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CSP_Rank/OpenMM_mini.py

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#!/usr/bin/env python
from pdbfixer import PDBFixer
from openmm import *
from openmm.app import *
from openmm import unit
import os
import re
import time
import datetime
import numpy as np
import math
"""
A program to minimize a PDB file/s with OpenMM (RTT, March 2023. V1.0)
Args:
-af2 Make all defaults to emulate AF2 relax
-afw2 Same as above with implicit water
-rtt Deafults to RT method
-inD <string> directory to get the PDB files from
-outD <string> directory write final minimized PDB files
-list <string> read from List the PDB file names to minimize
-steps <int> the number of steps for minimization, default 1000
-tolerance <float> tolerance in forces for minimization, default 10.0
-Ecut <float> Epot cutoff to report a list of good E ones
-ffield <string> Force field to use, default AMBER14
-water <string> Model for water molecules, default AMBER14
-box <float> Size of cubic box of explicit water (nm), def: 1.43
-restr <string> restrain atoms to original positions,
-cons <string> constrain atoms (not move at all),
-kf <float> value of k for force to restrain atoms, default 100.0
-NBmethod <string> nonbonded method to use. default: CutoffNonPeriodic
choices: NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME
-NBcut <float> nonbonded cut-off ")
-report Report minimization info/steps
-gr[oup] <string> File name for the multimodel file created at the end, if requested
"""
# ----------------------- help message -------------------------------
if ( len(sys.argv) < 2 ):
print("\n ** OpenMmini.py (RTT, March 2024. V1.0) \n")
print(" A python script to perform an energy minimization on a PDB file\n")
print(" Optional Args: options between (), defaults between brackets on the right")
print(" Special flags ")
print(" -af2 defaults to emulate AF2 relax protocol ")
print(" -af2w same as af2 plus implicit water in the protocol ")
print(" -rtt defaults to RTT relax protocol ")
print(" ")
print(" -inD <string> directory to get the PDB files from ")
print(" -outD <string> directory to write final mimized PDB files ")
print(" -list <string> read from List the PDB files to minimize ")
print(" -st[eps] <int> the number of steps for minimization, [0] ")
print(" -tol[erance] <float> tolerance in forces for minimization, [10.0] ")
print(" -Ecut <float> Epot cutoff to report a list of good E, [0.0] ")
print(" -ff[ield] <string> Force field to use (amber14, amber99) [AMBER14] ")
print(" -wa[ter] <string> Water model (implicit, amber14, amber99) [no default] ")
print(" -box <float> Size of cubic box of explicit water (nm), [1.43] ")
print(" -res[train] <string> restrain atoms around original positions, [no default] ")
print(" -con[strain] <string> Constrain atoms, no move at all [no default] ")
print(" (backbone, heavy, N,CA,C,O ) ")
print(" -kf <float> value of stiffness to restrain/constrain [10.0] ")
print(" -NBm[ethod] <string> nonbonded method to use. [CutoffNonPeriodic] ")
print(" (NoCutoff, CutoffNonPeriodic, CutoffPeriodic) ")
print(" -NBc[ut] <float> nonbonded cut-off [20 A]")
print(" -gr[oup] <string> File name for the multimodel file ")
print("")
print(" Defaults for flags: (note than can be changed at command line) ")
print(" -af2 -af2w -rtt no flag ")
print(" -------- ----------- ------------ ------------ ")
print(" Method AF2 AF2W RTT Custom ")
print(" Steps 100 100 0 (unlimited) 0 (unlimited) ")
print(" tolerance 2.39 2.39 1.0 1.0 ")
print(" restrained heavy heavy backbone -- ")
print(" stiffness 10.0 10.0 5.0 5.0 ")
print(" NBmethod NoCutoff NoCutoff NoCutoff NoCutoff ")
print(" ForceField amber99sb amber99sb amber99sb amber99sb ")
print(" FFwater -- implicit -- -- ")
print("")
print(" Use examples:")
print(" OpenMM_mini.py -af2 -inD Unrelaxed -list ListToMini -outD Minimized -gr AllPDBS.pdb ")
print(" OpenMM_mini.py -restr heavy -wat implicit ../SomeDir/*.pdb")
print(" OpenMM_mini.py -steps 1000 -tolerance 2.39 -list Lista -inD ../SomeDir/")
print("")
sys.exit(0)
# ----- General units and conversion constants
ENERGY = unit.kilocalories_per_mole
LENGTH = unit.angstroms
toKjnm2 = 100.0/0.239006
toKjmol = 4.184
toKcalmol = 0.239006
# ----------------------------------- defaults updated at command line
# ----- Special flags, report, plot
AF2 = False
AFw = False
RTT = False
Reporting = False # wether report (or not) on minimization steps
Grouping = False # wether group (or not) models into a multimodel file at the end
# ----- PDB or mmCIF formats
mmCIF = False
# ----- steps, tolerance, force field and water ff, integrator
steps = 99 # default number of steps, 0 means no limit, changed later
tolerance = 99.0 # default in OpenMM, AF2 uses 2.39, changed later
atomsrestrained = '' # default none
atomsconstrained = '' # default none
stiffness = 99.0 # Kf for restrained/constrained, changed laterº
Ecut = 1.0e99 # Cutoff for good Epot, changed later
ffield = 'amber99sb.xml'
ffwater = ''
Water = False
# ----- integrators, restrained and force or constrained atoms
integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
# ----- Others, dir for input/output, cutoff for E
indirname = './'
outdirname = './'
# -----
files = []
lEp = []
Files_to_group = []
# ----------------------------------- System Configuration general values
boxs = 1.43
#NBmethod = 'CutoffNonPeriodic'
NBmethod = ''
NBcut = 20
constraintTolerance = 0.0001
constraints = 'HBonds'
#rigidWater = True
#ewaldErrorTolerance = 0.0005
#hydrogenMass = 1.5*amu
# ----------------------------------- Simple parsing of args
#print("Full command:", sys.argv[0], sys.argv[1:])
i = 0
for tok in sys.argv[1:20]:
m = re.search(r'(?<=-)\w+', tok)
if ( m ):
i += 2
if ('ste' in m.group()): # steps for min
steps = int(sys.argv[i])
elif (m.group() == 'af2'): # AF2 imitate
AF2 = True
i -= 1
elif (m.group() == 'af2w'): # AF2 imitate plus implicit water
AFw = True
i -= 1
elif (m.group() == 'rtt'): # RTT method (more freedom)
RTT = True
i -= 1
elif (m.group() == 'cif'): # write in PDBx (CIF)
mmCIF = True
i -= 1
elif ('rep' in m.group()): # report on minimiztion steps
Reporting = True
i -= 1
elif ('gr' in m.group()): # group all files at the end into a single file
Grouping = True
Groupfname = sys.argv[i]
elif ('tol' in m.group()): # tolerance for min
tolerance = float(sys.argv[i])
elif ('NBm' in m.group() ): # NBmethod -- nonbondedMethod
NBmethod = sys.argv[i]
elif ('NBc' in m.group() ):
NBcut = float(sys.argv[i]) # NBcutoff -- nonbondedCutoff
elif (m.group() == 'inD'):
indirname = sys.argv[i]
elif (m.group() == 'outD'):
outdirname = sys.argv[i]
elif ('res' in m.group()): # restrain atoms (move a little)
atomsrestrained = (sys.argv[i])
elif ('con' in m.group()): # constrain atoms (no move at all)
atomsconstrained = (sys.argv[i])
elif (m.group() == 'kf'):
stiffness = float(sys.argv[i])
elif (m.group() == 'box'):
boxs = float(sys.argv[i])
elif (m.group() == 'Ecut'):
Ecut = float(sys.argv[i])
elif ('lis' in m.group()): # list
with open(sys.argv[i], mode="r") as lg:
for ln in lg.readlines():
files.append(ln.strip().split()[0])
lEp.append(ln.strip().split()[0])
elif ('for' in m.group() or 'ff' in m.group()): # forcefield
if ( sys.argv[i] == 'amber14'):
ffield = 'amber14-all.xml'
Water = False
else:
ffield = 'amber99sb.xml'
Water = False
elif ('wat' in m.group() ): # water
if ( sys.argv[i] == 'amber14'):
Water = True
ffwater = 'amber14/tip3pfb.xml' # tip3 real water
elif ( sys.argv[i] == 'amber99'):
Water = True
ffwater = 'tip3p.xml'
elif ( 'imp' in sys.argv[i] ): # implicit water
Water = False
ffwater = 'implicit/gbn2.xml'
else:
print("Option %s not recognized" % tok)
sys.exit(0)
# ---- Group all models into a single multimodel file
def GroupModels(Groupfname):
OldF = ""
nm = 0
it = 0
Ff = Files_to_group
with open(Groupfname, "w") as OA:
for f in Ff:
with open(f, "r") as IF:
if f != OldF:
nm += 1
OldF = f
OA.write(f"MODEL {nm}\n")
for line in IF:
if line.startswith("ATOM") or line.startswith("REMARK") or line.startswith("TER"):
OA.write(line)
OA.write("ENDMDL\n")
OA.write("END\n")
# ----------------------------------- Define a subclass of Minimization Reporter
class Reporter(MinimizationReporter):
interval = int
energies = [] # array to record progress
def report(self, iteration, x, grad, args):
# -- print current system energy to screen
if ( steps == 0 ):
interval = 50 # report interval
else:
interval = steps/10
if iteration % interval == 0:
print(" %12d %12.4e %12.4e" % (iteration, args['system energy']*toKcalmol, args['restraint energy']))
# -- save energy at each iteration to an array we can use later
self.energies.append(args['system energy'])
# -- The report method must return a bool specifying if minimization should be stopped.
# -- You can use this functionality for early termination.
return False
# -- Create an instance of our reporter
reporter = Reporter()
# ---------------------------------- if AF2 true mimetize all defaults as AF2 relax procedure
if AF2:
Method = 'AF2'
Water = False
ffield = 'amber99sb.xml'
if steps == 99: # adjust steps to 0 if not selected
steps = 100
else:
steps = steps
if ( tolerance == 99.0 ): # adjust tolerance to 2.39 if not selected
tolerance = 2.39 * ENERGY/(LENGTH)
else:
tolerance = tolerance * ENERGY/(LENGTH)
if ( stiffness == 99.0 ): # adjust stiffness, kf, if not selected
stiffness = 10.0 * ENERGY/(LENGTH**2)
else:
stiffness = stiffness * ENERGY/(LENGTH**2)
if Ecut == 1.0e99 : # adjust Ecutoff if not selected
Ecut = 0.0
else:
Ecut = Ecut
if ( atomsrestrained == '' ): # adjust restrained atoms
atomsrestrained = ('heavy')
if ( atomsconstrained != '' ):
atomsrestrained = ''
constraints = 'HBonds'
integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
NBmethod = 'NoCutoff'
NBcut = 999
elif AFw: # -- AF2 plus implicit water, unlim steps, choice of tolerance, etc
Method = 'AF2w'
Water = False
ffield = 'amber99sb.xml'
ffwater = 'implicit/gbn2.xml'
if steps == 99: # adjust steps to 0 if not selected
steps = 100
else:
steps = steps
if ( tolerance == 99.0 ): # adjust tolerance to 2.39 if not selected
tolerance = 2.39 * ENERGY/(LENGTH)
else:
tolerance = tolerance * ENERGY/(LENGTH)
if ( stiffness == 99.0 ): # adjust stiffness, kf, if not selected
stiffness = 10.0 * ENERGY/(LENGTH**2)
else:
stiffness = stiffness * ENERGY/(LENGTH**2)
if Ecut == 1.0e99 : # adjust Ecutoff if not selected
Ecut = 0.0
else:
Ecut = Ecut
if ( atomsrestrained == '' ): # adjust restrained atoms
atomsrestrained = ('heavy')
if ( atomsconstrained != '' ):
atomsrestrained = ''
constraints = 'HBonds'
integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
NBmethod = 'NoCutoff'
NBcut = 999
elif RTT: # -- RTT method
Method = 'RTT'
Water = False
if steps == 99: # adjust steps to 0 if not selected
steps = 0
else:
steps = steps
if ( tolerance == 99.0 ): # adjust tolerance to 2.39 if not selected
tolerance = 1.0 * ENERGY/(LENGTH)
else:
tolerance = tolerance * ENERGY/(LENGTH)
if ( stiffness == 99.0 ): # adjust stiffness, kf, if not selected
stiffness = 5.0 * ENERGY/(LENGTH**2)
else:
stiffness = stiffness * ENERGY/(LENGTH**2)
if Ecut == 1.0e99 : # adjust Ecutoff if not selected
Ecut = 0.0
else:
Ecut = Ecut
if ( atomsrestrained == '' ): # adjust restrained atoms
atomsrestrained = 'backbone'
if ( atomsconstrained != '' ):
atomsrestrained = ''
if ( ffield == '' ): # adjust force field
ffield = 'amber99sb.xml'
constraints = 'HBonds'
integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
NBmethod = 'NoCutoff'
NBcut = 99
else: # -- everything else, we call it Custom
Method = 'Custom'
Water = False
if steps == 99: # adjust steps to 0 if not selected
steps = 0
else:
steps = steps
if ( tolerance == 99.0 ): # adjust tolerance to 2.39 if not selected
tolerance = 1.0 * ENERGY/(LENGTH)
else:
tolerance = tolerance * ENERGY/(LENGTH)
if ( stiffness == 99.0 ): # adjust stiffness, kf, if not selected
stiffness = 5.0 * ENERGY/(LENGTH**2)
else:
stiffness = stiffness * ENERGY/(LENGTH**2)
if Ecut == 1.0e99 : # adjust Ecutoff if not selected
Ecut = 0.0
else:
Ecut = Ecut
# No atoms restrained nor constrained by default
if ( ffield == '' ): # adjust force field
ffield = 'amber99sb.xml'
if ( NBmethod == '' ):
NBmethod = 'NoCutoff'
NBcut = 99
# ------------------------------------ final selection of nonbonded based of NBmethod
if ( NBmethod == 'NoCutoff' ):
nonbondedMethod = NoCutoff
elif ( NBmethod == 'CutoffPeriodic' ):
nonbondedMethod = CutoffPeriodic
elif ( NBmethod == 'CutoffNonPeriodic'):
nonbondedMethod = CutoffNonPeriodic
elif ( NBmethod == 'PME' ):
nonbondedMethod = PME
elif ( NBmethod == 'Ewald' ):
nonbondedMethod = Ewald
else:
print(" **err* NBmethod:", NBmethod, " not available")
sys.exit(-1)
nonbondedCutoff = NBcut * LENGTH
# ------------------------------------ check whether directory already exists
# -- for outdir
if ( outdirname != './' ):
currdir = os.getcwd()
if not os.path.exists(currdir + '/' + outdirname):
os.mkdir(currdir + '/' + outdirname)
print("Folder %s created!" % (currdir + '/' + outdirname) )
else:
print("Folder %s already exists" % (currdir + '/' + outdirname))
print("Pick another name, please")
sys.exit(0)
# --- some header summarizing options being used
#print("\n ** OpenMM minimize: %d steps, tolerance %5.2f" % (steps,tolerance._value) )
print("\n **", sys.argv)
print(" ** OpenMM minimize: ")
print(" Method: %s" % Method )
if steps > 0 :
print(" Steps: %d" % steps )
else:
print(" Steps: %d" % steps,"(Unlimited)" )
print(" Tolerance: %.2f" % tolerance._value)
print(" ForceField: %-20s %-10s" % (ffield, ffwater))
if ( atomsrestrained != '' ):
print(" Atoms restrained: %-20s Kf(stiffness): %s" % (atomsrestrained, stiffness))
if ( atomsconstrained != '' ):
print(" Atoms constrained: %-20s" % (atomsconstrained))
if ( NBmethod == 'NoCutoff' ) :
print(" Nonbonded: %-20s" % nonbondedMethod)
else:
print(" Nonbonded: %-20s" % nonbondedMethod, " Cut-off:", nonbondedCutoff)
print(" E cutoff: %6.1e \n" % Ecut)
# ------------------------------------ cleaning of models with pdbfixer and then minimize it
if ( files == []):
files = sys.argv[i+1:]
startTime0 = float(time.time())
for f in files:
f = indirname + '/' + f
startTime = float(time.time())
# ---------- preparing cosmetic file name removing dir ----------
try:
idx = f.rindex('/')
myp = f[0:idx+1]
except:
myp = ""
name = f.removeprefix(myp)
name = name.removesuffix('.pdb')
name = name.removesuffix('_new') # remove final _new if present
name = name.removeprefix('relaxed_')
name = name.removeprefix('unrelaxed_')
# ------ fix structure with PDBfixer, add atoms as needed --------
fixer = PDBFixer(filename=f)
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.removeHeterogens(False) # removes all HETATMs
fixer.findMissingAtoms() # Finds ay missing heavy atom
fixer.addMissingAtoms() # will add heavy atoms for the missing residues
fixer.addMissingHydrogens(7.0) # will add hydrogens. pH = 7.0
# ----------- add cubic box of water if requested -----------------
if ( Water ):
maxSize = max(max((pos[i] for pos in fixer.positions))-
min((pos[i] for pos in fixer.positions)) for i in range(3))
boxSize = maxSize*Vec3(boxs, boxs, boxs)
fixer.addSolvent(boxSize)
# --------------------------------------------------- from PDB or mmCIF
if mmCIF:
fixed = outdirname+"/fixed_"+name+'.cif' # output file for fixed coords
outfile = outdirname+"/min_"+name+'.cif' # output file for minimized coords
else:
if AF2:
fixed = outdirname+"/fixed_"+name+'_af2.pdb' # output file for fixed coords
outfile = outdirname+"/min_"+name+'_af2.pdb' # output file for minimized coords
elif RTT:
fixed = outdirname+"/fixed_"+name+'_rtt.pdb' # output file for fixed coords
outfile = outdirname+"/min_"+name+'_rtt.pdb' # output file for minimized coords
else:
fixed = outdirname+"/fixed_"+name+'.pdb' # output file for fixed coords
outfile = outdirname+"/min_"+name+'.pdb' # output file for minimized coords
# ---------------------------------------------------
PDBFile.writeFile(fixer.topology, fixer.positions, open(fixed, 'w'))
pdb = PDBFile(fixed)
# ---------- adjust force field for explcit water if requested ----
if ( Water ) :
forcefield = ForceField(ffield,ffwater)
else:
forcefield = ForceField(ffield)
# ---------- Creation of the system based on coords from fixed PDB
modeller = Modeller(pdb.topology, pdb.positions)
#modeller.addHydrogens(forcefield,pH=7.0)
system = forcefield.createSystem(modeller.topology,
nonbondedMethod=nonbondedMethod,
nonbondedCutoff=nonbondedCutoff,
constraints=constraints)
print(" ---- File: %s \t (out: %s)" % (name, outfile))
totalparticles = system.getNumParticles()
# ----------- Restrain atoms in place if requested --------------------
restrainedparticles = 0
if ( atomsrestrained != '' ):
# -- for periodic boundadry conditions
force = CustomExternalForce("0.5 * k * ((x-x0)^2+(y-y0)^2+(z-z0)^2)")
force.addGlobalParameter("k", stiffness)
system.addForce(force)
for p in ["x0", "y0", "z0"]:
force.addPerParticleParameter(p)
for atom in pdb.topology.atoms():
if atomsrestrained == 'heavy':
if (atom.element.name != 'hydrogen'):
force.addParticle(atom.index, pdb.positions[atom.index])
restrainedparticles += 1
elif atomsrestrained in ('backbone','bb') :
if (atom.name == 'N') or (atom.name == 'CA') or (atom.name == 'C'):
force.addParticle(atom.index, pdb.positions[atom.index])
restrainedparticles += 1
else:
if atom.name.casefold() in (atomsrestrained.casefold()):
force.addParticle(atom.index, pdb.positions[atom.index])
restrainedparticles += 1
print(" Restrained: %s (%d/%d particles) k: %.2f %s" %
(atomsrestrained,restrainedparticles,totalparticles,stiffness._value, stiffness.unit))
# ---------- Constrain atoms to original position (no move) ------------
constrainedparticles = 0
if ( atomsconstrained != '' ):
for atom in pdb.topology.atoms():
if atomsconstrained == 'heavy':
if (atom.element.name != 'hydrogen'):
system.setParticleMass(atom.index, 0)
constrainedparticles += 1
elif atomsconstrained in ('backbone','bb') :
if (atom.name == 'N') or (atom.name == 'CA') or (atom.name == 'C'):
system.setParticleMass(atom.index, 0)
constrainedparticles += 1
else:
if atom.name.casefold() in (atomsconstrained.casefold()):
system.setParticleMass(atom.index, 0)
constrainedparticles += 1
print(" Constrained: %s (%d/%d particles) " %
(atomsconstrained,constrainedparticles, totalparticles))
# for later getting the forces
for i, frc in enumerate(system.getForces()):
frc.setForceGroup(i)
# -------- Build simulation context and minimize --------------------
if ( AF2 ): # make sure if AF2 mimic use the LangevinIntegrator
integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
else:
integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
# --- intial state
simulation = Simulation(modeller.topology, system, integrator)
simulation.context.setPositions(modeller.positions)
state = simulation.context.getState(getEnergy=True, getPositions=True)
Eti = state.getPotentialEnergy()
posini = state.getPositions(asNumpy=True).value_in_unit(LENGTH)
# ---- Minimize and report steps/Ep if requested
if Reporting:
print(" Iter Epotential Erestraint")
print(" ------ ---------- ----------")
simulation.minimizeEnergy(maxIterations=steps, tolerance=tolerance, reporter=reporter)
print(" ----------------------------------")
else:
simulation.minimizeEnergy(maxIterations=steps, tolerance=tolerance)
# --- final (minimized) state
state = simulation.context.getState(getEnergy=True, getPositions=True)
Etf = state.getPotentialEnergy()
positions = state.getPositions()
posmin = state.getPositions(asNumpy=True).value_in_unit(LENGTH)
# ---- evaluate RMSD for heavy
iat = 0
itot = 0
diffsqr = 0.0 ;
for atom in pdb.topology.atoms():
if (atom.element.name == 'hydrogen'): # avoid H's always
iat += 1
else:
for j in range(3):
diffsqr += (posini[iat][j] - posmin[iat][j])**2
itot += 1
iat += 1
rmsd = math.sqrt(diffsqr/itot)
# ---- as numpy thing, taking all atoms
rmsd_all = np.sqrt(np.sum((posini - posmin)**2) / posini.shape[0])
# ---- write down minimized file with Epot stored in REMARK record if
# the selected energy (Etf or Enb) is lower than cutoff (Ecut)
# ---- Getting Enb (nombonded term)
for i, frc in enumerate(system.getForces()):
state = simulation.context.getState(getEnergy=True, groups={i})
if frc.getName() in 'NonbondedForce' :
Enb = state.getPotentialEnergy()._value
# -- write CIF and/or PDB formats if model gets accepted
Epot = f'{Etf._value:10.2f} J/mol'
with open(outfile, mode="w") as file:
if mmCIF :
if Enb < Ecut :
PDBxFile.writeFile(simulation.topology, positions, file)
else:
os.remove(outfile)
else :
if Enb < Ecut :
if AF2:
file.write("REMARK File: " + "min_"+name+"_af2" + " Epot: " + Epot + "\n")
elif RTT:
file.write("REMARK File: " + "min_"+name+"_rtt" + " Epot: " + Epot + "\n")
else:
file.write("REMARK File: " + "min_"+name+ " Epot: " + Epot + "\n")
PDBFile.writeFile(simulation.topology, positions, file)
Files_to_group.append(outfile)
else:
os.remove(outfile)
# -------- output summary info ------------------
print(" Epot: %12.4e kcal/mole elapsed t: %12.4e s " %
(Etf._value*toKcalmol, float(time.time())-startTime))
# get report on current forces
print("\n -- Sumary of forces")
for i, frc in enumerate(system.getForces()):
state = simulation.context.getState(getEnergy=True, groups={i})
print(" %s \t %12.4e kcal/mol" % (frc.getName(), state.getPotentialEnergy()._value*toKcalmol))
print(" rmsd: %.3f (%d atoms)" % (rmsd,itot) )
print(" rmsd: %.3f (%d atoms)" % (rmsd_all,posini.shape[0]) )
print(" ")
# -------- remove intermediate fix PDB files (unrelaxed) ---
os.remove(fixed)
# -------- group good mini models into a single file if requested
if Grouping:
GroupModels(Groupfname)
print("\n Total time: ", str(datetime.timedelta(seconds=round(time.time()-startTime0))))
print('Done')