AutoAssign Version 2.4.0
Differences from pre 2.4.0 versions:
Differences from pre 2.3.0 versions:
Added "min_spin_system_peaks" keyword to the Properties: section of the control file. This keyword changes the minimum peaks check used to identify sidechain NH's.
Added pks2Xeasy.pl Perl program to convert AutoAssign peaklists into Xeasy format.
Added bmrb2XeasyRL.pl Perl program to convert bmrb assigned chemical shifts save frames into Xeasy prot format.
Fixed minor bug in sidechain identification.
Fixed minor bug that allowed link testing of GSs at the ends of the protein sequence.
Added support for the "no_referencing" and "no_sequential_intras" keywords in the Dataset Creation GUI.
Added "-residue num" feature to the createSparkyNoesyPks.pl Perl program.
Added "-bmrb" and "-alt" options to the create_bmrb.pl Perl program to facilitate conversion of assignments into bmrb format from earlier bmrb 2.1 formats and alternate formats where the residue type and residue number are in separate columns.
Fixed minor bug in bmrb2cmap.pl Perl program with the -interpret option.
Added "-author" option to the bmrb2cmap.pl Perl program that causes it to use the author indexing instead of the default indexing starting at 1.
Added "-shift" option to the dyanaUPL2cmap.pl Perl program to shift the indexing by a given amount.
Added "-noroot" option to the bmrb2cmap.pl Perl program that allows the "-interpret" option to work on residues (spin systems) without amide H and N values.
Updated validate_assignments.pl Perl program to recognize new methyl naming convention for resonances.
David Tolmie updated validate_assignments.pl Perl program to generate BMRB NMRStar 3.1 validation report tables.
Updated BMRBParsing.pm perl module to the BMRB NMRStar 3.1 format.
Added options to Examine and Save in BMRB NMRStar 3.1 format.
Fixed bug that allowed certain algorithms to break Typing Assignment Constraints (TACs).
Added "ignore_typing_constraints" and "ignore_mapping_constraints" keywords to the Properties: section of the control file. These two keywords turn off Typing Assignment Constraints (TACs) or Mapping Assignment Constraints (MACs) and Hammer Mapping Assignment Constraints (HMACs), respectively.
Added support for the "ignore_typing_constraints" and "ignore_mapping_constraints" keywords in the Dataset Creation GUI.
Added an Average residue "X" to the Sequence: section of the control file. It can be used when a mutation is suspected in the sequence but not known.
Fixed error in Dataset Creation GUI when generating the control file. The "print_ref" option had the wrong sign for correcting peak chemical shifts back to their original values before registration.
Fixed error in Save and Examine "Sidechain NH Roots" menu options.
Fixed error in sidechain identification methods that allowed GSs that were hammered (HMACs) into the sequence to still be identified as sidechain NH Roots.
Differences from pre 2.2.2 versions:
Removed deleted spins systems from the other lists in the Peak Lists Quality Asssessment Report generated from the examine_spin_systems.pl Perl program.
Fixed minor bug in Dataset Creation GUI where HSQC peak lists were being labeled as "NH-HSQC" versus "HSQC". HSQC is the recognized name in the examine_spin_systems.pl Perl program.
Differences from pre 2.2.1 versions:
Enhanced reading of the XML file ".peaklistConfig.xml" used for the AutoFill feature in the Dataset Creation GUI. It updates filepaths to the current working directory if the file exist there.
Fixed error message given when testing whether the current Dataset Creation GUI subdir is available. It now indicates the correct path it is testing.
Differences from pre 2.2.0 versions:
Rewrote/revamped all code related to the .AArc file and the Preferences dialog. Fixed numerous logical flaws that would prevent proper reading or writing of the .AArc file.
Fixed logical flaw in the AutoFill option in the Dataset Creation GUI. The location of the workingDir and scriptDir (internal variable) are now left alone by AutoFill. This is the proper behaviour so that it is easy to move a dataset and/or use a newer version of AutoAssign.
Improved parsing of the .AAhelp_files. Parser is more flexible with the input format of the file.
Fixed error in Dataset Creation GUI related to missing phase information that may occur when AutoFilling.
Fixed minor errors in how the workingDir is selected either by text window or Browse button. Now it is uniform.
Fixed flaws in window resizing of all windows and tabs in the Dataset Creation GUI. Internal text areas and layouts now resize with window resizing.
Fixed errors in the Dataset Creation GUI related to the picking of root spectra to register to.
Revamped the tree registration logic to handle intra_only experiments and to work without a single definable root spectrum for all resonance types in the Dataset Creation GUI. Added red highlighting to indicate lack of root spectra for a given resonance type.
Fixed errors in running examine_spin_systems.pl without HSQC or HNCO spectrum from the Dataset Creation GUI.
Added support for 4D and 5D peak lists and added HNCACACB and HNcoCACACB 4D GFT experiment types in the Dataset Creation GUI.
Fixed various errors in reading and writing the XML file ".peaklistConfig.xml" used for the AutoFill feature. AutoFill is more complete with respect to tolerances and registration information.
Fixed errors in reading, displaying, and using registration and tolerance values from calculate_registration in the Dataset Creation GUI.
Revamped text box sizes and layout to match the default system font used in the Dataset Creation GUI.
Adopted the system GUI look and feel parameters for all of AutoAssign, except the CMap Image Editor.
Patched error between CMap Image Editor and the new system GUI look and feel that caused 100% of the cpu to be used.
Added additional support for phased HNCACACB and HNcoCACACB experiments to both the Dataset Creation GUI and examine_spin_systems.pl .
Differences from pre 2.1.0 versions:
Rewrote and/or revamped all documentation. The reorganized documentation is now in fewer html files that are larger and better hyperlinked and include more screenshots. The documentation is now easier to browse and print.
Fixed error in phasing that would not properly use some phasing of peaks correctly (i.e. positive or negative intensities determined by local spin system
topology).
Improvement resonance assignment/classification algorithm to better filter out the presence of duplicate chemical shifts that could arise by picking peaks twice.
Fixed error in linking that would allow linking to ends of segments of GSs that had not been tested for compatible amino acid types nor compatible mapping constraints.
Fixed error in HB assignments that prevented two HB's from being assigned in certain circumstances.
Changed behavior of the program so that it would attempt assigning sequential CA's when an HNcoCACB and HNCA are present without the HNcoCA. This makes good sense if the HNcoCACB is a phased experiment.
Extended allowed range of assignable chemical shifts from 4std to 6std of the expected value when both intra and sequential shifts are present.
Made RACs (Resonance Assignment Constraints) override the 4std and 6std limits on assignable chemical shifts.
Added Peak picking Assignment Constraints or PACs using ";p" and ";-p" to indicate whether a peak should be used or not.
Added new peak deletion rule that only one peak for a set of peaks that exactly match in all dimension values and intensity will be allowed in a spectrum. All others will be deleted unless a PAC is used to keep some of the duplicates. Added the "Properties:" keyword "keep_duplicate_peaks" to override this behavior. Also revamped examine_spin_systems.pl Perl program to use these new peak deletion rules and PACs.
Removed use of the Java web browser. Now the user must supply the location of a viable web browser upon installation or in the preferences.
Fixed many bugs in the Dataset Conversion/Creation GUI.
Added Release Notes to the Help menu to aid the user in determining which version of AutoAssign they are running.
Added options to Examine and Save in older BMRB 2.1 format.
Added options to Examine and Save in "templated" BMRB 3.0 and 2.1 formats.
Fixed Sparky formatting errors in Sparky resonance lists and peak lists formats. The output now uses the author indexing for the protein sequence.
This is fixed in the AutoAssign Server and the Perl programs bmrb2SparkyRL.pl, bmrbACS2SparkyPks.pl, and bmrbSPL2SparkyPks.pl .
Added "print all" links to the html peak list quality assessment report generated by the examine_spin_systems.pl Perl program.
Fixed error in mapping algorithms that would allow an accidental mapping to a proline.
Fixed error in "WebBrowser:" keyword in the saving of the ".AArc" preferences file.
Added code from David Tolmie at the BioMagResBank for creating NMRStar 3.0 assignment validation save frames into the validate_assignments.pl Perl program.
Improved behavior of the create_bmrb.pl Perl program so that it will skip lines that do not contain numbers. This also affects the sparkyRL2bmrb.pl Perl program which calls create_bmrb.pl .
Added "-author" option to the bmrb2AutoStructure.pl Perl program which causes the program to use the author residue indexing instead of the internal residue indexing of the given BMRB file.
Fixed bug in saving the .AArc preferences file. The bug prevented saving if the old file was not in the valid format. This behavior prevents the user from using the GUI to fix format errors. This becomes an issue for anyone upgrading from pre 2.0.0 versions since the format changed in 2.0.0 .
Fixed bug in the "Set Defaults" button in the Preferences Window. The GUI was trying to read the defaults ".AArc" file from the wrong location if "Auto" was selected.
Fixed bug in the examine_spin_systems.pl Perl program involved with initial chemical shift assignment for calculating Linkage Uniqueness and Average PRTL Length scores. Added HB assignment to this scoring as well.
Removed all old code and options from the examine_spin_systems.pl Perl program related to the now defunct assignment constraints file which is no longer used by AutoAssign.
Added a "-author" option to the validate_assignments.pl and missing_shifts.pl Perl programs to print reports using author indexing.
Differences from pre 2.0.0 versions:
Added new Dataset Conversion/Creation GUI to java client. This is a major GUI addition that facilitates the creation of a dataset that AutoAssign can analyze.
Added views of Assignment Constraints into the Examine and Save submenus of the java client.
Fixed some GUI consistency issues in how files are open and saved.
Differences from pre 1.16.0 versions:
Added Properties keyword "ignore_constraints" to turn off all assignment constraints.
Removed the assignment constraints (override) file.
Revamped peak based assignment constraints and several new types including linking assignment constraints (LACs), resonance assignment constraints (RACs), and hammer mapping assignment constraints (HMACs).
Added error reporting and additional menu options for assignment constraints.
Fixed bug in BMRBParsing.pm associated with writing out "_Residue_author_seq_code" tags into BMRB files.
Added "STD:" section to the table file for indicating individual matching standard deviations for pairs of spectral dimensions.
Revamped all matching tolerances to use "STD:" settings over the "Tolerance:" settings in the table file.
Decoupled root and alternate root spectra from the HSQC and HNCO. The HNCO or even the HNcoCA can be used as the root spectrum.
Fixed alternate root spectrum issue with respect to overlapped spin systems with multiple root peaks.
Fixed "greedy" sidechain spin system identification methods making some glycine spin systems be classified as sidechain roots.
Made all BMRB and Sparky outputs have "C' instead of "B" and "U" residue symbols.
Added "alt_root" Properties keyword in order to specify another spectrum besides the "HNCO" as the alternate root spectrum.
Added "root_matching_std_units" Properties keyword to specify the number of standard deviation units to use in root HN matching for building spin systems.
Added "link_matching_std_units" Properties keyword to specify the number of standard deviation units to use in link matching for linking spin systems together.
Added "max_matching_multiplier" Properties keyword to specify the maximum tolerance to allow in matching (i.e. std * num_std_units * multiplier).
Added "min_matching_multiplier" Properties keyword to specify the minimum tolerance to allow in matching (i.e. std * num_std_units * multiplier).
Added comment feature to peak-based assignment constraints that causes all text after an "_" (underscore) to be ignored.
Fixed bug in typing_degeneracy.pl Perl program that made the "-sequence" option not work.
Fixed bug in create_bmrb.pl Perl program preventing the use of the "-diasterio" option.
Fixed bug in PeakParsing.pm Perl module in relationship to manipulating Sparky peak list files.
Added sparkyPks2bmrb.pl Perl program to convert Sparky peak list files to assigned spectral peak list save_frames in NMRStart format.
Changed some definitions of assignable aromatic and sidechain chemical shifts in the missing_shifts.pl Perl program.
Revamped the BMRB format generated by AutoAssign to full 3.0 compliance.
Revamped the BMRB format used by all Perl programs to full 3.0 compliance. Also rewrote a majority of the Perl programs and completely revamping the code base.
Removed tocsy_typing.pl Perl program.
Changed create_assigned_peaklist.pl to bmrb_assign_spl.pl which assigned spectral peak lists based on the given assignments. This and other tools provides the means to create a NMRStar 3.0 formatted BMRB file from scratch which includes assignments and assigned peak lists.
Added the ability for typing_degeneracy.pl Perl program to take a BMRB file with assignments and assigned peak lists.
Combined examine_expected_peaks.pl and examine_spin_systems.pl Perl program into one peak lists quality assessment tool (examine_spin_systems.pl) that uses phase information and peak-based grouping assignment constraints. It also generates a dynamic html report that is extensively hyperlinked and much easier to use.
Made spin systtem grouping assignment constraints (SGACs) override amide tolerances as far as grouping is concerned. In other words, a grouping constraint will group a peak into a spin system even if it is out of the tolerance boundary. The old behaviour can be restored by using the Properties keyword "tolerance_bound_grouping".
Added the keyword "NH2_PHASE" to the spectrum description in the table file. This keyword identifies the given experiment as having negative intensity when the peak arises from a sidechain NH2. AutoAssign will use this information when identifying sidechain spin systems.
Added Perl program bmrb2AutoStructure.pl that converts the BMRB assigned chemical shifts save frame into AutoStructure's resonance list format.
Fixed minor logic bugs in the code that would cause occasional crashes.
Fixed logical flaw in assigning resonances of a mapped GS. Now resonances used in linking have priority over resonances that better match the amino acid type.
Differences from pre 1.15.1 versions:
Fixed minor bug in create_peak_list.pl Perl program.
Added ability to save assigned peak lists in Sparky format. Added GUI options to examine and/or save specific or all peak lists in Sparky format.
Added ability to save assigned resonances in Sparky format.
Added "print_order" and "print_ref" keywords to dimension descriptions in the table file for describing how to print assigned peak lists in Sparky format.
Added better tracking of peak based spin system assignment constraints. More reports show the presence of these assignment constraints.
Added "Execute(Finish Assignments)" macro command.
Made all file selection and directory selection GUI windows uniform.
Differences from pre 1.15.0 versions:
Added minor error detection code to validate_assignments.pl perl program.
Added the createSparkyNOESYPks.pl Perl program to create hypothetical NOESY peak lists in Sparky format from the resonance assignments in bmrb format.
Added no_referencing keyword to list of possible Properties in the table file.
Revamped and mostly rewrote all the code associated with how chemical shifts are organized in GSs.
Fixed bugs in how sidechain GSs are recognized.
Fixed bugs in referencing.
Improved chemical shift selection for HA and HB resonances.
Implemented peak phasing. It actually works now. Updated table file format to handle dimension specific phasing descriptions.
Implemented dimension specific ladder descriptions of resonances in the table file.
Added peak based spin system assignment constraints. SGACs, STACS, SMACS, and SSACS can now be entered in the comment fields of peaks.
Changed the output format of the BMRB NMRStar format to include peak notes.
Changed the name of the Perl program bmrb2pks.pl to bmrbACS2pks.pl.
Changed the name of the Perl program bmrb2pks2.pl to bmrbSPL2pks.pl.
Changed the name of the Perl program bmrb2SparkyPks.pl to bmrbACS2SparkyPks.pl
Added the Perl program bmrbSPL2SparkyPks.pl which convert BMRB spectral peak list frames to sparky peak list format.
Improved the Perl program sparkyPks2pks.pl . It now incorporates Sparky notes correctly.
Fixed bugs and improved BMRBParsing.pm and PeakParsing.pm Perl modules.
Differences from pre 1.14.1 versions:
Fixed minor bug in SGACs (Spin system Grouping Assignment Constraints) implementation.
Fixed bug that allowed an inappropriate reuse of a peak in multiple assignments.
Rewrote and greatly improved methods for filling out assignments by using neighboring GSs.
Differences from pre 1.14.0 versions:
Made changes to linking algorithm which makes results more robust.
Made changes to the algorithm determining which peak to use for a specific chemical shift assignment. The changes makes AutoAssign more conservative and less error prone with complete data. Added the loose_sequential_intra_matching keyword to the list of Properties in the table file to mimic old behavior.
Added group keyword override feature to the override file format to aid in creating SGACs (Spin system Grouping Assignment Constraints).
Added the ability to define Assignment Constraints with the HNCO peaks even if they are not the root peak of the generic spin system.
Added the Spin system Sidechain Assignment Constraint (SSAC) for overriding which GSs that AutoAssign labels as sidechain GSs.
Removed Properties keywords "old", "deuterated_old", and "ILV_deuterated_old".
Updated statistics for HA and CO atom types based on RefDB statistics from Zhang and Wishart JBNMR 25, 172-195.
Added the ability to assign HBs and use them in the linking of GSs.
Updated BMRB output to include assigned peak list save frames.
Fixed string buffering bug in the information windows created by the Java GUI.
Fixed logic bug in specific resonance type identification cause improper reuse of a chemical shift value.
Added group keyword override feature to examine_spin_systems.pl Perl program.
Added ability to handle HNHAHB, HNcoHAHB, HNHB, and HNcoHB peak lists in examine_expected_peaks.pl Perl program.
Added ability to handle HNHAHB, HNcoHAHB, HNHB, and HNcoHB peak lists in examine_spin_systems.pl Perl program.
Fixed logic bug in determining which shifts are intra.
Differences from pre 1.13.2 versions:
Differences from pre 1.13.1 versions:
Fixed minor bug in validate_assignments.pl Perl program.
Fixed deeply buried runtime bug in AutoServer.
Improved missing_shifts.pl Perl program. Added more statistics of completeness and more options.
Differences from pre 1.13.0 versions:
Combined AutoAssign 1.12.0 with AutoPeak 1.5.0 to create a new combined distribution.
Recompiled calculate_registration for IRIX.
Added version for Darwin (MAC OS X).
Fixed nasty bug in typing_degeneracy.pl related to proper use of inter-residue chemical shifts in amino acid typing.
Improved quality scores produced by the examine_spin_systems.pl perl program.
Fixed minor bug in BMRBParsing.pm Perl module which was causing several scripts run under Solaris 8 not to work.
Differences from pre 1.12.0 versions:
Inverted sign of Consensus CSI in the CMap Image to match specification in Wishart and Sykes JBNMR 4, 171-180 (1994).
Corrected error in documentation. "C" residue type is for a disulfide bonded cysteine. "B" is for a non-disulfide (reduced) cysteine.
Added "U" residue type for cysteines of unknown state.
Added new amino acid typing statistics based on RefDB statistics from Zhang and Wishart JBNMR 25, 172-195. The old statistics tables are available by using the "Properties:" keywords: old, deuterated_old, ILV_deuterated_old.
Added non static Linux compiled versions of AutoServer and AsciiClient for versions of Linux that do not handle the static compile well.
Differences from pre 1.11.1 versions:
Made further changes to reports to facilitate use of assignment constraints.
Added no_sequential_intras keyword to list of possible Properties in the table file.
Recompiled under Linux RedHat 9.0 to fix bug created by new version of glibc libraries.
Fixed minor bug in sorting by HA in "Examine: Specific GS" dialog window.
Added sort by Reverse Order to "Examine: Specific GS" dialog window.
Differences from pre 1.11.0 versions:
Added linking overrides (assignment constraints) to AutoAssign and override file format.
Changed many reports to print spin system root ID's to aid in the creation of override files.
Added "Examine (List, All GSs)" and "Save (List, All GSs, path_filename)" to list of commands and menu items in AutoAssign GUI.
Differences from pre 1.10.1 versions:
There is updated documentation.
Another nasty bug was discovered and squashed all in a morning's work.
Fixed error in implementation of grouping overrides.
Differences from pre 1.10.0 versions:
Fixed minor bug in override file parsing.
Added @Set_CMap_Image_Color_Scheme macro command to macro language.
Fixed problem in creating GIF image of CMap. Problem due to changes between Java 1.3.1 and Java 1.4.1.
Added grouping overrides (assignment constraints) to AutoAssign and the override file format.
Made changes to code so that an HNCO peak list is no longer required to run AutoAssign.
Fixed minor bug in parsing the "Tolerances:" section of a table file.
Fixed minor Gly HA formating error in printing assignments in BMRB format.
Differences from pre 1.9.0 versions:
A lot of the CMap functionality does not work properly with versions AutoPeak before AutoPeak 1.1.0.Differences from pre 1.8.0 versions:
CMap Image Editor has been revamped. Secondary Structure, J Coupling, generic Graphics, and generic BarGraph Rows have been added. Also, the order of the rows can be changed. Various minor bugs where fixed as well. Also, subsequent "Assignment_Info" entries (after the first) do not need to have all residues listed nor for the residues to be in their correct order. Also better color options have been added.
Removed older Wishart plots and unimplemented Menu options.
Fixed bug in overriding Bayesian Typing priors of sequential (CO) ladders.
Added new deuteration table to handle amino acid typing of CA/CB's for samples that are deuterated with ILV methyl protonation.
The override (assignment constraint) file was added to the Properties section of the table file. With the override file, the user can override the Bayesian typing priors and the restrict the set of possible sequence sites for a specifc generic spin system.Differences from pre 1.7.8 versions:
Updated the BMRB (NMRStar) format created by AutoAssign. It now gives a better save frame template to use and works correctly with the updated BMRB parsing in AutoPeak 1.0.0 .
A very, very nasty run-time bug had shoes thrown at it for a day until I finally landed one good hit on the bug.
Differences from pre 1.7.7 versions:
Nasty run-time bug was squashed using dataset from Ron Nieman.
Made minor changes in the CMap editor.
Made minor adjustments in BMRB format.
Differences from pre 1.7.4 versions:
Added Save menu to MenuBar.Differences from pre 1.7.3 versions:Added the ability to set the location for temporary files in the Preferences.
Added -tmpDir feature to the autoclient script to override .AArc setting for the location of the temporary files.
Added AUTOASSIGN_HOST and AUTOASSIGN_PORT environmental variables that can override default host and port in the .AArc file.
Made the .AArc file format more flexible.
Warnings are now printed in the main window.
Fixed bug in the generated BMRB format.Differences from pre 1.7.2 versions:Made minor change to the generated CMap format.
Added secondary structure calculations and graphics to the CMap Image. Also
added ability to save results of calculations in a file.Added additional features to the CMap Editor including font size control.
Added dialog visibility option to the "Specific GS", "Specific Residue", and "Specific
Spectrum" menu options.Fixed bug in Connect to Server dialog on IRIX version.Differences from pre 1.7.1 versions:Client has a Connectivity Map editor for producing quality figures for publication.Differences from pre 1.7 versions:Client is revamped for Java 2.0 .Client has the ability to use AutoAssign macros.
Client has ability to use web browsers and text editors outside of Java.Differences from pre 1.6.1 versions:Client has a preferences file that can be modified.
There is Web-based Documentation.
The ability to handle fractional deuteration was added to a first approximation.Differences from pre 1.5.3 versions:Another nasty run-time bug was squashed.
Better error reporting for general use and in Sparky interface.Differences from pre 1.5.2 versions:Nasty run-time bug was squashed.
Version is compatible with Sparky.Differences from pre 1.5.0 versions:AutoAssign performs full 4-rung down to 2-rung matching when given 4-rungs to match with.Differences from pre 1.4.0 versions:Tools - Analyze - Link Discrepancies has a new look.
Ability to add "#" delimited comments to the peak files. Old peak files will need to have their header line delimited with a "#" now. The "upgrade_peak_file.pl" script in the AutoPeak directory will "upgrade" old peak files.
A new section has been added to the table file called the "Properties:" section. It is an optional section that must come before the "Sequence:" section.Differences from pre 1.3.0 versions:Ability to add "#" delimited comments has been added to the table file.
Simple handling of 100% deuteration has been added. You can completely turn it on by adding the keyword "deuterated" to the "Properties:" section.
The client does not change your working directory to the $AutoDir/Client directory anymore.
The startup scripts for the client (autoclient) and the server (autoserver) have various enhancements. They give more information about servers that are currently running.
AutoAssign is not as sensitive to spaces and tabs in the table and peak files.The Menu Bar has been radically reorganized.
The code has been optimized and runs about 6 times faster.
Differences from pre 1.5.0 versions:
Updated non-relevant list in missing_shifts.pl perl script.
Put better error reporting into BMRBParsing.pm perl module used by several perl scripts.
Differences from pre 1.4.0 versions:
Revamped typing_degeneracy.pl perl script. Algorithm has improved and fixed minor error in CA/CB/CG similarity table.
Output of program has improved as well.
Fixed help documenation for sparkyPks2pks.pl perl script.
Made missing_shifts.pl perl script print only information about NMR relevant resonances unless told otherwise.
Made a host of changes to examine_spin_systems.pl perl script. This includes handling additional workbook names, calculating ESS scores,
and using grouping overrides in splitting spin systems.
Added additional recognized workbook names to examine_expected_peaks.pl perl script.
Added "-diasterio" switch to create_bmrb.pl for giving disteriomer resonances an ambiguity code of 2.
Added sparkyRL2bmrb.pl perl script for converting Sparky resonance lists into BMRB files.
Added additional statistical evaluations to calculate_registration.
Added "-map" option to calculate_registration for saving the input peaks that map to root peaks and their mapping.
Differences from pre 1.3.1 versions:
Made minor changes to documentation for examine_spin_systems.pl perl program.
Added feature to create_peak_list.pl perl program for reporting lines that are skipped.
Added "-" option for using old workbook name to apply_shifting.pl perl program.
Added "-" option for using old workbook name to extract_by_filter.pl perl program.
Added "-" option for using old workbook name to extract_by_dup_count.pl perl program.
Added "-" option for using old workbook name to extract_by_intensity.pl perl program.
Added "-" option for using old workbook name to extract_by_intensity2.pl perl program.
Added "-" option for using old workbook name to extract_by_intensity3.pl perl program.
Added remove_peaks.pl perl program for removing peaks from peak lists in a way that gets recorded in the file history.
Differneces from pre 1.3.0 versions:
Added convert_rd_experiment C++ program that replaces the convert_rd_experiment.pl perl program and provides a better algorithm.
Added feature to concatenate.pl perl script.
Added examine_spin_systems.pl perl script for analyzing peaks lists before running AutoAssign.
Added examine_expected_peaks.pl to replace validate_peak_list.pl for comparing expected number of peaks to observed number of peaks in
certain types of peaklists.
Added new documentation to explain the major uses of AutoPeak.
Added extract_by_shift_range.pl to extract peaks that fall within given chemical shift ranges.
Added lost functionality back to bmrb2cmap.pl that works with current improved implementation.
Fixed small mistake in validate_assignments.pl, typing_degeneracy.pl, and tocsy_typing.pl.
Added pks2SparkyPks.pl to convert AutoAssign peak lists into Sparky peak lists.
Added compare_cmap.pl to compare CMap files for differences.
Improved dyanaUPL2cmap.pl to handle intraresidue NOEs.
Totally revamped calculate_registration, improving the algorithm and making it easier to use.
Differences from pre 1.2.0 versions:
Updated BMRBParsing.pm perl module to better handle peak list save frames.
Updated CMapParsing.pm perl module to better handle conversion from BMRB format.
Added DyanaParsing.pm perl module for reading DYANA NOE constraint files.
Added SparkyPeakParsing.pm module for reading Sparky Peak files.
Updated bmrb2cmap.pl to improve conversion of assigned peak lists into CMap representation, add J Rows, and add Secondary Structure Rows.
Added sparkyPks2pks.pl for converting spark peak lists into AutoAssign peak lists.
Improved cpu performance in convert_rd_experiment.pl. It is as much as 10 to 100 times faster in some cases.
Added create_assigned_peaklist.pl for assigning unassigned peak lists save frames in a BMRB file.
Added dyanaUPL2cmap.pl to convert DYANA UPL constraints into CMap format.
Updated pks2bmrb.pl to better convert AutoAssign peak lists into BMRB format.
Added sec2bmrb.pl to convert AutoStructure secondary structure format to BMRB format.
Added jval2bmrb.pl to convert AutoStructure HNHA J values into BMRB format.
Differences from pre 1.1.0 versions:
A lot of the CMap functionality does not work properly with versions of AutoAssign before AutoAssign 1.9.0.
Updated BMRBParsing.pm perl module with better support for spectral peak list save frames and better cloning subroutine.
Updated bmrb2pks.pl perl script.
Added bmrb2pks2.pl to convert spectral peak list save frames into AutoAssign peak lists.
Added pks2bmrb.pl to convert AutoAssign peak lists into spectral peak list save frames.
Fixed bug in calculate_registration C++ program and added better error reporting to the program.
Added better reporting of "unknown" and "duplicate" assigned chemical shifts to validate_assignments.pl perl script.
Enhanced create_bmrb.pl perl script to handle an option ambiguity code column.
Added cmap2bmrb.pl perl script to convert CMap files to BMRB files.
Updated CMapParsing.pm perl module to handle new CMap Image File Format.
Added calc_rdc.pl perl script to calculate RDCs given peak list with peak splittings dimension.
Added calc_resonance_splitting.pl perl script to calculate peak splittings from assigned split doublet.
Added create_split_doublet.pl perl script to create split doublets from assigned central peak with splittings dimension.
Added typing_degeneracy.pl perl script to analyze typing degeneracy in a given sequence.
Added extract_dup_assignments.pl to extract peaks with duplicate assignments in Notes column.
Added rdc2cns.pl to convert RDC peak lists to CNS RDC format.
Added rdc2pales.pl to convert RDC peak list to PALES input format.
Added pales2cns.pl to convert PALES output format to CNS RDC format.
Differences from pre 1.0.0 versions:
Added calculate_registration c++ program as a replacement for calculate_shifting.pl and apply_shifting.pl perl scripts.Differences from pre 0.8.0 versions:
Rewrote the BMRBParsing perl module and now all the scripts using BMRB files handles a more complete NMRStar format.
Added manage_bmrb.pl perl script for managing save frames inside BMRB files.
Changed name of concat_bmrb.pl to concat_bmrb_shifts.pl and updated the script to handle changes in BMRB parsing.
Fixed minor error in create_bmrb.pl perl script.
Added option to extract_duplicates.pl and concatenate.pl for peaks to keep old workbook name.
Added -printstats option to the missing_shifts.pl perl script.
Added the bmrb2SparkyPks.pl perl script to create Sparky peak list files from a BMRB NMRStar file.
validate_script.pl has been renamed to validate_peak_list.pl and added some more options.
Fixed option selection glitch in convert_rd_experiment.pl .
Changed tocsy_typing.pl perl script to only handle typing and assignment issues around the the hCCcoNH TOCSY.
Added validate_assignments.pl perl script to help validate the assignments in a BMRB NMRStar file.
Revamped tocsy_typing.pl perl script and added restricted peak assignment ability.Differences from pre 0.7.7 versions:Fixed a small bug in bmrb2pks.pl perl script.
Added a minor improvement in the validate_script.pl perl script.
Added an -abs option to the average_duplicates.pl perl script.
Expanded the convert_rd_experiment.pl perl script to handle residual dipolar coupling peak lists.
Added the two qualifier to the -template option for the convert_rd_experiment.pl perl script.
Added the change_intensity.pl perl script which allows the user to change peak intensities in defined ways.
Revamped the missing_shifts.pl perl script and added a lot of options.
Added the tag_peaks.pl perl script for tagging peaks that match a filter.
Added BMRB parsing capability to tocsy_typing.pl perl script and revamped part of its interface.
Added concat_bmrb.pl perl script which concatenates bmrb files together.
Added bmrb2cmap.pl perl script which converts bmrb files into cmap files.
Added bmrb2pks.pl perl script which creates peak lists from bmrb files.
Added create_bmrb.pl perl script which creates a bmrb file from an assigments file in 3 column format.
Added missing_shifts.pl perl script which reports which atom types are missing from a given bmrb file.
Added bmrb_extract_shifts.pl perl script which extracts shifts from a bmrb file to create a new bmrb file.
Added bmrb_apply_shifting.pl perl script which shifts chemical shifts of certain atom types.
Added bmrb_calculate_shifting.pl perl script which calculates the shifting between bmrb files.
Added compare_bmrb.pl perl script which compares pairs of matching shifts from two bmrb files.
Added bmrb2SparkyRL.pl perl script which converts a bmrb file into a Sparky Resonance List file.
Differences from pre 0.7.4 versions:
Fixed and enhanced the tocsy_typing.pl perl script. Added the ability to assign CD and CE chemical shifts.Changed the concatenate.pl perl script.
Added the file_history.pl perl script.
Changed the names of the apply_referencing.pl and calculate_referencing.pl perl scripts to apply_shifting.pl and calculate_shifting.pl .
Differences from pre 0.7.3 versions:Added revamped perl script for converting reduced dimensionality peak lists into standard peak lists.Differences from pre 0.7.2 versions:Added perl script for creating average peaks from a groups of similar peaks.
Fixed errors in validate_script.pl and tocsy_typing.pl perl scripts.
Added validate_script.pl perl script to provide additional peak file validation information.Added tocsy_typing.pl perl script to provide rigorous checking of amino acid typing of AutoAssign's results. It also provides facilities for performing sidechain assignments using (H)CC(CO)NH TOCSY data.
Differences from pre 0.7 versions:There are various improvements in the Perl scripts.Differences from pre 0.6.1 versions:The calculate_referencing.pl perl script was fixed and enhanced.Differences from pre 0.5.3 versions:More validation Perl scripts added.
More perl scripts added.Differences from pre 0.5.0 versions:Perl scripts have been added to allow easy creation of AutoAssign peak files. The scripts allow an expansion of the experimental strategies that AutoAssign can handle. This functionality will be directly incorporated into
AutoAssign in later versions.The "upgrade_peak_file.pl" script will "upgrade" old peak files.