/sample/sample_sessions/test01/2/acqu2s @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 121 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 00:37:56.542 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/acqu2s +$$ process /opt/topspin2.1/prog/mod/go +##$BF1= 60.810645 +##$FnMODE= 6 +##$NUC1= <15N> +##$O1= 5827.94102 +##$SFO1= 60.8176380097503 +##$SW= 34.9545034911622 +##$TD= 120 +##END= diff --git a/sample/sample_sessions/test01/2/acqus b/sample/sample_sessions/test01/2/acqus new file mode 100644 index 0000000..dbb4da3 --- /dev/null +++ b/sample/sample_sessions/test01/2/acqus @@ -0,0 +1,407 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 12 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 00:38:07.009 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/acqus +$$ process /opt/topspin2.1/prog/mod/shimcntl +##$ACQT0= 1000000 +##$AMP= (0..31) +100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 +100 100 100 100 100 100 100 100 100 100 100 100 100 100 +##$ANAVPT= -1 +##$AQSEQ= 0 +##$AQ_mod= 3 +##$AUNM= +##$AUTOPOS= <11 > +##$BF1= 600.13 +##$BF2= 150.902809 +##$BF3= 60.810645 +##$BF4= 600.13 +##$BF5= 600.13 +##$BF6= 600.13 +##$BF7= 600.13 +##$BF8= 600.13 +##$BYTORDA= 1 +##$CFDGTYP= 2 +##$CFRGTYP= 5 +##$CHEMSTR= +##$CNST= (0..63) +1 1 145 1 90 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +##$CPDPRG= <> +##$CPDPRG1= <> +##$CPDPRG2= <> +##$CPDPRG3= +##$CPDPRG4= +##$CPDPRG5= +##$CPDPRG6= +##$CPDPRG7= +##$CPDPRG8= +##$CPDPRGB= <> +##$CPDPRGT= <> +##$D= (0..63) +3e-06 1 0 0 0 0 0 0 0 0.06 0 0.03 0 4e-06 0 0 0.0002 0 0 0 0 0 0 0 0.00225 +0 0.002777778 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 +##$DATE= 1285553889 +##$DBL= (0..7) +120 120 120 120 120 120 120 120 +##$DBP= (0..7) +150 150 150 150 150 150 150 150 +##$DBP07= 0 +##$DBPNAM0= <> +##$DBPNAM1= <> +##$DBPNAM2= <> +##$DBPNAM3= <> +##$DBPNAM4= <> +##$DBPNAM5= <> +##$DBPNAM6= <> +##$DBPNAM7= <> +##$DBPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DBPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DE= 6.5 +##$DECBNUC= +##$DECIM= 16 +##$DECNUC= +##$DECSTAT= 4 +##$DIGMOD= 1 +##$DIGTYP= 8 +##$DL= (0..7) +0 120 120 120 120 120 120 120 +##$DP= (0..7) +150 150 150 150 150 150 150 150 +##$DP07= 0 +##$DPNAME0= <> +##$DPNAME1= <> +##$DPNAME2= <> +##$DPNAME3= <> +##$DPNAME4= <> +##$DPNAME5= <> +##$DPNAME6= <> +##$DPNAME7= <> +##$DPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$DPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$DQDMODE= 0 +##$DR= 18 +##$DS= 8 +##$DSLIST= +##$DSPFIRM= 0 +##$DSPFVS= 12 +##$DTYPA= 0 +##$EXP= +##$F1LIST= <111111111111111> +##$F2LIST= <222222222222222> +##$F3LIST= <333333333333333> +##$FCUCHAN= (0..9) +0 2 1 3 0 0 0 0 0 0 +##$FL1= 90 +##$FL2= 90 +##$FL3= 90 +##$FL4= 90 +##$FOV= 20 +##$FQ1LIST= +##$FQ2LIST= +##$FQ3LIST= +##$FQ4LIST= +##$FQ5LIST= +##$FQ6LIST= +##$FQ7LIST= +##$FQ8LIST= +##$FRQLO3= 1891778.52348993 +##$FRQLO3N= 0 +##$FS= (0..7) +83 83 83 83 83 83 83 83 +##$FTLPGN= 0 +##$FW= 125000 +##$FnMODE= 0 +##$FnTYPE= 0 +##$GP031= 0 +##$GPNAM0= +##$GPNAM1= +##$GPNAM10= +##$GPNAM11= +##$GPNAM12= +##$GPNAM13= +##$GPNAM14= +##$GPNAM15= +##$GPNAM16= +##$GPNAM17= +##$GPNAM18= +##$GPNAM19= +##$GPNAM2= +##$GPNAM20= +##$GPNAM21= +##$GPNAM22= +##$GPNAM23= +##$GPNAM24= +##$GPNAM25= +##$GPNAM26= +##$GPNAM27= +##$GPNAM28= +##$GPNAM29= +##$GPNAM3= +##$GPNAM30= +##$GPNAM31= +##$GPNAM4= +##$GPNAM5= +##$GPNAM6= +##$GPNAM7= +##$GPNAM8= +##$GPNAM9= +##$GPX= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GPY= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GPZ= (0..31) +0 50 80 8.1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$GRDPROG= +##$GRPDLY= -1 +##$HDDUTY= 20 +##$HDRATE= 20 +##$HGAIN= (0..3) +0 0 0 0 +##$HL1= 256 +##$HL2= 35 +##$HL3= 16 +##$HL4= 17 +##$HOLDER= 0 +##$HPMOD= (0..7) +0 0 0 0 0 0 0 0 +##$HPPRGN= 0 +##$IN= (0..63) +0.0002352 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 +0.001 0.001 0.001 0.001 +##$INF= (0..7) +0 470.4 0 0 0 0 0 0 +##$INP= (0..63) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$INSTRUM= +##$L= (0..31) +1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +##$LFILTER= 100 +##$LGAIN= -15 +##$LINPSTP= 10 +##$LOCKED= yes +##$LOCKFLD= 4675 +##$LOCKGN= 131.399993896484 +##$LOCKPOW= -10 +##$LOCKPPM= 4.69999980926514 +##$LOCNUC= <2H> +##$LOCPHAS= 269.6 +##$LOCSHFT= no +##$LOCSW= 0 +##$LTIME= 0.200000002980232 +##$MASR= 4200 +##$MASRLST= +##$NBL= 1 +##$NC= -2 +##$NLOGCH= 1 +##$NS= 64 +##$NUC1= <1H> +##$NUC2= <13C> +##$NUC3= <15N> +##$NUC4= +##$NUC5= +##$NUC6= +##$NUC7= +##$NUC8= +##$NUCLEI= 0 +##$NUCLEUS= +##$O1= 2818.21048 +##$O2= 7469.21502263831 +##$O3= 7175.65611 +##$O4= 2850.47650618253 +##$O5= 2850.47650618253 +##$O6= 2850.47650618253 +##$O7= 2850.47650618253 +##$O8= 2850.47650618253 +##$OBSCHAN= (0..9) +0 0 0 0 0 0 0 0 0 0 +##$OVERFLW= 0 +##$P= (0..63) +12 12 24 11 22 18.48 28 56 20000 25 50 80000 80000 0 500 250000 1000 2500 +10000 600 2500 32 64 0 2000 250 0 12 1000 1000 0 1730 20000 0 0 0 0 0 0 +160 2000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1500 +##$PACOIL= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAPS= 2 +##$PARMODE= 1 +##$PCPD= (0..9) +100 60 60 200 100 100 100 100 100 100 +##$PHCOR= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PHLIST= <> +##$PHP= 1 +##$PH_ref= 0 +##$PL= (0..63) +120 17.5 -0.5 -2 120 120 120 120 120 69.9 24.86 37.85 14.24 120 120 6.63 +13.92 120 17.5 31.48 120 120 120 1.88 120 120 120 37.85 120 120 14.24 8.21 +120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 120 +120 120 120 120 120 120 120 120 120 120 120 120 120 120 +##$PLSTEP= 0.1 +##$PLSTRT= -6 +##$POWMOD= 0 +##$PQPHASE= 0 +##$PQSCALE= 0 +##$PR= 1 +##$PRECHAN= (0..15) +-1 3 0 4 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$PRGAIN= 0 +##$PROBHD= <1.7 mm CPTCI 1H-13C/15N/D Z-GRD Z108160/0002 +> +##$PROSOL= no +##$PULPROG= +##$PW= 0 +##$PYNM= +##$QNP= 1 +##$RD= 0 +##$RECCHAN= (0..15) +0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$RECPH= 0 +##$RECPRE= (0..15) +-1 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$RECPRFX= (0..15) +-1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 +##$RECSEL= (0..15) +0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$RG= 512 +##$RO= 0 +##$ROUTWD1= (0..23) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 +##$ROUTWD2= (0..23) +0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 +##$RSEL= (0..9) +0 1 2 3 0 0 0 0 0 0 +##$S= (0..7) +83 4 83 83 83 83 83 83 +##$SEOUT= 0 +##$SFO1= 600.13281821048 +##$SFO2= 150.910278215023 +##$SFO3= 60.81782065611 +##$SFO4= 600.132850476506 +##$SFO5= 600.132850476506 +##$SFO6= 600.132850476506 +##$SFO7= 600.132850476506 +##$SFO8= 600.132850476506 +##$SOLVENT= +##$SP= (0..31) +1 86.27 80.25 6.83 4.69 0 75.92 6.83 120 0 51.32 51.32 0 0 8.31 0 150 150 +12.22 78.21 76.3 79.60999 72.28999 150 150 150 150 150 150 40.1 150 14.33 +##$SP07= 0 +##$SPECTR= 0 +##$SPNAM0= +##$SPNAM1= +##$SPNAM10= +##$SPNAM11= +##$SPNAM12= +##$SPNAM13= +##$SPNAM14= +##$SPNAM15= < > +##$SPNAM16= +##$SPNAM17= +##$SPNAM18= +##$SPNAM19= +##$SPNAM2= +##$SPNAM20= +##$SPNAM21= +##$SPNAM22= +##$SPNAM23= +##$SPNAM24= +##$SPNAM25= +##$SPNAM26= +##$SPNAM27= +##$SPNAM28= +##$SPNAM29= +##$SPNAM3= +##$SPNAM30= +##$SPNAM31= +##$SPNAM4= +##$SPNAM5= +##$SPNAM6= +##$SPNAM7= +##$SPNAM8= < > +##$SPNAM9= +##$SPOAL= (0..31) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$SPOFFS= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$SUBNAM0= <""> +##$SUBNAM1= <""> +##$SUBNAM2= <""> +##$SUBNAM3= <""> +##$SUBNAM4= <""> +##$SUBNAM5= <""> +##$SUBNAM6= <""> +##$SUBNAM7= <""> +##$SUBNAM8= <""> +##$SUBNAM9= <""> +##$SW= 13.9790084634634 +##$SWIBOX= (0..15) +0 1 2 3 0 0 6 0 0 0 0 0 0 0 0 0 +##$SW_h= 8389.26174496644 +##$SWfinal= 0 +##$TD= 1024 +##$TD0= 1 +##$TE= 293 +##$TE2= 300 +##$TE3= 300 +##$TEG= 300 +##$TL= (0..7) +0 120 120 120 120 120 120 120 +##$TP= (0..7) +150 150 150 150 150 150 150 150 +##$TP07= 0 +##$TPNAME0= <> +##$TPNAME1= <> +##$TPNAME2= <> +##$TPNAME3= <> +##$TPNAME4= <> +##$TPNAME5= <> +##$TPNAME6= <> +##$TPNAME7= <> +##$TPOAL= (0..7) +0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 +##$TPOFFS= (0..7) +0 0 0 0 0 0 0 0 +##$TUNHIN= 0 +##$TUNHOUT= 0 +##$TUNXOUT= 0 +##$USERA1= +##$USERA2= +##$USERA3= +##$USERA4= +##$USERA5= +##$V9= 5 +##$VALIST= +##$VCLIST= +##$VD= 0 +##$VDLIST= +##$VPLIST= +##$VTLIST= +##$WBST= 1024 +##$WBSW= 20 +##$XGAIN= (0..3) +0 0 0 0 +##$XL= 0 +##$YL= 0 +##$YMAX_a= 115504 +##$YMIN_a= -133374 +##$ZGOPTNS= <> +##$ZL1= 120 +##$ZL2= 120 +##$ZL3= 120 +##$ZL4= 120 +##END= diff --git a/sample/sample_sessions/test01/2/audita.txt b/sample/sample_sessions/test01/2/audita.txt new file mode 100644 index 0000000..749cb0c --- /dev/null +++ b/sample/sample_sessions/test01/2/audita.txt @@ -0,0 +1,23 @@ +##TITLE= Audit trail, TOPSPIN Version 2.1 +##JCAMPDX= 5.01 +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/audita.txt +##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT) +( 1,<2010-09-27 00:37:57.695 -0400>,,,,, + ) +( 2,<2010-09-27 00:38:07.366 -0400>,,,,, + ) +##END= + +$$ hash MD5 +$$ 52 B5 1D CD E1 CF C1 15 EA 29 FD D9 BB FE AC 2E diff --git a/sample/sample_sessions/test01/2/cpdprg3 b/sample/sample_sessions/test01/2/cpdprg3 new file mode 100644 index 0000000..c6eb071 --- /dev/null +++ b/sample/sample_sessions/test01/2/cpdprg3 @@ -0,0 +1,101 @@ +1 pcpd*0.339:0 + pcpd*0.613:180 + pcpd*2.864:0 + pcpd*2.981:180 + pcpd*0.770:0 + pcpd*0.691:180 + pcpd*0.944:0 + pcpd*1.020:180 + pcpd*1.494:0 + pcpd*2.846:180 + pcpd*0.738:0 + pcpd*0.510:180 + pcpd*0.283:0 + pcpd*0.808:180 + pcpd*1.328:0 + pcpd*1.536:180 + pcpd*2.871:0 + pcpd*0.721:180 + pcpd*0.788 :0 + pcpd*0.858:180 + pcpd*1.091:0 + pcpd*1.484:180 + pcpd*2.843:0 + pcpd*0.729:180 + pcpd*0.593:0 + pcpd*0.339:0 + pcpd*0.613:180 + pcpd*2.864:0 + pcpd*2.981:180 + pcpd*0.770:0 + pcpd*0.691:180 + pcpd*0.944:0 + pcpd*1.020:180 + pcpd*1.494:0 + pcpd*2.846:180 + pcpd*0.738:0 + pcpd*0.510:180 + pcpd*0.283:0 + pcpd*0.808:180 + pcpd*1.328:0 + pcpd*1.536:180 + pcpd*2.871:0 + pcpd*0.721:180 + pcpd*0.788 :0 + pcpd*0.858:180 + pcpd*1.091:0 + pcpd*1.484:180 + pcpd*2.843:0 + pcpd*0.729:180 + pcpd*0.593:0 + pcpd*0.339:180 + pcpd*0.613:0 + pcpd*2.864:180 + pcpd*2.981:0 + pcpd*0.770:180 + pcpd*0.691:0 + pcpd*0.944:180 + pcpd*1.020:0 + pcpd*1.494:180 + pcpd*2.846:0 + pcpd*0.738:180 + pcpd*0.510:0 + pcpd*0.283:180 + pcpd*0.808:0 + pcpd*1.328:180 + pcpd*1.536:0 + pcpd*2.871:180 + pcpd*0.721:0 + pcpd*0.788:180 + pcpd*0.858:0 + pcpd*1.091:180 + pcpd*1.484:0 + pcpd*2.843:180 + pcpd*0.729:0 + pcpd*0.593:180 + pcpd*0.339:180 + pcpd*0.613:0 + pcpd*2.864:180 + pcpd*2.981:0 + pcpd*0.770:180 + pcpd*0.691:0 + pcpd*0.944:180 + pcpd*1.020:0 + pcpd*1.494:180 + pcpd*2.846:0 + pcpd*0.738:180 + pcpd*0.510:0 + pcpd*0.283:180 + pcpd*0.808:0 + pcpd*1.328:180 + pcpd*1.536:0 + pcpd*2.871:180 + pcpd*0.721:0 + pcpd*0.788:180 + pcpd*0.858:0 + pcpd*1.091:180 + pcpd*1.484:0 + pcpd*2.843:180 + pcpd*0.729:0 + pcpd*0.593:180 + jump to 1 diff --git a/sample/sample_sessions/test01/2/format.temp b/sample/sample_sessions/test01/2/format.temp new file mode 100644 index 0000000..0bcc8cc --- /dev/null +++ b/sample/sample_sessions/test01/2/format.temp @@ -0,0 +1,382 @@ +EDIT_PAR COMMAND FILE + +DI_MODE LONG +ED_ENTRY ACQU +ORDER FILE + + +HEADER "F2 - Acquisition Parameters" +T_NAME Date_ + TYPE R64 + CLASS ACQU + SUBRANGE 0.0 50000000 + REL "Date_=itodate(DATE)" + INV_REL "DATE=datetoi(Date_,DATE)" + FORMAT "%14.0f" + TEXT " " +END +T_NAME Time + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000000 + REL "Time=itotime(DATE)" + INV_REL "DATE=timetoi(Time,DATE)" + FORMAT "%14.2f" + TEXT " " +END +NAME INSTRUM + TEXT " " +END +NAME PROBHD + FORMAT "%14.14s" + TEXT " " +END +NAME PULPROG + TEXT " " +END +NAME TD + TEXT " " +END +NAME SOLVENT + TEXT " " +END +NAME NS + TEXT " " +END +NAME DS + TEXT " " +END +T_NAME SWH + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e8 + REL "SWH=SW*SFO1" + INV_REL "SW=SWH/SFO1" + UNIT "Hz" + FORMAT "%14.3f Hz" + TEXT " " +END +T_NAME FIDRES + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 100000 + REL "FIDRES=SW*SFO1/TD" + INV_REL "TD = nextpow(SW*SFO1/FIDRES)" + UNIT "Hz" + FORMAT "%14.6f Hz" + TEXT " " +END +T_NAME AQ + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000 + REL "AQ=aqcalc(SW,SFO1,TD,DIGTYP)" + INV_REL "TD=tdcalc(SW,SFO1,1.0e6*AQ,DIGTYP)" + UNIT "sec" + FORMAT "%14.7f sec" + TEXT " " +END +NAME RG + TEXT " " +END +T_NAME DW + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1000000 + REL "DW=1/(2*SW*SFO1)" + INV_REL "SW=1000000/(2*(0.005+DW)*SFO1)" + UNIT "usec" + FORMAT "%14.3lf usec" + TEXT " " +END +NAME DE + FORMAT "%14.2f usec" + TEXT " " +END +NAME TE + FORMAT "%14.1f K" + TEXT " " +END +T_NAME CNST4 + TYPE R32 + CLASS ACQU + SUBRANGE -1e38 1e38 + REL "CNST4=CNST[4]" + INV_REL "CNST[4]=CNST4" + FORMAT "%14.7f" + TEXT " " +END +T_NAME D0 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D0=D[0]" + INV_REL "D[0]=D0" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D1 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D1=D[1]" + INV_REL "D[1]=D1" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D11 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D11=D[11]" + INV_REL "D[11]=D11" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D13 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D13=D[13]" + INV_REL "D[13]=D13" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D16 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D16=D[16]" + INV_REL "D[16]=D16" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D24 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D24=D[24]" + INV_REL "D[24]=D24" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME D26 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "D26=D[26]" + INV_REL "D[26]=D26" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +T_NAME IN0 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1e38 + REL "IN0=IN[0]" + INV_REL "IN[0]=IN0" + UNIT "sec" + FORMAT "%14.8f sec" + TEXT " " +END +NAME ZGOPTNS + TEXT " " +END +HEADER "======== CHANNEL f1 ========" +NAME NUC1 + NONEDIT + TEXT " " +END +T_NAME P1 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P1=P[1]" + INV_REL "P[1]=P1" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END +T_NAME P2 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P2=P[2]" + INV_REL "P[2]=P2" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END +T_NAME P28 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P28=P[28]" + INV_REL "P[28]=P28" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END +T_NAME PL1 + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL1=PL[1]" + INV_REL "PL[1]=PL1" + UNIT "dB" + FORMAT "%14.2f dB" + TEXT " " +END +T_NAME PL1W + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL1W=63.8*pow(10.0,(-6-PL[1])/10.0)" + INV_REL "PL[1]=-6-4.3425*log(PL1W/63.8)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +NAME SFO1 + FORMAT "%14.7f MHz" + TEXT " " +END +HEADER "======== CHANNEL f3 ========" +NAME CPDPRG3 + TEXT " " +END +NAME NUC3 + NONEDIT + TEXT " " +END +T_NAME P21 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P21=P[21]" + INV_REL "P[21]=P21" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END +T_NAME P22 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P22=P[22]" + INV_REL "P[22]=P22" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END +T_NAME PCPD3 + TYPE R32 + CLASS ACQU + SUBRANGE 0 1e38 + REL "PCPD3=PCPD[3]" + INV_REL "PCPD[3]=PCPD3" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END +T_NAME PL3 + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL3=PL[3]" + INV_REL "PL[3]=PL3" + UNIT "dB" + FORMAT "%14.2f dB" + TEXT " " +END +T_NAME PL16 + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL16=PL[16]" + INV_REL "PL[16]=PL16" + UNIT "dB" + FORMAT "%14.2f dB" + TEXT " " +END +T_NAME PL3W + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL3W=288*pow(10.0,(-6-PL[3])/10.0)" + INV_REL "PL[3]=-6-4.3425*log(PL3W/288)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +T_NAME PL16W + TYPE R32 + CLASS ACQU + SUBRANGE -6.0 1e38 + REL "PL16W=288*pow(10.0,(-6-PL[16])/10.0)" + INV_REL "PL[16]=-6-4.3425*log(PL16W/288)" + UNIT "no" + FORMAT "%14.8f W" + TEXT " " +END +NAME SFO3 + FORMAT "%14.7f MHz" + TEXT " " +END +HEADER "====== GRADIENT CHANNEL =====" +NAME GPNAM1 + TEXT " " +END +NAME GPNAM2 + TEXT " " +END +NAME GPNAM3 + TEXT " " +END +T_NAME GPZ1 + TYPE R32 + CLASS ACQU + SUBRANGE -100.0 100.0 + REL "GPZ1=GPZ[1]" + INV_REL "GPZ[1]=GPZ1" + UNIT "%" + FORMAT "%14.2f %" + TEXT " " +END +T_NAME GPZ2 + TYPE R32 + CLASS ACQU + SUBRANGE -100.0 100.0 + REL "GPZ2=GPZ[2]" + INV_REL "GPZ[2]=GPZ2" + UNIT "%" + FORMAT "%14.2f %" + TEXT " " +END +T_NAME GPZ3 + TYPE R32 + CLASS ACQU + SUBRANGE -100.0 100.0 + REL "GPZ3=GPZ[3]" + INV_REL "GPZ[3]=GPZ3" + UNIT "%" + FORMAT "%14.2f %" + TEXT " " +END +T_NAME P16 + TYPE R32 + CLASS ACQU + SUBRANGE 0.0 1.0e10 + REL "P16=P[16]" + INV_REL "P[16]=P16" + UNIT "usec" + FORMAT "%14.2f usec" + TEXT " " +END diff --git a/sample/sample_sessions/test01/2/pdata/1/2ii b/sample/sample_sessions/test01/2/pdata/1/2ii new file mode 100644 index 0000000..cf54eac Binary files /dev/null and b/sample/sample_sessions/test01/2/pdata/1/2ii differ diff --git a/sample/sample_sessions/test01/2/pdata/1/2ir b/sample/sample_sessions/test01/2/pdata/1/2ir new file mode 100644 index 0000000..deac384 Binary files /dev/null and b/sample/sample_sessions/test01/2/pdata/1/2ir differ diff --git a/sample/sample_sessions/test01/2/pdata/1/2ri b/sample/sample_sessions/test01/2/pdata/1/2ri new file mode 100644 index 0000000..b532e42 Binary files /dev/null and b/sample/sample_sessions/test01/2/pdata/1/2ri differ diff --git a/sample/sample_sessions/test01/2/pdata/1/2rr b/sample/sample_sessions/test01/2/pdata/1/2rr new file mode 100644 index 0000000..26bfd23 Binary files /dev/null and b/sample/sample_sessions/test01/2/pdata/1/2rr differ diff --git a/sample/sample_sessions/test01/2/pdata/1/auditp.txt b/sample/sample_sessions/test01/2/pdata/1/auditp.txt new file mode 100644 index 0000000..a88517d --- /dev/null +++ b/sample/sample_sessions/test01/2/pdata/1/auditp.txt @@ -0,0 +1,32 @@ +##TITLE= Audit trail, TOPSPIN Version 2.1 +##JCAMPDX= 5.01 +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/auditp.txt +##AUDIT TRAIL= $$ (NUMBER, WHEN, WHO, WHERE, PROCESS, VERSION, WHAT) +( 1,<2010-09-27 00:37:57.695 -0400>,,,,, + ) +( 2,<2010-09-27 00:38:07.366 -0400>,,,,, + ) +( 3,<2010-09-27 10:54:28.898 -0400>,,,,, + ) +( 4,<2010-09-27 15:02:16.968 -0400>,,,,, + ) +##END= + +$$ hash MD5 +$$ 5C BB 6C F7 27 6D B5 92 11 DE A2 17 D4 05 70 C8 diff --git a/sample/sample_sessions/test01/2/pdata/1/clevels b/sample/sample_sessions/test01/2/pdata/1/clevels new file mode 100644 index 0000000..fe79542 --- /dev/null +++ b/sample/sample_sessions/test01/2/pdata/1/clevels @@ -0,0 +1,33 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 16 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 15:02:27.405 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/clevels +$$ process /opt/topspin2.1/prog/mod/dataserver +##$LEVELS= (0..255) +-5800829716762.1 -3222683175979 -1790379542210.5 -994655301228.1 -552586278460 +-306992376922.2 -170551320512.4 -94750733618 -52639296454.4 -29244053585.8 +-16246696436.6 -9025942464.8 -5014412480.4 -2785784711.3 -1547658173 -859810096.1 +-477672275.6 -265373486.4 -147429714.7 -81905397.1 -45502998.4 -25279443.5 +-14044135.3 -7802297.4 -4334609.7 -2408116.5 -1337842.5 -743245.8 -412914.3 +-229396.9 -127442.7 -70801.5 70801.5 81421.7 93635 107680.2 123832.3 142407.1 +163768.2 188333.4 216583.4 249070.9 286431.6 329396.3 378805.7 435626.6 +500970.6 576116.2 662533.6 761913.6 876200.7 1007630.8 1158775.4 1332591.7 +1532480.5 1762352.5 2026705.4 2330711.2 2680317.9 3082365.6 3544720.4 4076428.5 +4687892.8 5391076.7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$LEVSIGN= 3 +##$MAXLEV= 60 +##$METHOD= 0 +##$NEGBASE= -70801.5 +##$NEGINCR= 1.8 +##$POSBASE= 70801.5 +##$POSINCR= 1.15 +##END= diff --git a/sample/sample_sessions/test01/2/pdata/1/outd b/sample/sample_sessions/test01/2/pdata/1/outd new file mode 100644 index 0000000..55c6d6d --- /dev/null +++ b/sample/sample_sessions/test01/2/pdata/1/outd @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-24 16:07:31.541 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/prog/curdir/changer/inmrchanger/Sep24-2010-1606-micro_screening/11/data/nmr/HR4762D.007_N_HSQC/1/pdata/1/outd +$$ process /opt/topspin2.1/prog/mod/xwish3 +##$CURPLOT= +##$CURPRIN= <$hp-laserjet-1300-1> +##$DFORMAT= +##$LAYOUT= <+/2D_inv.xwp> +##$LFORMAT= +##$PFORMAT= +##$SURQMSG= 1 +##END= diff --git a/sample/sample_sessions/test01/2/pdata/1/proc b/sample/sample_sessions/test01/2/pdata/1/proc new file mode 100644 index 0000000..b7d6205 --- /dev/null +++ b/sample/sample_sessions/test01/2/pdata/1/proc @@ -0,0 +1,110 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 7 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 15:02:16.968 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/proc +$$ process /opt/topspin2.1/prog/mod/proc2d +##$ABSF1= 4.6 +##$ABSF2= -100 +##$ABSG= 5 +##$ABSL= 3 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= +##$AXLEFT= 0 +##$AXNAME= <> +##$AXNUC= +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.1 +##$BCFW= 1 +##$BC_mod= 4 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 2 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 0 +##$FT_mod= 4 +##$GAMMA= 1 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 0.3 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 0 +##$MEAN= 0 +##$ME_mod= 0 +##$MI= 0 +##$NCOEF= 0 +##$NC_proc= 0 +##$NLEV= 6 +##$NOISF1= 8.174992 +##$NOISF2= 6.675002 +##$NSP= 1 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 11.68554 +##$PC= 1 +##$PHC0= 37.5853 +##$PHC1= -6.6 +##$PH_mod= 1 +##$PKNL= yes +##$PPARMOD= 1 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 4 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 600.13 +##$SI= 2048 +##$SIGF1= 5.6 +##$SIGF2= 5.2 +##$SINO= 400 +##$SIOLD= 2048 +##$SPECTYP= <> +##$SREGLST= <1H.H2O+D2O> +##$SSB= 2 +##$STSI= 0 +##$STSR= 0 +##$SW_p= 8389.26174496644 +##$SYMM= 0 +##$S_DEV= 0 +##$TDeff= 16384 +##$TDoff= 0 +##$TI= +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 4 +##$XDIM= 8192 +##$YMAX_p= 0 +##$YMIN_p= 0 +##END= diff --git a/sample/sample_sessions/test01/2/pdata/1/proc2 b/sample/sample_sessions/test01/2/pdata/1/proc2 new file mode 100644 index 0000000..f676dde --- /dev/null +++ b/sample/sample_sessions/test01/2/pdata/1/proc2 @@ -0,0 +1,109 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-24 16:07:31.541 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/prog/curdir/changer/inmrchanger/Sep24-2010-1606-micro_screening/11/data/nmr/HR4762D.007_N_HSQC/1/pdata/1/proc2 +$$ process /opt/topspin2.1/prog/mod/xwish3 +##$ABSF1= 1000 +##$ABSF2= -1000 +##$ABSG= 5 +##$ABSL= 3 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= < > +##$AXLEFT= 0 +##$AXNAME= <> +##$AXNUC= +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.5 +##$BCFW= 1 +##$BC_mod= 0 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 1 +##$DFILT= < > +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 0 +##$FT_mod= 0 +##$GAMMA= 1 +##$GB= 0.1 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 0.3 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 5 +##$MEAN= 0 +##$ME_mod= 2 +##$MI= 1 +##$NCOEF= 32 +##$NC_proc= 0 +##$NLEV= 6 +##$NOISF1= 0 +##$NOISF2= 0 +##$NSP= 1 +##$NTH_PI= 0 +##$NZP= 1 +##$OFFSET= 132.4757 +##$PC= 4 +##$PHC0= 0 +##$PHC1= 0 +##$PH_mod= 1 +##$PKNL= yes +##$PPARMOD= 1 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 1 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 60.810645 +##$SI= 256 +##$SIGF1= 0 +##$SIGF2= 0 +##$SINO= 16 +##$SIOLD= 256 +##$SPECTYP= <> +##$SREGLST= <.MeOH> +##$SSB= 2 +##$STSI= 0 +##$STSR= 0 +##$SW_p= 2125.85034013606 +##$SYMM= 0 +##$S_DEV= 0 +##$TDeff= 0 +##$TDoff= 0 +##$TI= < > +##$TILT= no +##$TM1= 0.1 +##$TM2= 0.9 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 4 +##$XDIM= 64 +##$YMAX_p= 0 +##$YMIN_p= 0 +##END= diff --git a/sample/sample_sessions/test01/2/pdata/1/proc2s b/sample/sample_sessions/test01/2/pdata/1/proc2s new file mode 100644 index 0000000..d7ae2a1 --- /dev/null +++ b/sample/sample_sessions/test01/2/pdata/1/proc2s @@ -0,0 +1,109 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 3 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 15:02:16.968 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/proc2s +$$ process /opt/topspin2.1/prog/mod/proc2d +##$ABSF1= 0 +##$ABSF2= 0 +##$ABSG= 0 +##$ABSL= 0 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= < > +##$AXLEFT= 0 +##$AXNAME= +##$AXNUC= <15N> +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.5 +##$BCFW= 0 +##$BC_mod= 0 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 0 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 256 +##$FT_mod= 6 +##$GAMMA= 0 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 0 +##$LEV0= 0 +##$LPBIN= 240 +##$MAXI= 10000 +##$MC2= 5 +##$MEAN= 0 +##$ME_mod= 2 +##$MI= 1 +##$NCOEF= 32 +##$NC_proc= -7 +##$NLEV= 6 +##$NOISF1= 0 +##$NOISF2= 0 +##$NSP= 0 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 132.4757 +##$PC= 4 +##$PHC0= 0 +##$PHC1= 0 +##$PH_mod= 1 +##$PKNL= no +##$PPARMOD= 1 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 1 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 60.810645 +##$SI= 256 +##$SIGF1= 0 +##$SIGF2= 0 +##$SINO= 16 +##$SIOLD= 256 +##$SPECTYP= <> +##$SREGLST= <.MeOH> +##$SSB= 2 +##$STSI= 256 +##$STSR= 0 +##$SW_p= 2125.85034013606 +##$SYMM= 0 +##$S_DEV= 3.127548e+07 +##$TDeff= 240 +##$TDoff= 0 +##$TI= < > +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 4 +##$XDIM= 128 +##$YMAX_p= 225681412 +##$YMIN_p= -132028372 +##END= diff --git a/sample/sample_sessions/test01/2/pdata/1/procs b/sample/sample_sessions/test01/2/pdata/1/procs new file mode 100644 index 0000000..60cb5fb --- /dev/null +++ b/sample/sample_sessions/test01/2/pdata/1/procs @@ -0,0 +1,110 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 5 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-27 15:02:16.967 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/pdata/1/procs +$$ process /opt/topspin2.1/prog/mod/proc2d +##$ABSF1= 0 +##$ABSF2= 0 +##$ABSG= 0 +##$ABSL= 0 +##$ALPHA= 0 +##$AQORDER= 0 +##$ASSFAC= 0 +##$ASSFACI= 0 +##$ASSFACX= 0 +##$ASSWID= 0 +##$AUNMP= +##$AXLEFT= 0 +##$AXNAME= +##$AXNUC= <1H> +##$AXRIGHT= 0 +##$AXTYPE= 0 +##$AXUNIT= <> +##$AZFE= 0.1 +##$AZFW= 0.1 +##$BCFW= 0 +##$BC_mod= 4 +##$BYTORDP= 0 +##$COROFFS= 0 +##$CY= 15 +##$DATMOD= 1 +##$DC= 0 +##$DFILT= <> +##$DTYPP= 0 +##$F1P= 0 +##$F2P= 0 +##$FCOR= 0.5 +##$FTSIZE= 2048 +##$FT_mod= 6 +##$GAMMA= 0 +##$GB= 0 +##$INTBC= 1 +##$INTSCL= 1 +##$ISEN= 128 +##$LB= 0 +##$LEV0= 0 +##$LPBIN= 0 +##$MAXI= 10000 +##$MC2= 0 +##$MEAN= 0 +##$ME_mod= 0 +##$MI= 0 +##$NCOEF= 0 +##$NC_proc= -7 +##$NLEV= 6 +##$NOISF1= 8.174992 +##$NOISF2= 6.675002 +##$NSP= 0 +##$NTH_PI= 0 +##$NZP= 0 +##$OFFSET= 11.68554 +##$PC= 1 +##$PHC0= 37.5853 +##$PHC1= -6.6 +##$PH_mod= 1 +##$PKNL= yes +##$PPARMOD= 1 +##$PPDIAG= 0 +##$PPIPTYP= 0 +##$PPMPNUM= 2147483647 +##$PPRESOL= 1 +##$PSCAL= 4 +##$PSIGN= 0 +##$PYNMP= +##$REVERSE= no +##$SF= 600.13 +##$SI= 2048 +##$SIGF1= 0 +##$SIGF2= 0 +##$SINO= 400 +##$SIOLD= 2048 +##$SPECTYP= <> +##$SREGLST= <1H.H2O+D2O> +##$SSB= 2 +##$STSI= 2048 +##$STSR= 0 +##$SW_p= 8389.26174496644 +##$SYMM= 0 +##$S_DEV= 3.127548e+07 +##$TDeff= 4096 +##$TDoff= 0 +##$TI= +##$TILT= no +##$TM1= 0 +##$TM2= 0 +##$TOPLEV= 0 +##$USERP1= +##$USERP2= +##$USERP3= +##$USERP4= +##$USERP5= +##$WDW= 4 +##$XDIM= 2048 +##$YMAX_p= 225681412 +##$YMIN_p= -132028372 +##END= diff --git a/sample/sample_sessions/test01/2/pdata/1/title b/sample/sample_sessions/test01/2/pdata/1/title new file mode 100644 index 0000000..439f677 --- /dev/null +++ b/sample/sample_sessions/test01/2/pdata/1/title @@ -0,0 +1,3 @@ +HR4762D.007 2D NH HSQC +HSQCETF3GPSIMS H2O+D2O /opt/topspin2.1 micro_screening 11 +Clear \ No newline at end of file diff --git a/sample/sample_sessions/test01/2/prosol_History b/sample/sample_sessions/test01/2/prosol_History new file mode 100644 index 0000000..b1d9b9f --- /dev/null +++ b/sample/sample_sessions/test01/2/prosol_History @@ -0,0 +1,173 @@ +#******************************************************************* +# +# $Source: /sc/CvsTree/sc/gen/src/prg/scripts/tix/prosol/lib/lists/default,v $ +# +# Copyright (c) 1999 +# BRUKER ANALYTIK GMBH +# D-76287 Rheinstetten, Germany +# +# All Rights Reserved +# +# +# $Id: default,v 1.15.2.2 2007/12/14 16:22:31 ber Exp $ +# +#******************************************************************* +#../conf/instr/spect/prosol/relations/default +#avance-version (07/12/14) +# +#pulses +# +P[0]=P90[F1]; # 90 deg pulse F1 +P[1]=P90[F1]; # 90 deg pulse F1 +P[2]=P90[F1]*2; # 180 deg pulse F1 +P[3]=P90[F2]; # 90 deg pulse F2 +P[4]=P90[F2]*2; # 180 deg pulse F2 +P[5]=PTOC[F1]*0.66; # 60 deg pulse F1, TOCSY +P[6]=PTOC[F1]; # 90 deg pulse F1, TOCSY +P[7]=PTOC[F1]*2; # 180 deg pulse F1, TOCSY +P[8]=PSH3[F1]; # 90 deg selective F1, WET +P[9]=PTOC[F2]; # 90 deg pulse F2, TOCSY +P[10]=PTOC[F2]*2; # 180 deg pulse F2, TOCSY +P[11]=PSH1[F1]; # 90 deg selective F1 +P[12]=PSH2[F1]; # 180 deg selective F1 +# +P[14]=PSH3[F2]; # 180 deg inversion, adiabatic +P[15]=TROE[F1]; # cw pulse F1, ROESY +P[18]=PSH7[F1]; # off-resonance presat F1 +P[21]=P90[F3]; # 90 deg pulse F3 +P[22]=P90[F3]*2; # 180 deg pulse F3 +P[23]=P90[F4]; # 90 deg pulse F4 +P[24]=PSH2[F2]; # 180 deg refocussing, adiabatic +P[25]=PROE[F1]*2; # 180 deg pulse, Shaka ROESY +P[26]=PSH12[F1]; # 180 deg inversion F1, adiabatic +P[27]=P90[F1]; # 90 deg pulse F1, WATERGATE +# +P[29]=PSH8[F1]; # flip back pulse +P[31]=PSH15[F2]; # 180 deg adiabatic, F2, 13C x-filter +P[32]=PSH16[F1]; # 180 deg adiabatic, F1, z-spoil +#P[33]=PSH[F1]; # 90 deg, F1, hadamard +#P[34]=PSH[F1]; # 180 deg, F1, hadamard +#P[35]=PSH[F2]; # 90 deg, F2, hadamard +#P[36]=PSH[F2]; # 180 deg, F2, hadamard +#P[37]=PSH[F3]; # 90 deg, F3, hadamard +#P[38]=PSH[F3]; # 180 deg, F3, hadamard +P[39]=PSH21[F2]; # 180 deg, F2, Bip +P[40]=PSH8[F1]*2; # 180 deg sel. F1, 1H (exc. scul) +# +P[63]=PSH11[F2]; # 180 deg adiabatic decoupling, F2, 13C +# +#decoupling pulses +# +PCPD[1]=PCPDP[F1]; # 90 deg pulse F1, dec. +PCPD[2]=PCPDP[F2]; # 90 deg pulse F2, dec. +PCPD[3]=PCPDP[F3]; # 90 deg pulse F3, dec. +# +#power levels +# +PL[1]=PL90[F1]; # high power, F1 +PL[2]=PL90[F2]; # high power, F2 +PL[3]=PL90[F3]; # high power, F3 +PL[4]=PL90[F4]; # high power, F4 +PL[9]=PLCW[F1]; # presat power, F1 +PL[10]=PLTOC[F1]; # TOCSY power, F1 +PL[11]=PLROE[F1]; # ROESY power, F1 +PL[12]=PLCPDP[F2]; # dec. power, F2 +PL[13]=PLCPD2[F2]; # dec. power 2, F2 +PL[14]=PLNOE[F2]; # low power cw, F2 +PL[15]=PLTOC[F2]; # TOCSY power, F2 +PL[16]=PLCPDP[F3]; # dec. power, F3 +PL[18]=PL90[F1]; # WATERGATE power, F1 +PL[19]=PLCPDP[F1]; # dec. power, F1 +PL[21]=PLCW[F2]; # +PL[23]=PLTOC[F3]; # TOCSY power, F3 +PL[24]=PLHD[F2]; # HD decoupling, F2 +PL[25]=PLSH8U[F2]; # Eretic, F2 +PL[27]=PLROE[F1]; # Shaka Spinlock +PL[30]=PLCPDP[F2]; # dec. power, F2, 13C (=pl12) +PL[31]=PLUSER2[F2]; # dec. power, F2, 13C, cw bilev +# +#shapes +# +SP[1]=PLSH1[F1]; # 90 deg selective F1 +SP[2]=PLSH2[F1]; # 180 deg selective F1 +SP[3]=PLSH3[F2]; # adiabatic 180 deg, F2, inversion +SP[4]=PLSH21[F2]; # 180 deg Bip, F2, inversion +SP[6]=PLSH7[F1]; # off-resonance presat F1 +SP[7]=PLSH2[F2]; # adiabatic 180 deg, F2, refocussing +SP[8]=PLSH12[F1]; # adiabatic 180 deg, F1, inversion +SP[10]=PLSH8[F1]; # flip-back pulse, F1, 1H +SP[11]=PLSH8[F1]; # flip-back pulse, F1, H +SP[14]=PLSH12[F2]; # adiab. bilev dec., F2, 13C +SP[18]=PLSH15[F2]; # adiabatic 180 deg, F2, 13C, x-filter +SP[19]=PLSH3[F1] +0.87; # 90 deg, F1, wet +SP[20]=PLSH3[F1] -1.04; # 90 deg, F1, wet +SP[21]=PLSH3[F1] +2.27; # 90 deg, F1, wet +SP[22]=PLSH3[F1] -5.05; # 90 deg, F1, wet +#SP[23]=PLSH[F1]; # 90 deg, F1, hadamard +#SP[24]=PLSH[F1]; # 180 deg, F1, hadamard +#SP[25]=PLSH[F2]; # 90 deg, F2, hadamard +#SP[26]=PLSH[F2]; # 180 deg, F2, hadamard +#SP[27]=PLSH[F3]; # 90 deg, F3, hadamard +#SP[28]=PLSH[F3]; # 180 deg, F3, hadamard +SP[29]=PLSH16[F1]; # adiabatic 180 deg, F1, z-spoil +SP[31]=PLSH11[F2]; # adiab. dec., F2, 13C +# +SPNAM1=PNSH1[F1]; # +SPNAM2=PNSH2[F1]; # +SPNAM3=PNSH3[F2]; # +SPNAM4=PNSH21[F2]; # +SPNAM6=PNSH7[F1]; # +SPNAM7=PNSH2[F2]; # +SPNAM8=PNSH12[F1]; # +SPNAM10=PNSH8[F1]; # +SPNAM11=PNSH8[F1]; # +SPNAM14=PNSH12[F2]; # +SPNAM15=PNSH8U[F2]; # Eretic, F2 +SPNAM18=PNSH15[F2]; # +SPNAM19=PNSH3[F1]; # +SPNAM20=PNSH3[F1]; # +SPNAM21=PNSH3[F1]; # +SPNAM22=PNSH3[F1]; # +#SPNAM23=PNSH[]; # +#SPNAM24=PNSH[]; # +#SPNAM25=PNSH[]; # +#SPNAM26=PNSH[]; # +#SPNAM27=PNSH[]; # +#SPNAM28=PNSH[]; # +SPNAM29=PNSH16[F1]; # +SPNAM31=PNSH11[F2]; # +# +SPOAL[1]=PASH1[F1]; # +SPOAL[2]=PASH2[F1]; # +SPOAL[3]=PASH3[F2]; # +SPOAL[4]=PASH21[F2]; # +SPOAL[6]=PASH7[F1]; # +SPOAL[7]=PASH2[F2]; # +SPOAL[8]=PASH12[F1]; # +SPOAL[10]=PASH8[F1]; +SPOAL[11]=PASH8[F1]; +SPOAL[14]=PASH12[F2]; # +SPOAL[18]=PASH15[F2]; # +SPOAL[19]=PASH3[F1]; # +SPOAL[20]=PASH3[F1]; # +SPOAL[21]=PASH3[F1]; # +SPOAL[22]=PASH3[F1]; # +#SPOAL[23]=PASH[]; # +#SPOAL[24]=PASH[]; # +#SPOAL[25]=PASH[]; # +#SPOAL[26]=PASH[]; # +#SPOAL[27]=PASH[]; # +#SPOAL[28]=PASH[]; # +SPOAL[29]=PASH16[F1]; # +SPOAL[31]=PASH11[F2]; # +# +#global +# +D[9]=TTOC[F1]; # +D[16]=D_grad; # +P[16]=P_grad1; # +P[17]=P_mlev; # +P[19]=P_grad2; # +P[20]=P_mlev; # +P[28]=P_hsqc; # +# diff --git a/sample/sample_sessions/test01/2/pulseprogram b/sample/sample_sessions/test01/2/pulseprogram new file mode 100644 index 0000000..1cfe5ac --- /dev/null +++ b/sample/sample_sessions/test01/2/pulseprogram @@ -0,0 +1,422 @@ +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" +;hsqcetf3gpsi +;avance-version (07/04/04) +;HSQC +;2D H-1/X correlation via double inept transfer +; using sensitivity improvement +;phase sensitive using Echo/Antiecho-TPPI gradient selection +;with decoupling during acquisition +;using trim pulses in inept transfer +;using f3 - channel +; +;A.G. Palmer III, J. Cavanagh, P.E. Wright & M. Rance, J. Magn. +; Reson. 93, 151-170 (1991) +;L.E. Kay, P. Keifer & T. Saarinen, J. Am. Chem. Soc. 114, +; 10663-5 (1992) +;J. Schleucher, M. Schwendinger, M. Sattler, P. Schmidt, O. Schedletzky, +; S.J. Glaser, O.W. Sorensen & C. Griesinger, J. Biomol. NMR 4, +; 301-306 (1994) +; +;$CLASS=HighRes +;$DIM=2D +;$TYPE= +;$SUBTYPE= +;$COMMENT= + + + +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/Avance.incl" 1 +;Avance2.incl +; for 1 +; +;avance-version (07/08/21) +; +;$CLASS=HighRes Incl +;$COMMENT= + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +;$Id: Avance2.incl,v 1.17.2.1 2007/09/14 16:17:35 ber Exp $ +# 27 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" 2 + +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/Grad.incl" 1 +;Grad2.incl - include file for Gradient Spectroscopy +; for 1 +; +;avance-version (07/01/17) +; +;$CLASS=HighRes Incl +;$COMMENT= + + + + + + + + + + + + + + + + + + + +define list EA= + + + +;$Id: Grad2.incl,v 1.12 2007/01/22 14:22:35 ber Exp $ +# 28 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" 2 + +# 1 "/opt/topspin2.1/exp/stan/nmr/lists/pp/Delay.incl" 1 +;Delay.incl - include file for commonly used delays +; +;version 00/02/07 +; +;$CLASS=HighRes Incl +;$COMMENT= + + +;general delays + +define delay DELTA +define delay DELTA1 +define delay DELTA2 +define delay DELTA3 +define delay DELTA4 +define delay DELTA5 +define delay DELTA6 +define delay DELTA7 +define delay DELTA8 + +define delay TAU +define delay TAU1 +define delay TAU2 +define delay TAU3 +define delay TAU4 +define delay TAU5 + + +;delays for centering pulses + +define delay CEN_HN1 +define delay CEN_HN2 +define delay CEN_HN3 +define delay CEN_HC1 +define delay CEN_HC2 +define delay CEN_HC3 +define delay CEN_HC4 +define delay CEN_HP1 +define delay CEN_HP2 +define delay CEN_CN1 +define delay CEN_CN2 +define delay CEN_CN3 +define delay CEN_CN4 +define delay CEN_CP1 +define delay CEN_CP2 + + +;loop counters + +define loopcounter COUNTER +define loopcounter SCALEF +define loopcounter FACTOR1 +define loopcounter FACTOR2 +define loopcounter FACTOR3 + + + +;$Id: Delay.incl,v 1.12 2005/11/10 12:16:58 ber Exp $ +# 29 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" 2 + + + +"p2=p1*2" +"p22=p21*2" +"d11=30m" +"d13=4u" +"d26=1s/(cnst4*4)" + + +"d0=3u" + +"in0=inf1/2" + + +"DELTA1=d13+p16+d16+4u" + + + + +"DELTA=p16+d16+p2+d0*2" + + + +# 1 "mc_line 53 file /opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi expanding definition part of mc command before ze" +define delay MCWRK +define delay MCREST +define loopcounter ST1CNT +"ST1CNT = td1 / (2)" +"MCWRK = 0.142857*d1" +"MCREST = d1 - d1" + dccorr +# 53 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" +1 ze +# 1 "mc_line 53 file /opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi expanding definition of mc command after ze" +# 54 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" + d11 pl16:f3 +# 1 "mc_line 55 file /opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi expanding start label for mc command" +2 MCWRK * 2 do:f3 +LBLSTS1, MCWRK * 4 +LBLF1, MCWRK + MCREST +# 56 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" +3 (p1 ph1) + d26 pl3:f3 + (center (p2 ph1) (p22 ph6):f3 ) + d26 setnmr3|0 setnmr0|34|32|33 ctrlgrad 0 + p28 ph1 + d13 + (p1 ph2) + 3u + p16:gp1 + d16 + (p21 ph3):f3 + d0 + + + + + (p2 ph7) + + + d0 + p16:gp2*EA + d16 + (p22 ph4):f3 + DELTA + (center (p1 ph1) (p21 ph4):f3 ) + d24 + (center (p2 ph1) (p22 ph1):f3 ) + d24 + (center (p1 ph2) (p21 ph5):f3 ) + d26 + (center (p2 ph1) (p22 ph1):f3 ) + d26 + (p1 ph1) + DELTA1 + (p2 ph1) + d13 + p16:gp3 + d16 pl16:f3 + 4u setnmr3^0 setnmr0^34^32^33 ctrlgrad 7 + go=2 ph31 cpd3:f3 +# 1 "mc_line 96 file /opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi expanding mc command in line" + MCWRK do:f3 wr #0 if #0 zd igrad EA MCWRK ip5*2 + lo to LBLSTS1 times 2 + MCWRK id0 MCWRK ip3*2 MCWRK ip6*2 MCWRK ip31*2 + lo to LBLF1 times ST1CNT + MCWRK +# 98 "/opt/topspin2.1/exp/stan/nmr/lists/pp/hsqcetf3gpsi" +exit + + +ph1=0 +ph2=1 +ph3=0 2 +ph4=0 0 2 2 +ph5=1 1 3 3 +ph6=0 +ph7=0 0 2 2 +ph31=0 2 2 0 + + +;pl1 : f1 channel - power level for pulse (default) +;pl3 : f3 channel - power level for pulse (default) +;pl16: f3 channel - power level for CPD/BB decoupling +;sp3: f2 channel - shaped pulse 180 degree (adiabatic) +;p1 : f1 channel - 90 degree high power pulse +;p2 : f1 channel - 180 degree high power pulse +;p14: f2 channel - 180 degree shaped pulse for inversion (adiabatic) +;p16: homospoil/gradient pulse [1 msec] +;p21: f3 channel - 90 degree high power pulse +;p22: f3 channel - 180 degree high power pulse +;p28: f1 channel - trim pulse [1 msec] +;d0 : incremented delay (2D) [3 usec] +;d1 : relaxation delay; 1-5 * T1 +;d11: delay for disk I/O [30 msec] +;d13: short delay [4 usec] +;d16: delay for homospoil/gradient recovery +;d24: 1/(4J)YH for YH +; 1/(8J)YH for all multiplicities +;d26: 1/(4J(YH)) +;cnst4: = J(YH) +;inf1: 1/SW(X) = 2 * DW(X) +;in0: 1/(2 * SW(X)) = DW(X) +;nd0: 2 +;NS: 1 * n +;DS: >= 16 +;td1: number of experiments +;FnMODE: echo-antiecho +;cpd3: decoupling according to sequence defined by cpdprg3 +;pcpd3: f3 channel - 90 degree pulse for decoupling sequence + + +;use gradient ratio: gp 1 : gp 2 : gp 3 +; 50 : 80 : 20.1 for C-13 +; 50 : 80 : 8.1 for N-15 + +;for z-only gradients: +;gpz1: 50% +;gpz2: 80% +;gpz3: 20.1% for C-13, 8.1% for N-15 + +;use gradient files: +;gpnam1: SINE.100 +;gpnam2: SINE.100 +;gpnam3: SINE.100 + + + ;preprocessor-flags-start +;LABEL_CN: for C-13 and N-15 labeled samples start experiment with +; option -DLABEL_CN (eda: ZGOPTNS) + ;preprocessor-flags-end + + + +;$Id: hsqcetf3gpsi,v 1.4 2007/04/11 13:34:30 ber Exp $ diff --git a/sample/sample_sessions/test01/2/scon2 b/sample/sample_sessions/test01/2/scon2 new file mode 100644 index 0000000..867251b --- /dev/null +++ b/sample/sample_sessions/test01/2/scon2 @@ -0,0 +1,17 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 1 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2010-09-26 22:16:43.586 -0400 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/data/micro_screening/nmr/HR4762D.007_N_HSQC/1/scon2 +$$ process /opt/topspin2.1/prog/mod/go +##$BLKTR= (0..15) +3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 +##$DE1= 4.5 +##$DEADC= 0.5 +##$DEPA= 4.5 +##$DERX= 1.5 +##$FILCOR= 0.2 +##END= diff --git a/sample/sample_sessions/test01/2/ser b/sample/sample_sessions/test01/2/ser new file mode 100644 index 0000000..09b1825 Binary files /dev/null and b/sample/sample_sessions/test01/2/ser differ diff --git a/sample/sample_sessions/test01/2/uxnmr.par b/sample/sample_sessions/test01/2/uxnmr.par new file mode 100644 index 0000000..c90a4f2 --- /dev/null +++ b/sample/sample_sessions/test01/2/uxnmr.par @@ -0,0 +1,527 @@ +##TITLE= Parameter file, TOPSPIN Version 2.1 +##JCAMPDX= 5.0 +##DATATYPE= Parameter Values +##NPOINTS= 104 $$ modification sequence number +##ORIGIN= Bruker BioSpin GmbH +##OWNER= nmrsu +$$ 2009-12-15 16:47:14.463 -0500 nmrsu@hector.cabm.rutgers.edu +$$ /opt/topspin2.1/conf/instr/spect/uxnmr.par +$$ process /opt/topspin2.1/prog/mod/hconfserver +##$ACB= 1 +##$ACBTAT= (0..15) +0 88 72 88 0 0 88 0 0 0 0 0 0 0 0 0 +##$ACBTBA= (0..15) +0 30 60 90 0 0 180 0 0 0 0 0 0 0 0 0 +##$ACBTBLK= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTCTL= (0..15) +0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 +##$ACBTDI= (0..15) +0 70 71 72 0 0 75 0 0 0 0 0 0 0 0 0 +##$ACBTDM= (0..15) +0 6 25 10 0 0 10 0 0 0 0 0 0 0 0 0 +##$ACBTFHI= (0..15) +0 365 600 365 0 0 365 0 0 0 0 0 0 0 0 0 +##$ACBTFL= (0..15) +0 249 249 249 0 0 249 0 0 0 0 0 0 0 0 0 +##$ACBTFLO= (0..15) +0 6 188 6 0 0 6 0 0 0 0 0 0 0 0 0 +##$ACBTINP= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTOUT= (0..15) +0 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 +##$ACBTPO= (0..15) +0 500000 100000 300000 0 0 300000 0 0 0 0 0 0 0 0 0 +##$ACBTPW= (0..15) +0 600 1000 1000 0 0 1000 0 0 0 0 0 0 0 0 0 +##$ACBTSB= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$ACBTY= +##$AQSBDCH= (0..95) +0 0 0 0 0 0 0 0 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDHW= (0..95) +1 4 4 4 0 1 4 4 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDID= (0..95) +88 83 83 83 89 88 83 83 89 80 80 66 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSBDNO= (0..95) +1 1 2 3 1 2 4 5 2 1 2 1 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSBDSL= (0..95) +4 5 6 7 8 10 11 12 15 17 18 19 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 +##$AQSBDTY= (0..95) +194 16 24 16 4 194 24 16 4 10 10 7 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSBUAD= (0..95) +52 36 37 38 60 53 39 40 61 33 34 32 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 +##$AQSECL= (0..95) +0 1 1 1 1 0 1 1 1 1 1 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSECLS= (0..95) +3 1 1 1 0 3 1 1 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 +##$AQSSPLT= no +##$ATT19F= (0..1) +0 0 +##$ATT1H= (0..1) +0 0 +##$ATT3H= (0..1) +0 0 +##$ATTX= (0..1) +0 0 +##$ATTY= (0..1) +0 0 +##$ATTZ= (0..1) +0 0 +##$BACSAIR= yes +##$BACSCAP= 60 +##$BACSDEL= 10 +##$BACSFCM= no +##$BACSOPT= +##$BACSTY= +##$BARPTY= +##$BFREQ= 600.13 +##$BGAETH1= +##$BGAETH2= +##$BGAETH3= +##$BGAETH4= +##$BGAETH5= +##$BGAETH6= +##$BGAETH7= +##$BGAETH8= +##$BIRDS= yes +##$BMPC= 0 +##$BMPCTY= +##$BPSUTY= +##$BSMS= 1 +##$BSMSETH= +##$BSMSTY= +##$CFASMOD= (0..7) +1 1 1 1 1 1 1 1 +##$CFASMUL= (0..7) +1 1 1 1 1 1 1 1 +##$CNFTXDR= (0..7) +6 6 6 6 6 0 0 0 +##$COMDIG2= 0 +##$CPDBTY= +##$CRCOTY= +##$CSW1= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$CSW2= (0..31) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$CSWNUM= (0..7) +0 0 0 0 0 0 0 0 +##$DATSTAT= no +##$DIGI140= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIB12= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIB16= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIFA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIHA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIHAF= (0..7) +1 0 0 0 0 0 0 0 +##$DIGIHRD= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIIA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGIO16= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISA= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISAF= (0..7) +0 0 0 0 0 0 0 0 +##$DIGISL= (0..7) +0 0 0 0 0 0 0 0 +##$DIGITYI= (0..7) +0 0 0 0 0 0 0 0 +##$DIGITYP= (0..7) +2 0 0 0 0 0 0 0 +##$DIGITZ= 0 +##$DRU= no +##$DRUETH01= +##$DRUETH02= +##$DRUETH03= +##$DRUETH04= +##$DRUETH05= +##$DRUETH06= +##$DRUETH07= +##$DRUETH08= +##$DRUETH09= +##$DRUETH10= +##$DRUETH11= +##$DRUETH12= +##$DRUETH13= +##$DRUETH14= +##$DRUETH15= +##$DRUETH16= +##$DRUETH17= +##$DRUETH18= +##$DRUETH19= +##$DRUETH20= +##$DRUETH21= +##$DRUETH22= +##$DRUETH23= +##$DRUETH24= +##$DRUETH25= +##$DRUETH26= +##$DRUETH27= +##$DRUETH28= +##$DRUETH29= +##$DRUETH30= +##$DRUETH31= +##$DRUETH32= +##$FCUMEM= (0..7) +2093056 2093056 2093056 2093056 2093056 2093056 0 0 +##$FCUPAL= (0..7) +260 260 260 260 260 260 0 0 +##$FGSVTY= +##$FQMIX= 0 +##$FUNCMOD= <> +##$GCUTYPE= 2 +##$GPREDEL= 0 +##$GPSCUTY= +##$GRADRES= 5 +##$GTUTY= +##$HFAC= 3 +##$HPCU= 0 +##$HPCUTY= +##$HPTXLP= (0..3) +-1 -1 -1 -1 +##$HPTXPI= (0..3) +0 0 0 0 +##$HPTXPO= (0..3) +0 0 0 0 +##$HPTXTY= (0..3) +0 0 0 0 +##$IF451= 0 +##$IFREQ= 1 +##$INTFPR= 0 +##$IPSOETH= <> +##$LOCKTY= +##$LOCSWID= 6 +##$LOCSWIF= 0 +##$M2FAC= 0 +##$MAS= 0 +##$MASETIME= 10 +##$MASITIME= 10 +##$MASTY= +##$MAS_CT= 0 +##$MAS_SG= 0 +##$MAS_TO= 0 +##$MEMPRM= 0 +##$MHFAC= 0 +##$MXFAC= 0 +##$NAMPD1= <1H LNA> +##$NAMPD10= <> +##$NAMPD11= <> +##$NAMPD12= <> +##$NAMPD13= <> +##$NAMPD14= <> +##$NAMPD15= <> +##$NAMPD16= <> +##$NAMPD2= +##$NAMPD3= <2H> +##$NAMPD4= <13C> +##$NAMPD5= <15N> +##$NAMPD6= <> +##$NAMPD7= <> +##$NAMPD8= <> +##$NAMPD9= <> +##$NFCU= 5 +##$NMRCH= 0 +##$NMRMEM= 0 +##$NRCU= 1 +##$NROUT= 2 +##$NSGU= 5 +##$PAMPF1= (0..15) +75 24 64 96 88 88 0 0 0 0 0 0 0 0 0 0 +##$PAMPF2= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF3= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF4= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF5= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF6= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF7= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PAMPF8= (0..15) +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +##$PH4= 0 +##$PHF4TY= +##$POWCHK= yes +##$PRAMD1= (0..7) +2 0 0 536870912 0 0 0 0 +##$PRAMD10= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD11= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD12= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD13= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD14= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD15= (0..7) +0 0 0 0 0 0 0 0 +##$PRAMD16= 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b/specdb/__pycache__/__init__.cpython-37.pyc differ diff --git a/specdb/__pycache__/__main__.cpython-37.pyc b/specdb/__pycache__/__main__.cpython-37.pyc new file mode 100644 index 0000000..c62f269 Binary files /dev/null and b/specdb/__pycache__/__main__.cpython-37.pyc differ diff --git a/specdb/__pycache__/specdb.cpython-37.pyc b/specdb/__pycache__/specdb.cpython-37.pyc new file mode 100644 index 0000000..869252a Binary files /dev/null and b/specdb/__pycache__/specdb.cpython-37.pyc differ diff --git a/specdb/specdb b/specdb/specdb new file mode 100755 index 0000000..64f6be2 --- /dev/null +++ b/specdb/specdb @@ -0,0 +1,379 @@ +#!/usr/bin/env python3 + +""" +SpecDB Command Line Interface. +""" + +import argparse +import json +import os +import sys + +import specdb + +env_keys = ['SPECDB_DB', 'SPECDB_ROOT', 'SPECDB_BACKUP', 'SPECDB_GS_CRED'] + +examples = """ +example command lines: + %(prog)s create --db my.db --backup /backups/my.backup.db + %(prog)s query --db my.db --sql "SELECT * FROM table users LIMIT 10" + %(prog)s insert --file specdb.yaml --env my.db --write + %(prog)s backup --db my.db --backup /backups/my.backup.db + %(prog)s forms --table user project --num 3 1 + %(prog)s summary --table user --db my.db +""" + +# top-level parser +sdb_top = argparse.ArgumentParser(prog='specdb', + description='Command line tool for interfacing with SpecDB', + formatter_class=argparse.RawDescriptionHelpFormatter, + epilog=examples) +sdb_subs = sdb_top.add_subparsers(dest='command', help='command description') +sdb_subs.required = False + +# configure level parser +sdb_configure = sdb_subs.add_parser('create', + help='instantiate a new database') +sdb_configure.add_argument('--db', type=str, metavar='', required=True, + help='path and name for a new database to be made created') +sdb_configure.add_argument('--backup', type=str, metavar='', + required=True, help='path where incremental backup will be saved') + +# forms level parser +sdb_forms = sdb_subs.add_parser('forms', + help=''.join(( + ("generate a template form for requested table\n"), + ('tables to generate forms for are: `user`, `project`, `target` '), + ('`construct`, `expression`, `batch`, `buffer`, `pst`, '), + ('`spectrometer`, and a JSON for a session')))) +sdb_forms.add_argument('--table', nargs='+', metavar='', required=True, + help=''.join(( + ('tables to generate a form for\n'), + ('tables to generate forms for are: `user`, `project`, `target` '), + ('`construct`, `expression`, `purification_batch`, `buffer`, '), + ('`buffer_components`, `pst`, `batch_components`, `spectrometer`, and'), + (' `session`')))) +sdb_forms.add_argument('--num', nargs='+', metavar='', required=False, + default=None, help=''.join(( + ('number of forms to generate for each requested table')))) + +# insert level parser +sdb_insert = sdb_subs.add_parser('insert', + help='insert a single json file into SpecDB') +sdb_insert.add_argument('--form', type=str, metavar='', required=True, + help='path to a single yaml file to insert') +sdb_insert.add_argument('--db', type=str, metavar='', required=True, + help=''.join(( + ('path to specific specdb database file to use for'), + (' insertion. use `specdb create` to create the .db file')))) +sdb_insert.add_argument('--write', action='store_true', required=False, + help=''.join(( + ('write new/altered information in JSON to database, used only once')))) + +# sumary level parser +sdb_summary = sdb_subs.add_parser('summary', + help=''.join(( + ("make a summary report for SpecDB database. if ran with no"), + (" table provided, then a summary for every table is made.")))) +sdb_summary.add_argument('--db', type=str, metavar='', required=True, + help=''.join(( + ('path to specific specdb database file to use.'), + (' use `specdb create` to create a new database file')))) +sdb_summary.add_argument('--table', type=str, metavar='', required=True, + help='provide which table a summary is needed for') + +# query level parser +sdb_query = sdb_subs.add_parser('query', + help=''.join(( + ("query records from SpecDB summary table. If no --output is given"), + (" then results are simply print to screen")))) +sdb_query.add_argument('--sql', nargs='+', type=str, metavar='', + required=True, help=''.join(( + ('query using sql syntax. The query can be on any table.'), + (' If no --output format is given, results are printed to screen.')))) +sdb_query.add_argument('--star', action='store_true', required=False, + help='whether to write a NMR-STAR file for each FID in the query results') +sdb_query.add_argument('--db', type=str, metavar='', required=True, + help=''.join(( + ('path to specific specdb database file to use.'), + (' use `specdb create` to create a new database file')))) +sdb_query.add_argument('--out', type=str, metavar='', required=True, + help='directory to place results of the query') + +# backup level parser +sdb_backup = sdb_subs.add_parser('backup', + help='perform incremental backup. specdb configure must be ran first') +sdb_backup.add_argument('--db', type=str, metavar='', required=True, + help=''.join(( + ('path to specific specdb database environment file to use for'), + (' backup operations. use `specdb configure` to create .env file')))) + +sdb_restore = sdb_subs.add_parser('restore', + help='perform database restoration from a SpecDB backup') +sdb_restore.add_argument('--db', type=str, metavar='', required=True, + help='provide path to the specific SpecDB database to be restored') + +sdb = sdb_top.parse_args() +## Commands ## + +if sdb.command == 'create': + if not sdb.db.endswith('.db'): + print(f'{sdb.db} does not end in .db') + print('change database name with .db at the end') + print('Aborting') + sys.exit() + + specdb_path = os.path.abspath(sdb.db) + + if os.path.isfile(specdb_path): + print(f'db file {sdb.db} already exists') + print(f'is there an already existing db at {sdb.db}?') + print('Aborting') + sys.exit() + + # initial SQLite database at SPECDB_DB location + specdb.init(location=specdb_path) + print('db configured and initialized') + print('Done') + +elif sdb.command == 'forms': + form = specdb.forms(table=sdb.table, num=sdb.num) + print(form) + +elif sdb.command == 'insert': + specdb.insert(file=os.path.abspath(sdb.form), db=sdb.db, write=sdb.write) + +elif sdb.command == 'summary': + specdb.summary(db=sdb.db, table=sdb.table) + +elif sdb.command == 'query': + specdb.query(db=sdb.db, sql=sdb.sql[0], star=sdb.star, output_dir=sdb.out) + +elif sdb.command == 'backup': + specdb.backup(env=sdb.env) + +elif sdb.command == 'restore': + specdb.restore(env=sdb.env) + +""" +# register level parser +sdb_register = sdb_subs.add_parser('register', + help='register a new record for a requested table') +sdb_register.add_argument('--env', type=str, metavar='', required=False, + help='provide a specdb environment file') +sdb_register.add_argument('--user', type=str, metavar='', required=False, + help='register a new user_id') +sdb_register.add_argument('--project', type=str, nargs='+', metavar='', + required=False, help='register a new project_id') +sdb_register.add_argument('--target', type=str, metavar='', + required=False, help='register a new target_id') +sdb_register.add_argument('--construct', type=str, metavar='', + required=False, help='register a new construct_id') +sdb_register.add_argument('--expression', type=str, metavar='', + required=False, help='register a new expression_id') +sdb_register.add_argument('--batch', type=str, metavar='', required=False, + help='register a new batch_id') +sdb_register.add_argument('--pst', type=str, metavar='', + required=False, help='register a new pst_id') +sdb_reg_subs = sdb_register.add_subparsers(dest='subcommand') +sdb_reg_subs.required = False +sdb_buffer_component = sdb_reg_subs.add_parser('buffer-component', + help='add a buffer component') +sdb_buffer_component.add_argument('--buffer', type=str, metavar='', + help='buffer-id this component goes to') +sdb_buffer_component.add_argument('--component', type=str, nargs='+', + metavar='', help='name of buffer component') +sdb_buffer_component.add_argument('--conc-value', type=float, metavar='', + help='concentration of component value') +sdb_buffer_component.add_argument('--unit', type=str, metavar='', + help='concentration unit for buffer component') +sdb_register.add_argument('--spectrometer', type=str, metavar='', + help='add an new spectrometer id') +sdb_register.add_argument('--probe', type=str, metavar='', + help='add a new probe id') + +# update level parser +sdb_update = sdb_subs.add_parser('update', + help='insert all new specdb.json files into SpecDB') +sdb_update.add_argument('--env', type=str, metavar='', required=True, + help=''.join(( + ('path to specific specdb database environment file to be updated.'), + (' use `specdb configure` to create .env file')))) +sdb_update.add_argument('--overwrite', action='store_true', + required=False, help=''.join(( + ('if a specdb.json conflicts with SpecDB, overwite SpecDB to match.'), + (' Otherwise, a conflict resuslts in the specdb.json not being'), + (' inserted into SpecDB and is filed in specdb.log')))) + +def register(table=None, table_id=None, env=None): + environ = read_config(file=env) + sql = f"SELECT table, id FROM register WHERE table == '{table}' AND", + sql += f" id == '{table_id}'" + + results = cursor.exectute(sql) + # if results empty INSERT + if len(results) == 0: + sql = f"INSERT register (table, id) VALUES({table}, {table_id})" + cursor.execute(sql) + print("Registered") + return + else: + print(f"id: {table_id} for table: {table} already registered") + print("Done") + return + +def update(overwrite=False): + # read environment + config = read_config() + + cmd = f'find {SPECDB_ROOT} -type f -name "{SPECDB_JSON}" -newermt {SPECB_LAST}' + new_jsons = subprocess.check_output(cmd, shell=True) + + for line in new_jsons: + line = line.rstrip() + insert(json=linef, overwrite=overwrite) + +if 'INSERT' in line: continue + if 'FROM' in line: continue + if 'VALUES' in line: continue + if 'PRAGMA' in line: continue + if len(line) == 0: continue + + if table == 'session': + if table_name != 'summary' and table_name != 'tubes': + form_dic[table_name] = list() + form_dic[table_name].append(dict()) + form_dic[table_name] + if table == table_name: + out = False + continue + else: + out = True + elif table_name == 'tubes': continue + elif table_name == 'summary': + + config['SPECDB_DB'] = os.path.abspath(sdb.db) + config['SPECDB_NAME'] = specdb_name + config['SPECDB_BACKUP'] = os.path.join( + os.path.abspath(sdb.backup), + f'{specdb_name}.backup.db') + config['SPECDB_LOG'] = os.path.join( + os.path.abspath(sdb.log), + f'{specdb_name}.log.json') + + specdb_env = os.path.join(sdb.log, f'{specdb_name}.specdb.env') + with open(specdb_env, 'w') as fp: + for k,v in config.items(): + fp.write(f'{k}={v}\n') + + log = [] + with open(config['SPECDB_LOG'], 'w') as fp: + json.dump(log, fp, indent=2) + +def read_config(file=None): + """""" + Read specdb.env and return dictionary with keys being SpecDB environemnt + variables. + + Parameters + ---------- + file path to .env file to read + + Returns + ------- + env dict, key/value pairs for SpecDB environemnt variables + """""" + with open(file, 'r') as fp: + env = {} + for line in fp.readlines(): + line = line.rstrip() + if '=' not in line: + print(f'{file} not formatted correctly') + print('Aborting') + sys.exit() + + params = line.split('=') + if params[0] not in env_keys: + print(f'unexpected environment variable {params[0]}') + print('Aborting') + sys.exit() + env[params[0]] = params[1] + + return env + + +def read_log(environment=None): + """""" + Read the SpecDB log file to check which specdb.json files experienced + problems. + + Parameters + ---------- + + environment path to environment file for SpecDB + + Returns + ------- + + log dictionary of specdb.json paths listed in log file + """""" + + environ = read_config(file=environment) + log = [] + with open(environ['SPECDB_LOG'], 'r') as fp: + log = json.load(fp) + + return log + + + sys.exit() + return +# # read template json file to check if provided json has expected keys +# specdb_path = os.path.abspath(os.path.dirname(__file__)) +# temp_json = os.path.join(specdb_path, '../sql/template_specdb.json') +# with open(temp_json, 'r') as fp: +# template_json = json.load(fp) + + for k1 in record: + if k1 not in template_json: + print(f'unknown key {k1} in {json}') + print('Aborting') + sys.exit() + if type(record[k1]) is dict: + for k2 in record[k1]: + if k2 not in template_json[k1]: + print(f'unknown key {k2} in {json}') + print('Aborting') + sys.exit() + return False + elif type(record[k1]) is list: + for item in record[k1]: + assert(type(item) is dict) + for k2 in item: + if k2 not in template_json[k1][0]: + print(f'unknown {k2} in {json}') + print('Aborting') + sys.exit() + return False + + new_fid['experiment_date'] = datetime.datetime.fromtimestamp( + os.path.getmtime( + os.path.join(zipped_path, time_domain[0]))) + +# if 'session' in table: +# if 'time_domain_dataset' not in table: +# print('session and time_domain_dataset must be together in a form') +# print('only session requested') +# print('Aborting') +# sys.exit() +# +# if 'time_domain_dataset' in table: +# if 'session' not in table: +# print('session and time_domain_dataset must be together in a form') +# print('only time_domain_dataset requested') +# print('Aborting') +# sys.exit() + + +""" + + + diff --git a/specdb/specdb.py b/specdb/specdb.py new file mode 100644 index 0000000..7028c2f --- /dev/null +++ b/specdb/specdb.py @@ -0,0 +1,1489 @@ +#!/usr/bin/env python3 + +""" +Module for performing all tasks in specdb +""" + +import datetime +import hashlib +import io +from io import StringIO +import json +import os +import re +import sys +import sqlite3 +import tarfile +import time + +import pandas as pd +import pynmrstar +from pynmrstar import utils, Loop +import ruamel.yaml + +SQL_TYPES = { + "TEXT" : "", + "FLOAT" : 0.0, + "INTEGER": 0, + "BLOB" : "" +} + +env_keys = ['SPECDB_DB', 'SPECDB_BACKUP', 'SPECDB_LOG', 'SPECDB_NAME'] + +table_order = [ + 'user', 'project', 'target', 'construct', 'expression', + 'purification_batch', 'buffer', 'buffer_components', 'pst', + 'batch_components', 'spectrometer', 'probe', 'pulse_sequence'] + +param_files = ['acqus', 'audita.txt', 'log', 'procpar'] + + +def init(location=""): + """ + Initialize a SpecDB database file. + + Parameters + ---------- + + location file-system location to initialize a db + + Returns + ------- + + Bool True if db was made, else False + """ + + assert(location) + specdb_path = os.path.abspath(os.path.dirname(__file__)) + sql_path = os.path.join(specdb_path, '../sql/specdb.sql') + + conn = sqlite3.connect(location) + c = conn.cursor() + with open(sql_path) as fp: + c.executescript(fp.read()) + return True + + +def forms(table=None, num=None): + """ + Create a YAML form for SpecDB tables + + Parameters + ---------- + + table list, table names to generate forms for + + num list, number of forms to make for each table + default 1, if any number is given then len(table) == len(num) + + Returns + ------- + form_out String of YAML form + """ + + if table is None: + print("Argument `table` cannot be none") + print("Aborting") + sys.exit() + + if num is not None: + if len(table) != len(num): + print("the num argument must be same length as table") + print("Aborting") + sys.exit() + + # read schema + specdb_path = os.path.abspath(os.path.dirname(__file__)) + sql_path = os.path.join(specdb_path, '../sql/specdb.sql') + + form_dic = ruamel.yaml.comments.CommentedMap() + table_name = "" + with open(sql_path, 'r') as fp: + + for line in fp.readlines(): + line = line.rstrip() + + if re.search(r'^CREATE ', line): + tr = line.split() + table_name = tr[2] + + if table_name in table: + comment_split = line.split(' -- ') + comment = comment_split[-1] + form_dic[table_name] = ruamel.yaml.comments.CommentedMap() + form_dic.yaml_add_eol_comment(comment, table_name) + + elif re.search(r' -- ', line): + if table_name in table: + sql_col = line.split(' -- ') + col_info = sql_col[0].split() + comment = sql_col[-1] + + column = col_info[0] + sql_type = col_info[1] + + form_dic[table_name][column] = SQL_TYPES[sql_type] + pad = 30 - len(column) + form_dic[table_name].yaml_add_eol_comment( + f"{' '*pad}{comment}", column) + + yaml = ruamel.yaml.YAML() + yaml.preserve_quotes = True + + if num is not None: + num = [int(i) for i in num] + form = ruamel.yaml.comments.CommentedMap() + for i, tbl in enumerate(table): + form[tbl] = ruamel.yaml.comments.CommentedMap() + comment = form_dic.ca.items[tbl][2].value + form.yaml_add_eol_comment(comment, tbl) + + for x in range(num[i]): + form[tbl][x] = ruamel.yaml.comments.CommentedMap() + for k,v in form_dic[tbl].ca.items.items(): + comment = v[2].value[1:] + form[tbl][x][k] = form_dic[tbl][k] + form[tbl][x].yaml_add_eol_comment(comment, k) + + string_stream = StringIO() + yaml.dump(form, string_stream) + form_out = string_stream.getvalue() + string_stream.close() + return form_out + else: + string_stream = StringIO() + yaml.dump(form_dic, string_stream) + form_out = string_stream.getvalue() + string_stream.close() + return form_out + + +def check_yaml(file=None): + """ + Check to see that requested YAML follows expected structure. + + Parameters + ---------- + + file path to YAML file to be checked + + Returns + ------- + + True if YAML file passes check + + False if YAML file fails check + """ + + if file is None: + print('no YAML file provided') + print('must provide a YAML file to be checked') + print('Aborting') + sys.exit() + + # read yaml file to be checked + with open(file, 'rt') as fp: + yaml = ruamel.yaml.YAML() + record = yaml.load(fp) + + # convert record to dictionary + rec = json.loads(json.dumps(record)) + + for tbl, dic in rec.items(): + + template = forms(table=tbl) + temp = ruamel.yaml.safe_load(template) + + temp = json.loads(json.dumps(temp)) + + rec_keys = list(rec[tbl].keys()) + + if isinstance(rec[tbl][rec_keys[0]], dict): + + for ind, data in record[tbl].items(): + for key in data: + if key not in temp[tbl]: + print(f'unknown key {key} in {file}') + print('Aborting') + print(key) + print(temp) + sys.exit() + return False + + else: + for key in dic: + if key not in temp[tbl]: + print(f'unknown key {key} in {file}') + print('Aborting') + print(key) + print(temp) + sys.exit() + return False + return True + + +def find_uniq_constraint(table=None, cursor=None): + """ + Find the columns in specified table with a unique constraint on it + + Parameters + ---------- + + table which table in database to look at + + cursor sqlite3 cursor object to perform the select + + Returns + ------- + + cols returns the columns in table that have a unique constraint + as a list + """ + sql = f"SELECT sql FROM sqlite_master WHERE type='table' AND name='{table}'" + cursor.execute(sql) + schema = cursor.fetchone() + entries = [ tmp.strip() for tmp in schema[0].splitlines() + if tmp.find("UNIQUE")>=0 ] + + assert(len(entries) > 0) + uniqs = entries[0][7:] + first = uniqs.split(')') + cols = first[0].split(', ') + + return cols + + +def condition_checker(columns=None, dic=None): + """ + Parameters + ---------- + + columns Name of SpecDB columns to query on + + dic Data structure to check for consistency with SpecDB database + + Returns + ------- + + col_str column to select on for the specific table requested + + condition string that is condition for the SQLite SELECT statement + """ + + if len(columns) == 1: + col_str = columns[0] + else: + col_str = ', '.join(columns) + + condition = '' + + for i in range(len(columns)): + + condition += f"{columns[i]} == '{dic[columns[i]]}'" + + if i < len(columns)-1: condition += " AND " + + return col_str, condition + + +def read_acqus(path=None): + """ + Read an acquisiton status file to find temperature in the experiment + + Parameters + ---------- + + path file path to acqus file + + Returns + ------- + + temp temperature float value + """ + if not os.path.isfile(path): return None + + temp = 0.0 + probe = '' + pulse = '' + with open(path, 'r') as fp: + for line in fp.readlines(): + line = line.rstrip() + if '##$TE= ' in line: + info = line.split('= ') + temp = info[-1] + temp = float(temp) + + if '##$PULPROG= ' in line: + info = line.split('= ') + pulse = info[-1] + pulse = pulse.replace('<','') + pulse = pulse.replace('>','') + + if '##$PROBHD= ' in line: + info = line.split('= ') + probe = info[-1] + probe = probe.replace(' ','_') + probe = probe.replace('<','') + probe = probe.replace('>','') + + return temp, probe, pulse + + return None + + +def read_audita(path=None): + """ + Read a Bruker `audita.txt` file for when pulse sequence started + + Parameters + ---------- + + path path to `audita.txt` to parse + + Returns + + time string of when pulse sequence started + """ + + if not os.path.isfile(path): return None + + time = '' + with open(path, 'r') as fp: + for line in fp.readlines(): + line = line.rstrip() + if 'started at ' in line: + info = line.split() + time = ' '.join(( + info[2], + info[3])) + return time + + +def insert_fid(files=None, cursor=None, dic=None): + """ + Insert time domain data into database + + Parameters + ---------- + + files list of files in FID directory + + cursor SQLite cursor object to perform database operations + + dic dictionary of information to insert into time_domain_datasets + table + + Returns + ------- + + success True/False if/ifnot insert successful + + str/dic depends on the errors from table_inserter() + """ + + found = {} + for f in files: + if os.path.isfile(f): + name = os.path.basename(f) + + if name in param_files: found[name] = f + + if 'acqus' in found and 'audita.txt' in found: + temp, probe, pulse = read_acqus(path=found['acqus']) + exp_time = read_audita(path=found['audita.txt']) + + dic['temperature_from_data'] = temp + dic['probe_info'] = probe + dic['pulse_sequence'] = pulse + dic['experiment_date'] = exp_time + +# if 'procpar' in found and 'log' in found: +# temp, probe, pulse = read_procpar(path=found['procpar']) +# + fid_dirs = files[0].split('/') + zipped_path = '/'.join(fid_dirs[:-1]) + up_path = '/'.join(fid_dirs[:-2]) + cwd = os.getcwd() + os.chdir(up_path) + + cmd = f"find ./{dic['subdir_name']} -maxdepth 1" + cmd += f" -type f -print0 | xargs -0" + cmd += f" tar -zcvf specdb.tar.gz" + os.system(cmd) + + with open('specdb.tar.gz', 'rb') as fp: fbytes = fp.read() + + dic['zipped_dir'] = fbytes + time_domain = [f for f in os.listdir(zipped_path) + if os.path.isfile(os.path.join(zipped_path, f))] + + time_domain = [f for f in time_domain if f == 'fid' or f == 'ser'] + assert(len(time_domain) == 1) + + with open(os.path.join(zipped_path, time_domain[0]), 'rb') as fp: + fbytes = fp.read() + + readable_hash = hashlib.md5(fbytes).hexdigest() + dic['md5checksum'] = readable_hash + + success, last_row = table_inserter( # go ahead and insert + table='time_domain_dataset', + record=dic, + cursor=cursor) + + os.remove('specdb.tar.gz') + if success is True: return success, dic + else: return success, last_row + + +def insert_constructor(col_names, row): + """ + Construct the SQL insert statement for data to be inserted in a SpecDB + table. + + Parameters + ---------- + + col_names names of columns for the specific table we are inserting + into. these strings are used as keys into the dictionary + `row`. + + row key/value pairs to be inserted into the SQLite table. + + Returns + ------- + + cols table column names to be inserted. + + VALS `,?` placeholder in SQLite Insert statement. + + vals the actual values to be inserted into the table. + """ + cols = '(' + vals = [] + VALS = '(' + + for i, c in enumerate(col_names): + if c == 'id': continue + if c == 'isotopic_labeling': continue + cols += f'{c}' + VALS += '?' + + if type(row[c]) == str: + if len(row[c]) == 0: + vals.append(None) + else: + vals.append(row[c]) + else: + vals.append(row[c]) + + if i+1 < len(col_names): + cols += ', ' + VALS += ', ' + else: + cols += ')' + VALS += ')' + + return cols, VALS, vals + + +def table_inserter(table=None, record=None, cursor=None): + """ + Insert data into SQLite table from SpecDB + + Parameters + ---------- + + table name of table to insert into + + record key/value pairs to be inserted into table + keys are table column names, values are the data to be inserted + for the respective column + + cursor sqlite3 cursor object + + Returns + ------- + int last rowid of row inserted + """ + assert(table is not None) + assert(record is not None) + assert(cursor is not None) + #print('record', record) + cursor.execute(f"select * from {table} limit 1") + table_cols = [i[0] for i in cursor.description] + if table == 'buffer_components': + assert('isotopic_labeling' in table_cols) + table_cols.remove('isotopic_labeling') + #print('table_cols', record.keys()) + columns, vals_place, values = insert_constructor(table_cols, record) + #print('columns', columns) + #print('vals_place', vals_place) + if values == [None] * len(values): return None + sql = f"INSERT INTO {table} {columns} VALUES{vals_place}" + #print(sql) + #print(values) + try: + cursor.execute(sql, values) + return True, cursor.lastrowid + except sqlite3.Error as e: + return False, e.args[0] + + +def table_updater(table=None, record=None, cursor=None): + """ + Update data in a SQLite table from SpecDB + + Parameters + ---------- + + table name of table to update + + record keye/value pairs to be used to update table + + cursor sqlite3 cursor object + + Returns + ------- + int rowid of row that was updated + """ + assert(table is not None) + assert(record is not None) + assert(cursor is not None) + + cursor.execute(f"SELECT * from {table} limit 1") + table_cols = [i[0] for i in cursor.description] + + columns, vals_place, values = insert_constructor(table_cols, record) + if values == [None] * len(values): return None + sql = f"INSERT OR REPLACE INTO {table} {columns} VALUES{vals_place}" + try: + cursor.execute(sql, values) + return True, cursor.lastrowid + except sqlite3.Error as e: + return False, e.args[0] + + +def insert_logic(table=None, dic=None, write=False, cursor=None): + """ + Control logic for insertion into each of the tables + + Parameters + ---------- + + table which table to insert into + + dic which data structure is given, read from JSON file + + write whether to write new/update items in the database + + cursor sqlite3 cursor object + + Returns + ------ + + status True/False + True if insertion was successful + False otherwise + + value The lastrowid of table after successful insert + OR + dictionary of updated record + OR + dictionary of errors to write to LOG file + """ + + # if nothing is filled out for this table/row, abort + all_none = [] + for v in dic.items(): + if type(v) == str: + if len(v) == 0: all_none.append(True) + elif type(v) == int: + if v == 0: all_none.append(True) + elif type(v) == float: + if v == 0.0: all_none.append(True) + + if len(all_none) == len(dic): + msg = f"Table: {table} is completely empty" + msg += "\nAborting" + return False, msg + + # find the columns that serve as unique constraints + uniq_cols = find_uniq_constraint(table=table, cursor=cursor) + + # determine if they are defined in dic + uniq_pres = [True for uc in uniq_cols if len(dic[uc]) > 0] + if len(uniq_pres) == len(uniq_cols): + # if they are defined, check if the remaining columns are empty + # if they are, assume that the user wanted to pull in the info + # for that table entity + # otherwise, insert as normal + + col_names, cond = condition_checker( # build strings for SELECT command + columns=uniq_cols, + dic=dic + ) + + # checking if all but uniq columns are empty + empty = True + for k,v in dic.items(): + if k in uniq_cols: continue + if type(v) == str: + if len(v) > 0: + empty = False + break + elif type(v) == int: + if v != 0: + empty = False + break + elif type(v) == float: + if v != 0.0: + empty = False + break + + if empty: # attempt to fill JSON file with database info + sql = f"SELECT {col_names} FROM {table} WHERE {cond}" + cursor.execute(sql) + results = cursor.fetchall() + if len(results) == 0: # uniq col values don't exist and empty + + status = False + msg = f"nothing to insert on table {table}" + msg += f"\nwhat was given:\n" + msg += f"{json.dumps(dic)}" + msg += "\n" + + return status, msg + + else: # they are in the database and rest are empty + assert(len(results) == 1) + + sql = f"SELECT * FROM {table} WHERE {cond}" + cursor.execute(sql) + results = cursor.fetchall() + assert(len(results) == 1) + + # set the JSON data to what is in db + tmp_results = dict(results[0]) + del tmp_results['id'] + for k,v in tmp_results.items(): + if v is None: tmp_results[k] = "" + + dic = tmp_results + return True, dic + + else: # not empty, user supplied some information, attempt to insert + sql = f"SELECT * FROM {table} WHERE {cond}" + cursor.execute(sql) + results = cursor.fetchall() + + if len(results) == 0: # supplied info not in database + if not write: + msg = "information provided is new\n" + msg += json.dumps(dic, indent='\t') + msg += "\nMust set --write to insert provided information" + msg += " to database\nAborting" + return False, msg + + else: + success, last_row = table_inserter( # go ahead and insert + table=table, + record=dic, + cursor=cursor) + + if type(last_row) is str: + assert(success is False) + + msg = f"SQLite error on insert on table {table}" + msg += "\nErr Message:\n" + msg += f"{last_row}" + msg += "\ncheck the template form for instructions and " + msg += "examples\n" + msg += "ensure all ids this table relates to (i.e " + msg += "constructs relate to targets) are inserter " + msg += "already\n" + msg += "Aborting" + + return success, msg + + return success, last_row + + else: # table unique columns actually in db, make sure they match + assert(len(results) == 1) + tmp_results = dict(results[0]) + del tmp_results['id'] + for k,v in dic.items(): + if type(v) == str: + if len(v) == 0: dic[k] = None + + if tmp_results != dic: + + if not write: + success = False + msg = f"requested data is different than the database" + msg += "\ninput information:\n" + msg += json.dumps(dic, indent='\t') + msg += "\ndatabase information:\n" + msg += json.dumps(tmp_results, indent='\t') + msg += "\nAborting" + + return success, msg + + else: + success, last_row = table_updater( + table=table, + record=dic, + cursor=cursor + ) + + if type(last_row) is str: + assert(success is False) + + msg = f"SQLite error on insert on table {table}" + msg += "\nErr Message:\n" + msg += f"{last_row}" + msg += "\ncheck the template form for examples and " + msg += "instructions\n" + msg += "ensure all ids this table relates to (i.e " + msg += "constructs relate to targets) are inserted " + msg += "already\n" + msg += "Aborting" + + return success, msg + + return success, last_row + + else: return True, results[0]['id'] + else: + + msg = f"unique column ids {uniq_cols} cannot be blank" + msg += "\nmust provide some string for them" + msg += "\nAborting" + + return False, msg + + +def insert(file=None, db=None, write=False): + """ + Add a single YAML file into SpecDB SQLite database. + Could be used for any data item type in database. + + Parameters + ---------- + + file path to YAML file to be inserted + + db path to specdb database file + + write whether to write new SpecDB records into the SpecDB + database, or to update records in database + Expires after each new write + + Returns + ------- + True If insertion successful + False If insertion is unsuccessful + """ + if file is None: + print('no YAML file provided') + print('must provide a YAML file to insert for specdb add') + print('Aborting') + sys.exit() + + if db is None: + print('no specdb database file provided') + print('must provide a .db file for insert to work') + print('Aborting') + sys.exit() + + # connect to database + conn = sqlite3.connect(os.path.abspath(db)) + conn.row_factory = sqlite3.Row + c = conn.cursor() + + # enforce foreign key constraints + sql = "PRAGMA foreign_keys = ON" + c.execute(sql) + + # check yaml file to be inserted that it has the expected keys + if not check_yaml(file=file): + print(f"JSON file {file} does not have expected keys") + print("Aborting") + sys.exit() + + # read json file to be inserted + with open(file, 'rt') as fp: + yaml = ruamel.yaml.YAML() + record = yaml.load(fp) + + # convert record to plain dictionary + record = json.loads(json.dumps(record)) + + # insert data from yaml in the specific table order + for tbl in table_order: + # some information in specd.json is entered as a single dictionary + # others require a list of dictionaries + + # not all tables need to be inserter at the same time + # for example user information can be inserted separately + if tbl not in record: continue + + rec_keys = list(record[tbl].keys()) + + if isinstance(record[tbl][rec_keys[0]], dict): + + for ind, data in record[tbl].items(): + + status, value = insert_logic( + table=tbl, + dic=data, + write=write, + cursor=c + ) + + if status is True: + if type(value) is dict: + record[tbl][ind] = value + conn.commit() + elif type(value) is int: + conn.commit() + continue + else: + print("Unexpected type") + print("Aborting") + return False + + elif status is False: + if value == 0: + return False + + assert(type(value) is not dict) + + print(value) + return False + + else: + print(f"Unexpected value {status}") + print("Aborting") + return False + + else: + + status, value = insert_logic( + table=tbl, + dic=record[tbl], + write=write, + cursor=c + ) + + if status is True: + if type(value) is dict: + conn.commit() + record[tbl] = value + elif type(value) is int: + conn.commit() + continue + else: + print("Unexpected type") + print("Aborting") + return False + + elif status is False: + if value == 0: + print(value) + return False + + assert(type(value) is not dict) + + print(value) + return False + + else: + print(f"Unexpected value {status}") + print("Aborting") + return False + + # now insert sessions if present + if 'session' in record: + + file_path = os.path.abspath(file) + dirs = file_path.split('/') + session_folder = dirs[-2] + #print(session_folder) + session_path = '/'.join(dirs[:-1]) + + rec_keys = list(record['session'].keys()) + + if isinstance(record['session'][rec_keys[0]], dict): + record['session']['0']['folder_name'] = session_folder + session_dic = record['session']['0'] + + else: + record['session']['folder_name'] = session_folder + session_dic = record['session'] + + status, value = insert_logic( + table='session', + dic=session_dic, + cursor=c, + write=write + ) + + if status is True: + if type(value) is dict: + record['session']['0'] = value + conn.commit() + + elif type(value) is int: + conn.commit() + + else: + print("Unexpected type") + print("Aborting") + return False + + elif status is False: + if value == 0: return False + + assert(type(value) is not dict) + + print(value) + return False + + else: + print(f"Unexpected value {status}") + print("Aborting") + return False + + session_id = value + if 'time_domain_dataset' not in record: + + record['time_domain_data'] = dict() + for sub in os.listdir(session_path): + + if os.path.isdir(os.path.join(session_path, sub)): + + subpath = os.path.join(session_path, sub) + if 'fid' in os.listdir(subpath) or 'ser' in os.listdir(subpath): + + new_fid = { + 'subdir_name': sub, + 'pulse_sequence_nickname': None, + 'probe_id': None, + 'session_id': session_id, + 'zipped_dir': None, + 'md5checksum': None, + 'temperature_from_data': None, + 'experiment_date': None, + 'pulse_sequence': None, + 'probe_info': None, + 'pst_id': session_dic['pst_id'] + } + + files = [ + os.path.join(subpath, f) for f in os.listdir( + subpath) + ] + + status, value = insert_fid( + files=files, + dic=new_fid, + cursor=c) + + if status is True: + assert(type(value) is dict) + del value['zipped_dir'] + record['time_domain_data'][ + value['subdir_name']] = value + conn.commit() + #print(status, sub) + + elif status is False: + print("Err message") + print(value) + print("moving to next fid") + continue + + else: + print("Unexpected type") + print("Aborting") + return False + else: + rec_keys = list(record['time_domain_dataset'].keys()) + if isinstance(record['time_domain_dataset'][rec_keys[0]], dict): + for ind, data in record['time_domain_dataset'].items(): + new_fid = { + 'subdir_name': None, + 'pulse_sequence_nickname': None, + 'probe_id': None, + 'session_id': session_id, + 'zipped_dir': None, + 'md5checksum': None, + 'temperature_from_data': None, + 'experiment_date': None, + 'pulse_sequence': None, + 'probe_info': None, + 'pst_id': session_dic['pst_id'] + } + + for k, v in data.items(): new_fid[k] = v + + files = [ + os.path.join( + session_path, + new_fid['subdir_name'], + f) for f in os.listdir( + os.path.join( + session_path, + new_fid['subdir_name']))] + + status, value = insert_fid( + files=files, + dic=new_fid, + cursor=c) + + if status is True: + assert(type(value) is dict) + del value['zipped_dir'] + record['time_domain_data'][ind] = value + conn.commit() + + elif status is False: + print("Err message") + print(value) + print("moving to next fid") + continue + + else: + print("Unexpected type") + print("Aborting") + return False + + conn.commit() + conn.close() + print(f"Inserted data from form file at {file}") + + with open(file, 'w') as fp: + yaml = ruamel.yaml.YAML() + yaml.dump(record, fp) + + else: + + conn.commit() + conn.close() + print(f"Inserted data from json file at {file}") + + with open(file, 'w') as fp: + yaml = ruamel.yaml.YAML() + yaml.dump(record, fp) + + return True + + +def summary(db=None, table=None): + """ + Display contents of a SpecDB table + + Parameters + ---------- + + db path to a specdb database file + + table str, name of table to display contents of + + Returns + ------- + print to stdout dataframe of SpecDB table contents, order alphabetically + """ + if db is None: + print("Must provide a database file") + print("Aborting") + sys.exit() + + if table is None: + print("Must provide a table to summarize") + print("Aborting") + sys.exit() + + pd.set_option('display.max_columns', None) + pd.set_option('max_colwidth', 20) + pd.set_option('display.max_rows', None) + pd.set_option('display.width', 110) + pd.set_option('max_rows', None) + + # connect to database + conn = sqlite3.connect(os.path.abspath(db)) + conn.row_factory = sqlite3.Row + c = conn.cursor() + + # collect the columns that define unique constraint for the table + if table == 'summary': + sql = f"SELECT * FROM {table}" + else: + uniq_cols = find_uniq_constraint(table=table, cursor=c) + + # perform sql select * query from provided table + if len(uniq_cols) == 1: + sql = f"SELECT * FROM {table} ORDER BY {uniq_cols[0]} ASC" + elif len(uniq_cols) == 2: + sql = f"SELECT * FROM {table} ORDER BY {uniq_cols[0]} ASC," + sql += f" {uniq_cols[1]} ASC" + else: + sql = f"SELECT * from {table}" + + df = pd.read_sql(sql, conn) + blankindex = [''] * len(df) + df.index = blankindex + df = df.rename(columns=lambda x: x[:14]) + + print() + print(df) + print() + + return + + +def flatten_query(sql, col, table, cursor): + #print(sql) + cursor.execute(sql) + results = cursor.fetchall() + flat = dict() + + for rr in results: + for k in rr.keys(): + if k == 'id': continue + if k == col: continue + if (table, k) not in flat: flat[(table, k)] = list() + flat[(table, k)].append(rr[k]) + + + return flat + + +def query_dbview(view, curr_view, table, fkeys, cursor): + #all_fkeys[ctable][child] = {'parent':parent, 'ptable':ptable} + for k, v in curr_view.items(): + #print(k,v) + #continue + if table in fkeys: + if k[1] in fkeys[table]: + view[k] = v + parent_key = fkeys[table][k[1]]['parent'] + parent_table = fkeys[table][k[1]]['ptable'] + assert(type(v) == list and len(v) == 1) + sql = f"select * from {parent_table} where {parent_key} = '{v[0]}' order by id ASC" + #print(sql) + fq = flatten_query(sql, '', parent_table, cursor) + for k1 in fq: + if k1 not in view: view[k1] = fq[k1] + view = query_dbview(view, fq, parent_table, fkeys, cursor) + del fkeys[table][k[1]] + else: + view[k] = v + else: + view[k] = v + return view + + +def star_loop_constructor(tags, view, cat): + + if cat not in view: return {} + + loop_data = dict() + + maxlen = -1 + for t in view[cat]: + if len(view[cat][t]) > maxlen: + maxlen = len(view[cat][t]) + + for col in view[cat]: + if len(view[cat][col]) < maxlen: + view[cat][col] += ['.'] * (len(view[cat][col]) - maxlen) + + loop_data = {t:view[cat][t] for t in tags if t in view[cat]} + + for k in loop_data: + for i, val in enumerate(loop_data[k]): + if type(val) != str: continue + if '<' in val: + print(val.replace('<','')) + loop_data[k][i] = val.replace('<','') + if '>' in val: + loop_data[k][i] = val.replace('>','') + + #print(json.dumps(loop_data,indent=2)) + return loop_data + + +def fid2star(data=None, cursor=None, save=None): + """ + Take FID information from SpecDB into STAR + + Parameters + ---------- + + data SQLite row object from SpecDB summary query + + cursor SQLite cursor object to perform queries + + save path to save resulting STAR file + + Returns + ------- + True if STAR creation successful + """ + + sql = "SELECT m.name, p.* FROM sqlite_master m JOIN" + sql += " pragma_foreign_key_list(m.name) p ON m.name != p.'table' WHERE" + sql += " m.type = 'table' ORDER BY m.name" + cursor.execute(sql) + all_fks = cursor.fetchall() + + all_fkeys = dict() + for fk in all_fks: + #print(dict(fk)) + child = fk[4] + parent = fk[5] + ptable = fk[3] + ctable = fk[0] + + if ctable not in all_fkeys: + all_fkeys[ctable] = dict() + + if child not in all_fkeys[ctable]: + all_fkeys[ctable][child] = {'parent':parent, 'ptable':ptable} + + #print(json.dumps(all_fkeys, indent=2)) + #sys.exit() + + # gather conversion table + cursor.execute("SELECT * from star_conversion") + mappings = cursor.fetchall() + + translator = dict() + for k in mappings: + table = k[2] + col = k[1] + tag = k[3] + frame = k[4] + + if table not in translator: translator[table] = dict() + if col not in translator[table]: translator[table][col] = dict() + if frame not in translator[table][col]: translator[table][col][frame] = [] + translator[table][col][frame].append(tag) + + #print(json.dumps(translator,indent=2)) + sql = f"SELECT * FROM time_domain_dataset where id == '{data['id']}'" + cursor.execute(sql) + results = cursor.fetchall() + + #print(dict(results[0])) + + view = dict() + flat = flatten_query(sql, '', 'time_domain_dataset', cursor) + dbview = query_dbview(view, flat, 'time_domain_dataset', all_fkeys, cursor) + + #print(list(dbview.keys())) + #print(len(list(dbview.keys()))) + + #print(dbview[('time_domain_dataset','pst_id')]) + sql = f"SELECT * FROM batch_components WHERE pst_id == '{dbview[('time_domain_dataset','pst_id')][0]}'" + flat = flatten_query(sql, '', 'batch_components', cursor) + moreview = query_dbview(dbview, flat, 'batch_components', all_fkeys, cursor) + + #print(json.dumps(list(moreview.keys()),indent=2)) + #print(len(list(moreview.keys()))) + + sql = f"SELECT * from buffer_components WHERE buffer_id == '{dbview[('pst','buffer_id')][0]}'" + flat = flatten_query(sql, 'buffer_id', 'buffer_components', cursor) + fullview = query_dbview(moreview, flat, 'buffer_components', all_fkeys, cursor) + + #print(json.dumps(list(fullview.keys()),indent=2)) + #print(len(list(fullview.keys()))) + + specdb_path = os.path.abspath(os.path.dirname(__file__)) + star_path = os.path.join(specdb_path, '../sql/template.str') + + # Fill up the STAR file + # Load the template + with open(star_path, 'r') as fp: + entry = pynmrstar.Entry.from_file(fp) + + entry.entry_id = 'SpecDBQuery' + # Obtain schema version + schema = utils.get_schema() + fullview['nmr_star_version'] = schema.version + + # Fill in timedomain specific tags not given in schema + fullview['title'] = fullview[('project', 'project_id')][0] + fullview['data_file_content_type'] = 'timedomain_data' + + """ + _Experiment_file.Name + _Experiment_file.Directory_path + _Upload_data.Data_file_name + _Upload_data.Data_file_content_type + + """ + #print(save) + save_split = save.split('/') + save_path = '/'.join(save_split[:-1]) + if 'fid' in os.listdir(save_path): + tdname = 'fid' + elif 'ser' in os.listdir(save_path): + tdname = 'ser' + + file_dir_path = '/'.join(save_split[-3:-1])+'/'+tdname + #sys.exit() + + #print(json.dumps(translator, indent=2)) + + specdb = dict() + for k in fullview.keys(): + #print(k) + if k[0] in translator: + if k[1] in translator[k[0]]: + for frame in translator[k[0]][k[1]]: + if frame not in specdb: specdb[frame] = dict() + for tag in translator[k[0]][k[1]][frame]: + if tag not in specdb[frame]: specdb[frame][tag] = list() + specdb[frame][tag].extend(fullview[k]) + + specdb['nmr_star_version'] = schema.version + specdb['title'] = fullview[('project', 'project_id')][0] + specdb['experiment_list']['_Experiment_file.Name'] = [tdname] + specdb['experiment_list']['_Experiment_file.Type'] = ['free-induction decay'] + specdb['experiment_list']['_Experiment_file.Directory_path'] = [file_dir_path] + + #print(json.dumps(specdb, indent=2)) + #sys.exit() + for frame in entry: + #print(frame.tag_prefix) + #print(frame._category) + cat = frame._category + #print(cat) + #if cat not in specdb: continue + + #continue + for ftags in frame.tag_dict.keys(): + + tt = ftags.capitalize() + #print(ftags) + #print(frame.tag_prefix+'.'+ftags) + #print(frame[frame.tag_prefix+'.'+ftags]) + + full_tag = frame.tag_prefix+'.'+tt + + if ftags in specdb: + frame[ftags] = specdb[ftags][0] + #print(full_tag) + if cat in specdb: + #print(cat) + if full_tag in specdb[cat]: + #print(cat, full_tag) + frame[ftags] = specdb[cat][full_tag][0] + + if len(list(frame.loop_iterator())) > 0: + for loop in frame.loop_iterator(): + tags = loop.get_tag_names() + + if '_Upload_data.Data_file_name' in tags: + data_to_add = { + '_Upload_data.Data_file_name':[tdname], + '_Upload_data.Data_file_content_type':['free-induction decay'] + } + loop.add_data(data_to_add) + continue + + data_to_add = star_loop_constructor(tags, specdb, cat) + + if not data_to_add: continue + else: + #print(tags) + loop.add_data(data_to_add) + #print(loop) + + + + + entry.add_missing_tags() + #entry.normalize() + entry.write_to_file(save) + print("done") + + #print(entry.validate()) + + return + + +def query(db=None, sql=None, star=False, output_dir=None): + """ + Perform a query against summary view of database + Format the query results either in a directory hierarchy or in NMR-STAR + for each retrieved FID + + Parameters + ---------- + + db path to a specdb database file + + sql user provided SQL select statement, must be on summary + + star whether to output a STAR file for each FID in the query + + output_dir where to put the results + + Returns + ------- + Directory structure of results with NMR-STAR at the end for each FID + """ + + if db is None: + print("Must provide a database file") + print("Aborting") + sys.exit() + + if sql is None: + print("Must provide a SQL SELECT statement to execute") + print("Aborting") + sys.exit() + + if output_dir is None: + print("Must provide an output directory to place query results") + print("Aborting") + sys.exit() + + if not re.search(r'^SELECT', sql): + print(f"provided SQL does not look like a SELECT statement") + print(f"provided SQL: {sql}") + print("Aborting") + sys.exit() + + if not re.search(r' summary ', sql): + print("provided SQL does not appear to SELECT on summary") + print(f" provided SQL: {sql}") + print("Aborting") + sys.exit() + + # connect to database + conn = sqlite3.connect(db) + conn.row_factory = sqlite3.Row + c = conn.cursor() + + # execute query + c.execute(sql) + + results = c.fetchall() + results = [dict(res) for res in results] + + if not os.path.isdir(os.path.abspath(output_dir)): + os.mkdir(os.path.abspath(output_dir)) + + output_dir = os.path.abspath(output_dir) + + for res in results: + date_info = res['experiment_date'].split() + date = date_info[0].split('-') + date = ''.join(date) + ids = [res['pst_preparer'], res['pst_id'], date] + + dir_name = '_'.join(ids) + + if not os.path.isdir(os.path.join(output_dir, dir_name)): + os.mkdir(os.path.join(output_dir, dir_name)) + + f = io.BytesIO() + tar_file = tarfile.open(fileobj=f, mode='w:') + tar_info = tarfile.TarInfo('data_zipped') + tar_info.size = len(res['zipped_dir']) + tar_info.mtime = time.time() + tar_file.addfile(tar_info, io.BytesIO(res['zipped_dir'])) + tar_file.close() + os.chdir(os.path.join(output_dir, dir_name)) + + with open('stream.tar.gz', 'wb') as fp: + fp.write(f.getvalue()) + + os.system("tar -xf stream.tar.gz") + os.system("tar -xf data_zipped") + + os.remove("stream.tar.gz") + os.remove("data_zipped") + print(os.getcwd()) + + sql = f"SELECT subdir_name FROM time_domain_dataset WHERE" + sql += f" id='{res['id']}'" + + c.execute(sql) + subname = c.fetchall()[0] + #print(subname['subdir_name']) + if star: + star_path = os.path.join( + output_dir, dir_name, subname['subdir_name'], 'fid.star') + #print(output_dir) + #print(dir_name) + #print(star_path) + #print(os.getcwd()) + #sys.exit() + out = fid2star( + data=res, + cursor=c, + save=star_path + ) + + +def backup(): + pass + + +def restore(): + pass + diff --git a/sql/specdb.sql b/sql/specdb.sql new file mode 100644 index 0000000..470c442 --- /dev/null +++ b/sql/specdb.sql @@ -0,0 +1,363 @@ +PRAGMA foreign_keys = ON; + +CREATE TABLE user ( -- provide information about a user, REQUIRED: `user_id` + id INTEGER PRIMARY KEY NOT NULL, + user_id TEXT CHECK( user_id NOT LIKE '% %' and length(user_id) <= 8 ) NOT NULL, -- no spaces, must be unique, len <= 8, Ex: KJF + given_name TEXT CHECK( length(given_name) <= 64 ), -- len <= 64, Ex: Keith + family_name TEXT CHECK( length(family_name) <= 64 ), -- len <= 64, Ex: Fraga + middle_initials TEXT CHECK( length(middle_initials) <= 16 ), -- len <= 16, Ex: J + department_and_institution TEXT CHECK( length(department_and_institution) <= 128 ), -- len <= 128, Ex: MCB UCD + country TEXT CHECK( length(country) <= 32 ), -- len <= 32, Ex: USA + state_province TEXT CHECK( length(state_province) <= 32 ), -- len <= 32, Ex: NY + city TEXT CHECK( length(city) <= 32 ), -- len <= 32, Ex: Troy + postal_code TEXT CHECK( length(postal_code) <= 32 ), -- len <= 32, Ex: 12180 + role TEXT CHECK( length(role) <= 64 ), -- len <= 64, Ex: postdoc + organization_type TEXT CHECK( length(organization_type) <= 64 ), -- len <= 64, Ex: academic + email_address TEXT CHECK( email_address NOT LIKE '% %' and email_address LIKE '%@%' and length(email_address) <= 64 ), -- no spaces, must have `@`, len <= 64, Ex: user@mail.com + UNIQUE(user_id) +); + +CREATE TABLE project ( -- provide information describing a project, REQUIRED: `project_id` + id INTEGER PRIMARY KEY NOT NULL, + structural_genomics TEXT CHECK( structural_genomics IN ('yes', 'no') ), -- not required, only yes or no + project_id TEXT CHECK( project_id NOT LIKE '% %' and length(project_id) <= 32 ) NOT NULL, -- required, must be unique, no spaces, len <= 32, Ex: SpikeFraga + project_details TEXT CHECK( length(project_details) <= 128 ), -- not required, short description, len <= 128, Ex: Spike protein project 2022 + UNIQUE(project_id) +); + +CREATE TABLE target ( -- molecular target information, REQUIRED: `target_id` + id INTEGER PRIMARY KEY NOT NULL, + target_id TEXT CHECK( target_id NOT LIKE '% %' and length(target_id) <= 32 ) NOT NULL, -- text identifier for target, must be unique, no spaces, len <= 32, Ex: Db0515 + target_comment TEXT CHECK( length(target_comment) <= 128 ), -- free field comment, anything to note about target, len <= 128, Ex: from UW-Madison + target_sequence TEXT CHECK( target_sequence NOT LIKE '% %' and length(target_sequence) <= 1024 ), -- target's molecular seq., any type of code/alphabet, no spaces, len <= 1024, Ex: MGSHHHHILVAM + organism_source TEXT CHECK( length(organism_source) <= 128 ), -- organism name for target source, can indicate if target is synthetic, len <= 128, Ex: synthetic + gene_name TEXT CHECK( length(gene_name) <= 64 ), -- gene name, len <= 64, Ex: SpikeCoV2 + project_id TEXT NOT NULL, -- `project_id` target is a member of, must be in project table, Ex: SpikeFraga + target_preparer TEXT , -- `user_id` that assigned the target, must be in user table, Ex: KJF + UNIQUE(target_id), + FOREIGN KEY ([project_id]) REFERENCES "project" ([project_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([target_preparer]) REFERENCES "user" ([user_id]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE TABLE construct ( -- molecular construct from a target, REQUIRED: `construct_id`, `construct_sequence`, `target_id` + id INTEGER PRIMARY KEY NOT NULL, + construct_id TEXT CHECK( construct_id NOT LIKE '% %' and length(construct_id) <= 32 ) NOT NULL, -- text identifier for construct, must be unique, no spaces, len <= 32, Ex: Db0515A + construct_sequence TEXT CHECK( construct_sequence NOT LIKE '% %' and length(construct_sequence) <= 1024 ) NOT NULL, -- construct sequence, any type of code/alphabet, no spaces, len <= 1024, Ex: MGSHHHINLVAE + target_id TEXT NOT NULL, -- `target id` this construct was made for, must already be in target table, Ex: Db0515 + ext_coefficient_280 FLOAT , -- extinction coefficient at 280 nm, Ex: 108.7 + expected_mw FLOAT , -- expected molecular weight of construct in Da, Ex: 1211.8 + construct_comment TEXT CHECK( length(construct_comment) <= 128 ), -- free field comment, anything to note about construct, len <= 128, Ex: with primers RE1A/RE1B + plasmid_id TEXT CHECK( length(plasmid_id) <= 64 ), -- plasmid construct DNA sequence is cloned in, len <= 64, Ex: pET218(+) + plasmid_id_comment TEXT CHECK( length(plasmid_id_comment) <= 128 ), -- comments on plasmid, len <= 256, Ex: from Underwood lab + construct_preparer TEXT , -- `user_id` who prepared the construct, must already be in user table, Ex: KJF + construct_company TEXT CHECK( length(construct_company) <= 128 ), -- if the construct was produced by a company, indicate where it came from, len <= 128, Ex: Genscript + UNIQUE(construct_id), + FOREIGN KEY ([target_id]) REFERENCES "target" ([target_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([construct_preparer]) REFERENCES "user" ([user_id]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE TABLE expression ( -- describe a molecular expression experiment/results, REQUIRED: `expression_id`, `construct_id` + id INTEGER PRIMARY KEY NOT NULL, + expression_id TEXT CHECK( expression_id NOT LIKE '% %' and length(expression_id) <= 32 ) NOT NULL, -- text identifier for expression, must be unique, no spaces, len <= 32, Ex: Db0515A.X + expression_comment TEXT CHECK( length(expression_comment) <= 128 ), -- free field comment, anything of note for expression, len <= 128, Ex: reached 4.5 OD + construct_id TEXT , -- `construct_id` this expression was for, must already be in construct table, Ex: Db0515A + expression_media TEXT CHECK( length(expression_media) <= 32 ), -- growth media expression was in, len <= 32, Ex: MJ9 + strain TEXT CHECK( length(strain) <= 32 ), -- cellular strain expression was in, len <= 32, Ex: BL21A (+) + expression_organism TEXT CHECK( length(expression_organism) <= 32 ), -- organism expression was in, len <- 32, Ex: E. colli + expression_preparer TEXT , -- `user_id` of person who did the expression, must already be in user table, Ex: KJF + UNIQUE(expression_id), + FOREIGN KEY ([construct_id]) REFERENCES "construct" ([construct_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([expression_preparer]) REFERENCES "user" ([user_id]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE TABLE purification_batch ( -- describe the purification run for an expression product, REQUIRED: `batch_id`, `expression_id`, `sample_sequence` + id INTEGER PRIMARY KEY NOT NULL, + batch_id TEXT CHECK( batch_id NOT LIKE '% %' and length(batch_id) <= 32 ) NOT NULL, -- text identifier for batch, must be unique, no spaces, len <= 32, Ex: Db0515.X.batch + expression_id TEXT , -- expression run this purification batch is for, must already be in expression table Ex: Db0515.X + sample_sequence TEXT CHECK( sample_sequence NOT LIKE '% %' and length(sample_sequence) <= 1024 ) NOT NULL, -- sequence of molecule after purification (i.e if there was tag cleaving), any type of code/alphabet, no spaces, len <= 1024, Ex: MQNGPILA + purif_comment TEXT CHECK( length(purif_comment) <= 128 ), -- free text comment about the purification, len <= 128, Ex: HPLC in RM 204 + production_method TEXT CHECK( length(production_method) <= 64 ), -- indicate the purification method, len <= 64, Ex: Ni column only + isotopic_labeling_remark TEXT CHECK( length(isotopic_labeling_remark) <= 64 ), -- provide the isotopic labeling, preferred method to indicate labeling in the appropriate column below, len <= 64, Ex: NC5 + iso_13c_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_13c_enrichment LIKE '%.% 13C%' ESCAPE '.' ), -- 13C labeling percentage, must contain `% 13C`, len <= 32, Ex: 100% 13C + iso_15n_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_15n_enrichment LIKE '%.% 15N%' ESCAPE '.' ), -- 15N labeling percentage, must contain `% 15N`, len <= 32, Ex: 99% 15N + iso_2h_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_2h_enrichment LIKE '%.% 2H%' ESCAPE '.' ), -- 2H labeling percentage, must contain `% 2H`, len <= 32, Ex: 100% 2H + iso_19f_Trp_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_19f_Trp_enrichment LIKE '%.% 19F-Trp%' ESCAPE '.' ), -- 19F-Trp labeling percentage, must contain `% 19F-Trp`, len <= 32, Ex: 11% 19F-Trp + iso_19f_Phe_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_19f_Phe_enrichment LIKE '%.% 19F-Phe%' ESCAPE '.' ), -- 19F-Phe labeling percentage, must contain `% 19F-Phe`, len <= 32, Ex: 9.1% 19F-Phe + iso_1hd1_Leu_methyl_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_1hd1_Leu_methyl_enrichment LIKE '%.% 1HD1-Leu%' ESCAPE '.' ), -- 1HD1-Leu stereospecific labeling percentage, must contain `% 1HD1-Leu`, len <= 32, Ex: 13.3% 1HD1-Leu + iso_1hd2_Leu_methyl_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_1hd2_Leu_methyl_enrichment LIKE '%.% 1HD2-Leu%' ESCAPE '.' ), -- 1HD2-Leu stereospecific labeling percentage, must contain `% 1HD2-Leu`, len <= 32, Ex: 15% 1HD2-Leu + iso_1hd_Ile_methyl_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_1hd_Ile_methyl_enrichment LIKE '%.% 1HD-Ile%' ESCAPE '.' ), -- 1HD-Ile labeling percentage, must contain `% 1HD-Ile`, len <= 32, Ex: 50% 1HD-Ile + iso_1hg1_Val_methyl_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_1hg1_Val_methyl_enrichment LIKE '%.% 1HG1-Val%' ESCAPE '.' ), -- 1HG1-Val stererospecific labeling percentage, must contain `% 1HG1-Val`, len <= 32, Ex: 25% 1HG1-Val + iso_1hg2_Val_methyl_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_1hg2_Val_methyl_enrichment LIKE '%.% 1HG2-Val%' ESCAPE '.' ), -- 1HG2-Val stereospecific labeling percentage, must contain `% 1HG2-Val`, len <= 32, Ex: 27%% 1HG2-Val + iso_1hb_Ala_methyl_enrichment TEXT CHECK( length(iso_13c_enrichment) <= 32 and iso_1hb_Ala_methyl_enrichment LIKE '%.% 1HB-Ala%' ESCAPE '.' ), -- 1HB-Ala labeling percentage, must contain `% 1HB-Ala`, len <= 32, Ex: 100% 1HB-Ala + batch_preparer TEXT , -- `user_id` of person who did the purification, must already be in user table, Ex: KJF + UNIQUE(batch_id), + FOREIGN KEY ([expression_id]) REFERENCES "expression" ([expression_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([batch_preparer]) REFERENCES "user" ([user_id]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE TABLE buffer ( -- store all buffers used, their id and their pH, REQUIRED: `buffer_id`, `buffer_pH`, NOTE: the buffer components go in the `buffer_components` table + id INTEGER PRIMARY KEY NOT NULL, + buffer_id TEXT CHECK( buffer_id NOT LIKE '% %' and length(buffer_id) <= 32 ) NOT NULL, -- text identifier for the buffer, must be unique, no spaces, len <= 32, Ex: hn4071 + buffer_ph FLOAT NOT NULL, -- pH of buffer, must be a number, Ex: 8.1 + buffer_comment TEXT CHECK( length(buffer_comment) <= 128 ), -- free text field for any notes about the buffer, len <= 128, Ex: made by KJF 12/04 + UNIQUE(buffer_id) +); + +CREATE TABLE buffer_components ( -- describe the component(s) of a buffer, REQUIRED: `buffer_id`, `buffer_component`, `buffer_component_value`, `buffer_component_unit` + id INTEGER PRIMARY KEY NOT NULL, + buffer_id TEXT NOT NULL, -- `buffer_id` this component goes to, must already be in buffer table, Ex: hn4071 + buffer_component TEXT CHECK( length(buffer_component) <= 64 ) NOT NULL, -- name of the component, len <= 64, Ex: NaCl + buffer_component_value FLOAT NOT NULL, -- the numeric concentration value of the component, Ex: 100.0 + buffer_component_unit TEXT CHECK( buffer_component_unit in ('mM', '% (v/v)', 'mg/mL') ) NOT NULL, -- unit of concentration, one of (`mM`, `% (v/v)`, `mg/mL`), Ex: mM + isotopic_labeling TEXT DEFAULT "natural abundance", + UNIQUE(buffer_id, buffer_component), + FOREIGN KEY ([buffer_id]) REFERENCES "buffer" ([buffer_id]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE TABLE tubes ( + id INTEGER PRIMARY KEY NOT NULL, + tube_type TEXT NOT NULL, + UNIQUE(tube_type) +); + +INSERT INTO tubes (tube_type) +VALUES + ("0.5 mL Eppendorf"), + ("1.7 mL Eppendorf"), + ("15 mL cent. tube"), + ("50 mL cent. tube"), + ("1 L cent. tube"), + ("8-well PCR strip"), + ("NMR tube"), + ("plate well"), + ("1-mm NMR tube"), + ("1.7-mm NMR tube"), + ("3-mm NMR tube"), + ("3-mm Shigemi tube"), + ("4-mm NMR tube"), + ("4-mm Shigemi tube"), + ("5-mm NMR tube"), + ("5-mm Shigemi tube"), + ("8-mm NMR tube"), + ("8-mm Shigemi tube"), + ("10-mm NMR tube"), + ("10-mm Shigemi tube"); + +CREATE TABLE pst ( -- description of a protein sample tube, not only proteins, REQUIRED: `pst_id`, `pst_preparer`, `sample_ph`, `total_volume`, `volume_unit`, `tube_type` + id INTEGER PRIMARY KEY NOT NULL, + pst_id TEXT CHECK( pst_id NOT LIKE '% %' and length(pst_id) <= 32 ) NOT NULL, -- text identifier for the pst, must be unique, no spaces, len <= 32, Ex: Db0515A.001 + prev_pst_id TEXT , -- if pst derived from another pst, give previous `pst_id`, must already be in pst table, Ex: Db0515A.000 + pst_preparer TEXT NOT NULL, -- `user_id` of user that prepared the sample tube, must be in user table, Ex: KJF + pst_comment TEXT CHECK( length(pst_comment) <= 128 ), -- free field comment about pst, len <= 128, Ex: new sample + sample_type TEXT CHECK( sample_type IN ('solution', 'solid state') ), -- is sample a solution or solid-state sample, one of (`solution`, `solid state`), Ex: solution + solvent_system TEXT CHECK( length(solvent_system) <= 64 ), -- solvent system for the sample, len <= 64, Ex: DMSO + sample_ph FLOAT , -- pst pH, can be different from buffer ph, Ex: 7.1 + total_volume FLOAT NOT NULL, -- numeric volume for total volume in tube, Ex: 2.2 + volume_unit TEXT CHECK( volume_unit IN ('nL', 'uL', 'mL', 'L') ) NOT NULL, -- unit of volume for volume in tube, one of (`nL`, `uL`, `mL`, `L`), Ex: mL + curr_location TEXT CHECK( length(curr_location) <= 64 ), -- current location of tube, len <= 64, Ex: NMR room + prev_location TEXT CHECK( length(prev_location) <= 64 ), -- previous location of tube, len <= 64, Ex: Underwood lab + create_date TEXT CHECK( create_date LIKE '____-__-__' ), -- date record added to database, format "YYYY-MM-DD", Ex: 2022-01-01 + buffer_id TEXT , -- id of buffer in the tube, must already be in `buffer` table, no spaces, len <= 32, Ex: hn4071 + tube_type TEXT NOT NULL, -- the tube type for sample tube, use `specdb summary --table tubes` to find allowable tube types, Ex: 1-mm Shigemi tube + UNIQUE(pst_id), + FOREIGN KEY ([pst_preparer]) REFERENCES "user" ([user_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([prev_pst_id]) REFERENCES "pst" ([pst_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([buffer_id]) REFERENCES "buffer" ([buffer_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([tube_type]) REFERENCES "tubes" ([tube_type]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE TABLE batch_components ( -- describe the purification batches in a pst, REQUIRED: `pst_id`, `batch_id`, `volume`, `volume_unit`, `conc`, `conc_unit` + id INTEGER PRIMARY KEY NOT NULL, + pst_id TEXT NOT NULL, -- text id of sample tube being described, must already be in pst table, Ex: Db0515A.001 + batch_id TEXT NOT NULL, -- text id of batch in the `pst_id` above, must already be in purification_batch table, Ex: Db0515A.X.batch + conc FLOAT NOT NULL, -- concentration of sample in the sample tube, numeric, Ex: 10.2 + conc_unit TEXT CHECK( conc_unit IN ('ug/mL', 'mg/mL', 'nM', 'uM', 'mM') ) NOT NULL, -- concentration units, one of (`ug/mL`, `mg/mL`, `nM`, `uM`, `mM`), Ex: mM + mass FLOAT , -- mg of protein sample in tube, Ex: 101.1 + UNIQUE(pst_id, batch_id) + FOREIGN KEY ([pst_id]) REFERENCES "pst" ([pst_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([batch_id]) REFERENCES "purification_batch" ([batch_id]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE TABLE spectrometer ( -- spectrometer information, REQUIRED: `spectrometer_id`, `manufacturer``, `field_strength` + id INTEGER PRIMARY KEY NOT NULL, + spectrometer_id TEXT CHECK( spectrometer_id NOT LIKE '% %' and length(spectrometer_id) <= 32 ) NOT NULL, -- text identifier for spectrometer, must be unique, no spaces, len <= 32, EX: HU800 + manufacturer TEXT CHECK( manufacturer IN ('Bruker', 'Varian') ), -- spectrometer manufacturer, one of 'Bruker' or 'Varian' + model TEXT CHECK( length(model) <= 32 ), -- spectrometer model, len <= 32, Ex: Bruker + serial_number TEXT CHECK( length(serial_number) <= 64 ), -- spectrometer serial number, len <= 64, Ex: 16Z001 + field_strength TEXT CHECK( field_strength LIKE '%Hz' and length(field_strength) <= 16 ) NOT NULL, -- spectrometer field strength, text must end in `Hz`, len <=16, Ex: 800 MHz + spectrometer_comment TEXT CHECK( length(spectrometer_comment) <= 128 ), -- free field comment about the spectrometer, len <= 128, Ex: located in Briggs + UNIQUE(spectrometer_id) +); + +CREATE TABLE probe ( -- describe the NMR probe, REQUIRED: `probe_id` + id INTEGER PRIMARY KEY NOT NULL, + probe_id TEXT CHECK( probe_id NOT LIKE '% %' and length(probe_id) <= 32 ) NOT NULL, -- text identifier for probe, no spaces, len <= 32, must be unique, Ex: probe_bruker_12 + model TEXT CHECK( length(model) <= 64 ), -- probe model, len <= 64 + manufacturer TEXT CHECK( length(manufacturer) <= 64 ), -- probe manufacturer, len <= 64 + serial_number TEXT CHECK( length(serial_number) <= 64 ), -- probe serial number, len <= 64 + diameter TEXT CHECK( length(diameter) <= 8 ), -- diameter of probe, len <= 8 + rotor_length TEXT CHECK( length(rotor_length) <= 8 ), -- rotor length, len <= 8 + rotor_composition TEXT CHECK( length(rotor_composition) <= 64 ), -- len <= 64 + internal_vol TEXT CHECK( length(internal_vol) <= 16 ), -- len <= 16 + spacer_present TEXT CHECK( length(spacer_present) <= 8 ), -- len <= 8 + UNIQUE(probe_id) +); + +CREATE TABLE session ( -- describe a data collection session, REQUIRED: `session_preparer`, `spectrometer_id`, `pst_id` + id INTEGER PRIMARY KEY NOT NULL, + folder_name TEXT , + session_preparer TEXT NOT NULL, -- `user_id` of the person who prepared and collected the session, must already be in user table, Ex: KJF + spectrometer_id TEXT NOT NULL, -- `spectrometer_id` session was collected at, must already be in spectrometer table, Ex: Hu800 + pst_id TEXT NOT NULL, -- `pst_id` the session is for + UNIQUE(folder_name, session_preparer, spectrometer_id), + FOREIGN KEY ([session_preparer]) REFERENCES "user" ([user_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([spectrometer_id]) REFERENCES "spectrometer" ([spectrometer_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([pst_id]) REFERENCES "pst" ([pst_id]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE TABLE time_domain_dataset ( -- record information about a time domain dataset, REQUIRED: `subdir_name` + id INTEGER PRIMARY KEY NOT NULL, + subdir_name TEXT CHECK( length(subdir_name) <= 128 ) NOT NULL, -- path to where fid/ser file is, can be a relative path, len <= 128, Ex: 1/ + pst_id TEXT , -- `pst_id` of sample, must already be in pst table, Ex: Db0515.001 + pulse_sequence_nickname TEXT CHECK( length(pulse_sequence_nickname) <= 32 ), -- nickname/short name for pulse sequence, len <= 32, Ex: NOESY + probe_id TEXT , -- `probe_id` for the probe, if blank probe information pulled from fid directory + pulse_sequence TEXT CHECK( length(pulse_sequence) <= 128 ), + zipped_dir BLOB NOT NULL, + md5checksum TEXT NOT NULL, + session_id INTEGER, + temperature_from_data FLOAT, + experiment_date TEXT , + probe_info TEXT CHECK( length(probe_info) <= 256 ), + UNIQUE(md5checksum), + FOREIGN KEY ([session_id]) REFERENCES "session" ([id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([pst_id]) REFERENCES "pst" ([pst_id]) ON DELETE NO ACTION ON UPDATE CASCADE + FOREIGN KEY ([probe_id]) REFERENCES "probe" ([probe_id]) ON DELETE NO ACTION ON UPDATE CASCADE +); + +CREATE VIEW summary +AS +SELECT + time_domain_dataset.id AS id, + time_domain_dataset.experiment_date AS experiment_date, + time_domain_dataset.pulse_sequence_nickname AS pulse_sequence_nickname, + time_domain_dataset.pulse_sequence AS pulse_sequence, + time_domain_dataset.md5checksum AS md5checksum, + time_domain_dataset.session_id AS session_id, + session.session_preparer AS session_preparer, + temperature_from_data AS temperature, + pst.buffer_id AS buffer_id, + time_domain_dataset.pst_id AS pst_id, + pst.pst_preparer AS pst_preparer, + purification_batch.batch_id AS batch_id, + purification_batch.batch_preparer AS batch_preparer, + purification_batch.sample_sequence AS sample_sequence, + expression.expression_id AS expression_id, + expression.expression_preparer AS expression_preparer, + construct.construct_id AS construct_id, + construct.construct_preparer AS construct_preparer, + target.target_id AS target_id, + target.target_preparer AS target_preparer, + target.target_sequence AS target_sequence, + target.project_id AS project, + construct.construct_sequence AS construct_sequence, + session.spectrometer_id AS spectrometer_id, + spectrometer.field_strength AS field, + time_domain_dataset.probe_id AS probe_id, + time_domain_dataset.probe_info AS probehd, + pst.tube_type AS tube_type, + zipped_dir +FROM + time_domain_dataset +INNER JOIN session ON session.id = time_domain_dataset.session_id +INNER JOIN pst ON pst.pst_id = time_domain_dataset.pst_id +INNER JOIN batch_components ON batch_components.pst_id = pst.pst_id +INNER JOIN purification_batch ON purification_batch.batch_id = batch_components.batch_id +INNER JOIN expression ON expression.expression_id = purification_batch.expression_id +INNER JOIN construct ON construct.construct_id = expression.construct_id +INNER JOIN target ON target.target_id = construct.target_id +INNER JOIN project ON project.project_id = target.project_id +INNER JOIN spectrometer ON spectrometer.spectrometer_id = session.spectrometer_id; + +CREATE TABLE star_conversion ( + id INTEGER PRIMARY KEY NOT NULL, + specdb_col TEXT, + specdb_table TEXT, + star_tag TEXT, + star_frame TEXT +); + +INSERT INTO star_conversion (specdb_col,specdb_table,star_tag,star_frame) +VALUES + ("pst_comment", "pst", "_Assembly.Details", "assembly"), + ("pst_id", "pst", "_Assembly.Name", "assembly"), + ("pst_id", "pst", "_Assembly.Sf_framecode", "assembly"), + ("target_id", "target", "_Entity_assembly.Entity_assembly_name", "assembly"), + ("target_id", "target", "_Entity_assembly.Entity_label", "assembly"), + ("sample_sequence", "purification_batch", "_Entity.Polymer_seq_one_letter_code_can", "entity"), + ("construct_comment", "construct", "_Entity.Details", "entity"), + ("target_id", "target", "_Entity.Name", "entity"), + ("target_id", "target", "_Entity.Sf_framecode", "entity"), + ("project_id", "target", "_Entry_src.Project_name", "entry_information"), + ("project_details", "project", "_Entry_information.Details", "entry_information"), + ("given_name", "user", "_Contact_person.Given_name", "entry_information"), + ("family_name", "user", "_Contact_person.Family_name", "entry_information"), + ("given_name", "user", "_Entry_author.Given_name", "entry_information"), + ("family_name", "user", "_Entry_author.Family_name", "entry_information"), + ("middle_initials", "user", "_Entry_author.Middle_initials", "entry_information"), + ("department_and_institution","user", "_Contact_person.Department_and_institution", "entry_information"), + ("country", "user", "_Contact_person.Country", "entry_information"), + ("state_province", "user", "_Contact_person.State_province", "entry_information"), + ("city", "user", "_Contact_person.City", "entry_information"), + ("postal_code", "user", "_Contact_person.Postal_code", "entry_information"), + ("role", "user", "_Contact_person.Role", "entry_information"), + ("organization_type", "user", "_Contact_person.Organization_type", "entry_information"), + ("email_address", "user", "_Contact_person.Email_address", "entry_information"), + ("structural_genomics", "project", "_Entry_interview.Structural_genomics", "entry_interview"), + ("batch_id", "purification_batch", "_Experiment.Sample_label", "experiment_list"), + ("volume", "pst", "_Experiment.Sample_volume", "experiment_list"), + ("volume_unit", "pst", "_Experiment.Sample_volume_units", "experiment_list"), + ("sample_type", "pst", "_Experiment.Sample_state", "experiment_list"), + ("tube_type", "pst", "_Experiment.NMR_tube_type", "experiment_list"), + ("spectrometer_id", "session", "_Experiment.NMR_spectrometer_label", "experiment_list"), + ("probe_info", "time_domain_dataset","_Experiment.NMR_spectrometer_probe_label", "experiment_list"), + ("pulse_sequence", "time_domain_dataset","_Experiment.Name", "experiment_list"), + ("pulse_sequence", "time_domain_dataset","_Experiment_file.Experiment_name", "experiment_list"), + ("target_id", "target", "_Entity_experimental_src.Entity_label", "experimental_source"), + ("plasmid_id", "construct", "_Entity_experimental_src.Vector_name", "experimental_source"), + ("plasmid_id_comment", "construct", "_Entity_experimental_src.Vector_details", "experimental_source"), + ("strain", "expression", "_Entity_experimental_src.Host_org_strain", "experimental_source"), + ("expression_organism", "expression", "_Entity_experimental_src.Host_org_name_common","experimental_source"), + ("production_method", "purification_batch", "_Entity_experimental_src.Production_method", "experimental_source"), + ("target", "target", "_Entity_natural_src.Entity_label", "natural_source"), + ("organism_source", "target", "_Entity_natural_src.Organism_name_common", "natural_source"), + ("gene_name", "target", "_Entity_natural_src.Gene_mnemonic", "natural_source"), + ("spectrometer_id", "session", "_NMR_spectrometer.Sf_framecode", "NMR_spectrometer"), + ("spectrometer_id", "session", "_NMR_spectrometer.Name", "NMR_spectrometer"), + ("manufacturer", "spectrometer", "_NMR_spectrometer.Manufacturer", "NMR_spectrometer"), + ("model", "spectrometer", "_NMR_spectrometer.Model", "NMR_spectrometer"), + ("serial_number", "spectrometer", "_NMR_spectrometer.Serial_number", "NMR_spectrometer"), + ("field_strength", "spectrometer", "_NMR_spectrometer.Field_strength", "NMR_spectrometer"), + ("spectrometer_comment", "spectrometer", "_NMR_spectrometer.Details", "NMR_spectrometer"), + ("probe_info", "time_domain_dataset","_NMR_spectrometer_probe.Sf_framecode", "NMR_spectrometer_probe"), + ("probe_info", "time_domain_dataset","_NMR_spectrometer_probe.Details", "NMR_spectrometer_probe"), + ("probe_model", "probe", "_NMR_spectrometer_probe.Model", "NMR_spectrometer_probe"), + ("manufacturer", "probe", "_NMR_spectrometer_probe.Manufacturer", "NMR_spectrometer_probe"), + ("serial_number", "probe", "_NMR_spectrometer_probe.Serial_number", "NMR_spectrometer_probe"), + ("diameter", "probe", "_NMR_spectrometer_probe.Diameter", "NMR_spectrometer_probe"), + ("rotor_length", "probe", "_NMR_spectrometer_probe.Rotor_length", "NMR_spectrometer_probe"), + ("rotor_composition", "probe", "_NMR_spectrometer_probe.Rotor_composition", "NMR_spectrometer_probe"), + ("internal_vol", "probe", "_NMR_spectrometer_probe.Internal_volume", "NMR_spectrometer_probe"), + ("spacer_present", "probes", "_NMR_spectrometer_probe.Spacer_present", "NMR_spectrometer_probe"), + ("batch_id", "purification_batch", "_Sample.Sf_framecode", "sample"), + ("create_date", "pst", "_Sample.Preparation_date", "sample"), + ("solvent_system", "pst", "_Sample.Solvent_system", "sample"), + ("target_id", "target_id", "_Sample_component.Entity_label", "sample"), + ("conc", "batch_components", "_Sample_component.Concentration_val", "sample"), + ("conc_unit", "batch_components", "_Sample_component.Concentration_val_units", "sample"), + ("isotopic_labeling_remark", "purification_batch", "_Sample_component.Isotopic_labeling", "sample"), + ("isotopic_labeling", "buffer_components", "_Sample_component.Isotopic_labeling", "sample"), + ("sample_ph", "pst", "_Sample_condition_variable.Val", "sample"), + ("buffer_component", "buffer_components", "_Sample_component.Mol_common_name", "sample"), + ("target_id", "target", "_Sample_component.Mol_common_name", "sample"), + ("buffer_component_value", "buffer_components", "_Sample_component.Concentration_val", "sample"), + ("buffer_component_unit", "buffer_components", "_Sample_component.Concentration_val_units", "sample"); \ No newline at end of file diff --git a/sql/template.str b/sql/template.str new file mode 100644 index 0000000..6e27fc6 --- /dev/null +++ b/sql/template.str @@ -0,0 +1,405 @@ +data_new_templ + +save_entry_interview_1 + _Entry_interview.Sf_category entry_interview + _Entry_interview.Sf_framecode entry_interview_1 + _Entry_interview.Entry_ID . + _Entry_interview.ID 1 + _Entry_interview.PDB_deposition no + _Entry_interview.BMRB_deposition yes + _Entry_interview.View_mode 'BMRB Only' + _Entry_interview.Structural_genomics . + _Entry_interview.Timedomain_data yes + +save_ + +save_deposited_data_files_1 + _Deposited_data_files.Sf_category deposited_data_files + _Deposited_data_files.Sf_framecode deposited_data_files_1 + _Deposited_data_files.Entry_ID . + _Deposited_data_files.ID 1 + + loop_ + _Upload_data.Data_file_ID + _Upload_data.Data_file_name + _Upload_data.Data_file_content_type + _Upload_data.Data_file_Sf_category + _Upload_data.Data_file_syntax + _Upload_data.Data_file_immutable_flag + _Upload_data.Sf_ID + _Upload_data.Entry_ID + _Upload_data.Deposited_data_files_ID + + stop_ + +save_ + +####################### +# Entry information # +####################### + +save_entry_information_1 + _Entry.Sf_category entry_information + _Entry.Sf_framecode entry_information_1 + _Entry.ID . + _Entry.Title . + _Entry.Type macromolecule + _Entry.Version_type original + _Entry.Submission_date . + _Entry.Accession_date . + _Entry.Last_release_date . + _Entry.Original_release_date . + _Entry.Origination author + _Entry.Format_name . + _Entry.NMR_STAR_version . + _Entry.Experimental_method NMR + _Entry.Experimental_method_subtype solution + _Entry.Details . + + loop_ + _Contact_person.ID + _Contact_person.Email_address + _Contact_person.Given_name + _Contact_person.Family_name + _Contact_person.Department_and_institution + _Contact_person.Country + _Contact_person.State_province + _Contact_person.City + _Contact_person.Postal_code + _Contact_person.Role + _Contact_person.Organization_type + + stop_ + + loop_ + _Entry_author.Ordinal + _Entry_author.Given_name + _Entry_author.Family_name + _Entry_author.First_initial + _Entry_author.Middle_initials + _Entry_author.Family_title + _Entry_author.ORCID + _Entry_author.Entry_ID + + stop_ + + loop_ + _Entry_src.ID + _Entry_src.Project_name + _Entry_src.Organization_full_name + _Entry_src.Organization_initials + _Entry_src.Entry_ID + + stop_ + +save_ + + +############################################# +# Molecular system (assembly) description # +############################################# + +save_assembly_1 + _Assembly.Sf_category assembly + _Assembly.Sf_framecode assembly_1 + _Assembly.Entry_ID . + _Assembly.ID 1 + _Assembly.Name . + _Assembly.BMRB_code . + _Assembly.Number_of_components 1 + _Assembly.Molecular_mass . + _Assembly.Details . + + loop_ + _Entity_assembly.ID + _Entity_assembly.Entity_assembly_name + _Entity_assembly.Entity_ID + _Entity_assembly.Entity_label + _Entity_assembly.Asym_ID + _Entity_assembly.PDB_chain_ID + _Entity_assembly.Experimental_data_reported + _Entity_assembly.Physical_state + _Entity_assembly.Conformational_isomer + _Entity_assembly.Chemical_exchange_state + _Entity_assembly.Magnetic_equivalence_group_code + _Entity_assembly.Role + _Entity_assembly.Details + _Entity_assembly.Entry_ID + _Entity_assembly.Assembly_ID + + stop_ + +save_ + + #################################### + # Biological polymers and ligands # + #################################### + +save_entity_1 + _Entity.Sf_category entity + _Entity.Sf_framecode entity_1 + _Entity.Entry_ID . + _Entity.ID 1 + _Entity.BMRB_code . + _Entity.Name . + _Entity.Type polymer + _Entity.Polymer_type polypeptide(L) + _Entity.Polymer_type_details . + _Entity.Polymer_seq_one_letter_code_can . + _Entity.Polymer_seq_one_letter_code . + _Entity.Polymer_author_seq_details . + _Entity.Details . + + loop_ + _Entity_comp_index.ID + _Entity_comp_index.Auth_seq_ID + _Entity_comp_index.Comp_ID + _Entity_comp_index.Comp_label + _Entity_comp_index.Entry_ID + _Entity_comp_index.Entity_ID + + stop_ + +save_ + + #################### + # Natural source # + #################### + +save_natural_source_1 + _Entity_natural_src_list.Sf_category natural_source + _Entity_natural_src_list.Sf_framecode natural_source_1 + _Entity_natural_src_list.Entry_ID . + _Entity_natural_src_list.ID 1 + + loop_ + _Entity_natural_src.ID + _Entity_natural_src.Entity_ID + _Entity_natural_src.Entity_label + _Entity_natural_src.NCBI_taxonomy_ID + _Entity_natural_src.Type + _Entity_natural_src.Organism_name_scientific + _Entity_natural_src.Organism_name_common + _Entity_natural_src.Organism_acronym + _Entity_natural_src.Superkingdom + _Entity_natural_src.Kingdom + _Entity_natural_src.Genus + _Entity_natural_src.Species + _Entity_natural_src.Strain + _Entity_natural_src.Variant + _Entity_natural_src.Subvariant + _Entity_natural_src.Cell_line + _Entity_natural_src.Cell_type + _Entity_natural_src.Plasmid + _Entity_natural_src.Plasmid_details + _Entity_natural_src.Gene_mnemonic + _Entity_natural_src.Details + _Entity_natural_src.Entry_ID + _Entity_natural_src.Entity_natural_src_list_ID + + stop_ + +save_ + + ######################### + # Experimental source # + ######################### + +save_experimental_source_1 + _Entity_experimental_src_list.Sf_category experimental_source + _Entity_experimental_src_list.Sf_framecode experimental_source_1 + _Entity_experimental_src_list.Entry_ID . + _Entity_experimental_src_list.ID 1 + + loop_ + _Entity_experimental_src.ID + _Entity_experimental_src.Entity_ID + _Entity_experimental_src.Entity_label + _Entity_experimental_src.Production_method + _Entity_experimental_src.Host_org_scientific_name + _Entity_experimental_src.Host_org_name_common + _Entity_experimental_src.Host_org_details + _Entity_experimental_src.Host_org_NCBI_taxonomy_ID + _Entity_experimental_src.Host_org_genus + _Entity_experimental_src.Host_org_species + _Entity_experimental_src.Host_org_strain + _Entity_experimental_src.Host_org_variant + _Entity_experimental_src.Host_org_subvariant + _Entity_experimental_src.Host_org_cell_line + _Entity_experimental_src.Host_org_cell_type + _Entity_experimental_src.Vector_type + _Entity_experimental_src.Vector_name + _Entity_experimental_src.Vector_details + _Entity_experimental_src.Details + _Entity_experimental_src.Entry_ID + _Entity_experimental_src.Entity_experimental_src_list_ID + + stop_ + +save_ + +##################################### +# Sample contents and methodology # +##################################### + + ######################## + # Sample description # + ######################## + +save_sample_1 + _Sample.Sf_category sample + _Sample.Sf_framecode sample_1 + _Sample.Entry_ID . + _Sample.ID 1 + _Sample.Name sample1 + _Sample.Type solution + _Sample.Details . + _Sample.Aggregate_sample_number 1 + _Sample.Solvent_system . + _Sample.Preparation_date . + _Sample.Preparation_expiration_date . + _Sample.Storage_protocol . + + loop_ + _Sample_component.ID + _Sample_component.Mol_common_name + _Sample_component.Isotopic_labeling + _Sample_component.Assembly_ID + _Sample_component.Assembly_label + _Sample_component.Entity_ID + _Sample_component.Entity_label + _Sample_component.Type + _Sample_component.Concentration_val + _Sample_component.Concentration_val_min + _Sample_component.Concentration_val_max + _Sample_component.Concentration_val_units + _Sample_component.Concentration_val_err + _Sample_component.Entry_ID + _Sample_component.Sample_ID + + stop_ + +save_ + +####################### +# Sample conditions # +####################### + +save_sample_conditions_1 + _Sample_condition_list.Sf_category sample_conditions + _Sample_condition_list.Sf_framecode sample_conditions_1 + _Sample_condition_list.Entry_ID . + _Sample_condition_list.ID 1 + _Sample_condition_list.Name condition-1 + _Sample_condition_list.Details . + + loop_ + _Sample_condition_variable.Type + _Sample_condition_variable.Val + _Sample_condition_variable.Val_err + _Sample_condition_variable.Val_units + _Sample_condition_variable.Entry_ID + _Sample_condition_variable.Sample_condition_list_ID + + stop_ + +save_ + + +######################### +# Experimental detail # +######################### + + ################################## + # NMR Spectrometer definitions # + ################################## + +save_NMR_spectrometer_1 + _NMR_spectrometer.Sf_category NMR_spectrometer + _NMR_spectrometer.Sf_framecode NMR_spectrometer_1 + _NMR_spectrometer.Entry_ID template + _NMR_spectrometer.ID . + _NMR_spectrometer.Name . + _NMR_spectrometer.Details . + _NMR_spectrometer.Manufacturer . + _NMR_spectrometer.Model . + _NMR_spectrometer.Serial_number . + _NMR_spectrometer.Field_strength . + + +save_ + + +save_NMR_spectrometer_probe_1 + _NMR_spectrometer_probe.Sf_category NMR_spectrometer_probe + _NMR_spectrometer_probe.Sf_framecode NMR_spectrometer_probe_1 + _NMR_spectrometer_probe.Entry_ID template + _NMR_spectrometer_probe.ID . + _NMR_spectrometer_probe.Name . + _NMR_spectrometer_probe.Details . + _NMR_spectrometer_probe.Manufacturer . + _NMR_spectrometer_probe.Model . + _NMR_spectrometer_probe.Serial_number . + _NMR_spectrometer_probe.Diameter . + _NMR_spectrometer_probe.Rotor_length . + _NMR_spectrometer_probe.Rotor_composition . + _NMR_spectrometer_probe.Internal_volume . + _NMR_spectrometer_probe.Spacer_present . + +save_ + + ############################# + # NMR applied experiments # + ############################# + +save_experiment_list_1 + _Experiment_list.Sf_category experiment_list + _Experiment_list.Sf_framecode experiment_list_1 + _Experiment_list.Entry_ID . + _Experiment_list.ID 1 + _Experiment_list.Details . + + loop_ + _Experiment.ID + _Experiment.Name + _Experiment.Raw_data_flag + _Experiment.NUS_flag + _Experiment.Interleaved_flag + _Experiment.NMR_spec_expt_ID + _Experiment.NMR_spec_expt_label + _Experiment.Sample_ID + _Experiment.Sample_label + _Experiment.Sample_state + _Experiment.Sample_volume + _Experiment.Sample_volume_units + _Experiment.Sample_condition_list_ID + _Experiment.Sample_condition_list_label + _Experiment.Sample_spinning_rate + _Experiment.Sample_angle + _Experiment.NMR_tube_type + _Experiment.NMR_spectrometer_ID + _Experiment.NMR_spectrometer_label + _Experiment.NMR_spectrometer_probe_ID + _Experiment.NMR_spectrometer_probe_label + _Experiment.NMR_spectral_processing_ID + _Experiment.NMR_spectral_processing_label + _Experiment.Details + _Experiment.Entry_ID + _Experiment.Experiment_list_ID + + stop_ + + loop_ + _Experiment_file.Experiment_ID + _Experiment_file.Experiment_name + _Experiment_file.Name + _Experiment_file.Type + _Experiment_file.Content + _Experiment_file.Directory_path + _Experiment_file.Details + _Experiment_file.Entry_ID + _Experiment_file.Experiment_list_ID + + stop_ + +save_