def main(filename, ExpNMR, nfiles):
print "=========================="
print "PyDP4 script,\nintegrating Tinker/MacroModel,"
print "Gaussian/NWChem/Jaguar and DP4\nv0.7"
print "\nCopyright (c) 2015-2018 Kristaps Ermanis, Jonathan M. Goodman"
print "Distributed under MIT license"
print "==========================\n\n"
if nfiles < settings.NTaut or nfiles % settings.NTaut != 0:
print "Invalid number of tautomers/input files - number of input files\
must be a multiple of number of tautomers"
quit()
SetTMSConstants()
#Check the number of input files, generate some if necessary
if nfiles == 1:
import InchiGen
if len(settings.SelectedStereocentres) > 0:
numDS, inpfiles = InchiGen.GenSelectDiastereomers(
filename, settings.SelectedStereocentres)
else:
numDS, inpfiles = InchiGen.GenDiastereomers(filename)
if settings.GenTaut:
newinpfiles = []
for ds in inpfiles:
print "Generating tautomers for " + ds
settings.NTaut, files = InchiGen.GenTautomers(ds)
newinpfiles.extend(files)
inpfiles = list(newinpfiles)
if settings.GenProt:
newinpfiles = []
for ds in inpfiles:
print "Generating protomers for " + ds
settings.NTaut, files = InchiGen.GenProtomers(
ds, settings.BasicAtoms)
newinpfiles.extend(files)
inpfiles = list(newinpfiles)
else:
inpfiles = filename
if settings.GenTaut:
numDS = nfiles
import InchiGen
newinpfiles = []
for ds in inpfiles:
print "Generating tautomers for " + ds
settings.NTaut, files = InchiGen.GenTautomers(ds)
newinpfiles.extend(files)
inpfiles = list(newinpfiles)
else:
numDS = int(nfiles / settings.NTaut)
if numDS == 1:
import InchiGen
for f in filename:
tdiastereomers = []
numDS, tinpfiles = InchiGen.GenDiastereomers(f)
tdiastereomers.append(tinpfiles)
tinpfiles = zip(*tdiastereomers)
inpfiles = []
for ds in tinpfiles:
inpfiles.extend(list(ds))
print inpfiles
#Check the existence of mm output files
MMRun = False
if settings.MMTinker:
#Check if there already are Tinker output files with the right names
tinkfiles = glob.glob('*.tout')
mminpfiles = []
for f in inpfiles:
if f + '.tout' in tinkfiles and (f + 'rot.tout' in tinkfiles
or settings.Rot5Cycle is False):
if len(mminpfiles) == 0:
MMRun = True
else:
MMRun = False
mminpfiles.append(f)
else:
#Check if there already are MacroModel output files with the right names
mmfiles = glob.glob('*.log')
mminpfiles = []
for f in inpfiles:
if f + '.log' in mmfiles and (f + 'rot.log' in mmfiles
or settings.Rot5Cycle is False):
if len(mminpfiles) == 0:
MMRun = True
else:
MMRun = False
mminpfiles.append(f)
if MMRun or settings.AssumeDone or settings.UseExistingInputs:
print 'Conformation search has already been run for these inputs.\
\nSkipping...'
if settings.GenOnly:
print "Input files generated, quitting..."
quit()
else:
if settings.MMTinker:
print 'Some Tinker files missing.'
print '\nSeting up Tinker files...'
Tinker.SetupTinker(len(inpfiles), settings, *mminpfiles)
if settings.GenOnly:
print "Input files generated, quitting..."
quit()
print '\nRunning Tinker...'
Tinker.RunTinker(len(inpfiles), settings, *mminpfiles)
else:
print 'Some Macromodel files missing.'
print '\nSetting up Macromodel files...'
MacroModel.SetupMacromodel(len(inpfiles), settings, *mminpfiles)
if settings.GenOnly:
print "Input files generated, quitting..."
quit()
print '\nRunning Macromodel...'
MacroModel.RunMacromodel(len(inpfiles), settings, *mminpfiles)
if settings.OnlyConfS:
print "Conformational search completed, quitting as instructed."
quit()
if (not settings.AssumeDone) and (not settings.UseExistingInputs):
if settings.ConfPrune and not settings.Cluster:
if settings.DFT == 'z' or settings.DFT == 'g' or settings.DFT == 'd':
adjRMSDcutoff = Gaussian.AdaptiveRMSD(inpfiles[0], settings)
elif settings.DFT == 'n' or settings.DFT == 'w' or settings.DFT == 'm':
adjRMSDcutoff = NWChem.AdaptiveRMSD(inpfiles[0], settings)
elif settings.DFT == 'j':
adjRMSDcutoff = Jaguar.AdaptiveRMSD(inpfiles[0], settings)
print 'RMSD cutoff adjusted to ' + str(adjRMSDcutoff)
else:
adjRMSDcutoff = settings.InitialRMSDcutoff
#Run DFT setup script for every diastereomer
print '\nRunning DFT setup...'
i = 1
for ds in inpfiles:
if settings.DFT == 'z' or settings.DFT == 'g' or settings.DFT == 'd':
print "\nGaussian setup for file " + ds + " (" + str(i) +\
" of " + str(len(inpfiles)) + ")"
if settings.Cluster == False:
Gaussian.SetupGaussian(ds, ds + 'ginp', 3, settings,
adjRMSDcutoff)
else:
Gaussian.SetupGaussianCluster(ds, ds + 'ginp', 3, settings)
elif settings.DFT == 'n' or settings.DFT == 'w' or settings.DFT == 'm':
print "\nNWChem setup for file " + ds +\
" (" + str(i) + " of " + str(len(inpfiles)) + ")"
NWChem.SetupNWChem(ds, ds + 'nwinp', 3, settings,
adjRMSDcutoff)
elif settings.DFT == 'j':
print "\nJaguar setup for file " + ds +\
" (" + str(i) + " of " + str(len(inpfiles)) + ")"
Jaguar.SetupJaguar(ds, ds + 'jinp', 3, settings, adjRMSDcutoff)
i += 1
QRun = False
elif settings.AssumeDone:
QRun = True
else:
QRun = False
if settings.DFT == 'z' or settings.DFT == 'g' or settings.DFT == 'd':
Files2Run = Gaussian.GetFiles2Run(inpfiles, settings)
elif settings.DFT == 'n' or settings.DFT == 'w' or settings.DFT == 'm':
Files2Run = NWChem.GetFiles2Run(inpfiles, settings)
elif settings.DFT == 'j':
Files2Run = Jaguar.GetFiles2Run(inpfiles, settings)
print Files2Run
if len(Files2Run) == 0:
if (settings.DFT == 'z' or settings.DFT == 'g' or settings.DFT == 'd') and\
(settings.DFTOpt or settings.PM6Opt or settings.HFOpt or settings.M06Opt)\
and not settings.AssumeDone:
print "Checking if all geometries have converged"
Ngeoms, Nunconverged, unconverged = Gaussian.CheckConvergence(
inpfiles)
if Nunconverged > 0:
print "WARNING: Not all geometries have achieved convergence!"
print ','.join([x[:-8] for x in unconverged])
print "Number of geometries: " + str(Ngeoms)
print "Unconverged: " + str(Nunconverged)
Gaussian.ResubGeOpt(unconverged, settings)
Files2Run = Gaussian.GetFiles2Run(inpfiles, settings)
QRun = False
else:
QRun = True
else:
QRun = True
#QRun = True
if len(Files2Run) > settings.HardConfLimit:
print "Hard conformation count limit exceeded, DFT calculations aborted."
quit()
if QRun:
print 'DFT has already been run for these inputs. Skipping...'
else:
if settings.DFT == 'g':
print '\nRunning Gaussian locally...'
Gaussian.RunLocally(Files2Run, settings)
elif settings.DFT == 'z':
print '\nRunning Gaussian on Ziggy...'
#Run Gaussian jobs on Ziggy cluster in folder named after date
#and time in the short 1processor job queue
#and wait until the last file is completed
MaxCon = settings.MaxConcurrentJobs
if settings.DFTOpt or settings.PM6Opt or settings.HFOpt or settings.M06Opt:
for i in range(len(Files2Run)):
Files2Run[i] = Files2Run[i][:-5] + '.com'
if len(Files2Run) < MaxCon:
Gaussian.RunOnZiggy(0, settings.queue, Files2Run, settings)
else:
print "The DFT calculations will be done in " +\
str(math.ceil(len(Files2Run)/MaxCon)) + " batches"
i = 0
while (i + 1) * MaxCon < len(Files2Run):
print "Starting batch nr " + str(i + 1)
Gaussian.RunOnZiggy(
str(i + 1), settings.queue,
Files2Run[(i * MaxCon):((i + 1) * MaxCon)], settings)
i += 1
print "Starting batch nr " + str(i + 1)
Gaussian.RunOnZiggy(str(i + 1), settings.queue,
Files2Run[(i * MaxCon):], settings)
elif settings.DFT == 'd':
print '\nRunning Gaussian on Darwin...'
#Run Gaussian jobs on Darwin cluster in folder named after date
#and title and wait until the last file is completed
MaxCon = settings.MaxConcurrentJobsDarwin
if settings.DFTOpt or settings.PM6Opt or settings.HFOpt or settings.M06Opt:
for i in range(len(Files2Run)):
Files2Run[i] = Files2Run[i][:-5] + '.com'
if len(Files2Run) < MaxCon:
Gaussian.RunOnDarwin(0, Files2Run, settings)
else:
print "The DFT calculations will be done in " +\
str(math.ceil(len(Files2Run)/MaxCon)) + " batches"
i = 0
while (i + 1) * MaxCon < len(Files2Run):
print "Starting batch nr " + str(i + 1)
Gaussian.RunOnDarwin(
str(i + 1), Files2Run[(i * MaxCon):((i + 1) * MaxCon)],
settings)
i += 1
print "Starting batch nr " + str(i + 1)
Gaussian.RunOnDarwin(str(i + 1), Files2Run[(i * MaxCon):],
settings)
elif settings.DFT == 'n':
print '\nRunning NWChem locally...'
NWChem.RunNWChem(Files2Run, settings)
elif settings.DFT == 'w':
print '\nRunning NWChem on Ziggy...'
#Run NWChem jobs on Ziggy cluster in folder named after date
#and time in the short 1 processor job queue
#and wait until the last file is completed
now = datetime.datetime.now()
MaxCon = settings.MaxConcurrentJobs
if len(Files2Run) < MaxCon:
NWChem.RunOnZiggy(now.strftime('%d%b%H%M'), settings.queue,
Files2Run, settings)
else:
print "The DFT calculations will be done in " +\
str(math.ceil(len(Files2Run)/MaxCon)) + " batches"
i = 0
while (i + 1) * MaxCon < len(Files2Run):
print "Starting batch nr " + str(i + 1)
NWChem.RunOnZiggy(
now.strftime('%d%b%H%M') + str(i + 1), settings.queue,
Files2Run[(i * MaxCon):((i + 1) * MaxCon)], settings)
i += 1
print "Starting batch nr " + str(i + 1)
NWChem.RunOnZiggy(
now.strftime('%d%b%H%M') + str(i + 1), settings.queue,
Files2Run[(i * MaxCon):], settings)
elif settings.DFT == 'm':
print '\nRunning NWChem on Medivir cluster...'
#Run NWChem jobs on Medivir cluster
MaxCon = settings.MaxConcurrentJobs
if len(Files2Run) < MaxCon:
NWChem.RunOnMedivir(Files2Run, settings)
else:
print "The DFT calculations will be done in " +\
str(math.ceil(len(Files2Run)/MaxCon)) + " batches"
i = 0
while (i + 1) * MaxCon < len(Files2Run):
print "Starting batch nr " + str(i + 1)
NWChem.RunOnMedivir(
Files2Run[(i * MaxCon):((i + 1) * MaxCon)], settings)
i += 1
print "Starting batch nr " + str(i + 1)
NWChem.RunOnMedivir(Files2Run[(i * MaxCon):], settings)
elif settings.DFT == 'j':
print '\nRunning Jaguar locally...'
Jaguar.RunJaguar(Files2Run, settings)
if numDS < 2:
print "DP4 requires at least 2 candidate structures!"
else:
allargs = []
for i in range(numDS):
allargs.append(settings.NTaut)
allargs.extend(inpfiles[i * settings.NTaut:(i + 1) *
settings.NTaut])
allargs.append(ExpNMR)
DP4outp = NMRAnalysis.main(numDS, settings, *allargs)
print '\nWriting the DP4 output to DP4outp'
DP4_ofile = open(allargs[-1] + '.dp4', 'w')
DP4_ofile.write(DP4outp)
DP4_ofile.close()
print 'DP4 process completed successfully.'
def main(settings):
print("Current working directory: " + os.getcwd())
print("Initial input files: " + str(settings.InputFiles))
print("NMR file: " + str(settings.NMRsource))
print("Workflow: " + str(settings.Workflow))
# Read in any text inputs and add these to the input file list
import StructureInput
if settings.Smiles:
settings.InputFiles.extend(
StructureInput.GenerateSDFFromTxt(settings.Smiles, 'Smiles'))
if settings.Smarts:
settings.InputFiles.extend(
StructureInput.GenerateSDFFromTxt(settings.Smarts, 'Smarts'))
if settings.InChIs:
settings.InputFiles.extend(
StructureInput.GenerateSDFFromTxt(settings.InChIs, 'InChI'))
# Clean up input files if c in workflow - this generates a new set of 3d coordinates as a starting point
if 'c' in settings.Workflow and len(settings.InputFiles) > 0:
import StructureInput
# if requested generate 3d coordinates to define any stereochemistry
settings.InputFiles = StructureInput.CleanUp(settings.InputFiles)
# if no structure inputs have been found at this point quit
if len(settings.InputFiles) == 0:
print(
"\nNo input files were found please use -h for help with input options quitting..."
)
quit()
# if g in workflow check number of stereocentres for each input and generate and diastereomers
if ('g' in settings.Workflow):
import InchiGen
print("\nGenerating diastereomers...")
FinalInputFiles = []
nStereo = [
StructureInput.NumberofStereoCentres(InpFile)
for InpFile in settings.InputFiles
]
if len(settings.InputFiles) == 1:
FinalInputFiles.extend(
InchiGen.GenDiastereomers(settings.InputFiles[0], nStereo[0],
settings.SelectedStereocentres))
else:
for InpFile, nStereoCentres in zip(settings.InputFiles, nStereo):
FinalInputFiles.extend(
InchiGen.GenDiastereomers(InpFile, nStereoCentres, []))
settings.InputFiles = list(FinalInputFiles)
print("Generated input files: " + str(settings.InputFiles) + '\n')
# Create isomer data structures
Isomers = [Isomer(f.split('.sdf')[0]) for f in settings.InputFiles]
print("Assuming all computations are done? ... ", settings.AssumeDone)
print("Using preexisting DFT data? ... ", settings.UseExistingInputs)
# Run conformational search, if requested
if ('m' in settings.Workflow) and not (settings.AssumeDone
or settings.UseExistingInputs):
print("Performing conformational search using ", end="")
if settings.MM == 't':
print("Tinker")
print('\nSetting up Tinker files...')
TinkerInputs = Tinker.SetupTinker(settings)
print('\nRunning Tinker...')
TinkerOutputs = Tinker.RunTinker(TinkerInputs, settings)
Isomers = Tinker.ReadConformers(TinkerOutputs, Isomers, settings)
elif settings.MM == 'm':
print("MacroModel")
print('\nSetting up MacroModel files...')
MacroModelInputs = MacroModel.SetupMacroModel(settings)
print("MacroModel inputs: " + str(MacroModelInputs))
print('Running MacroModel...')
MacroModelOutputs = MacroModel.RunMacroModel(
MacroModelInputs, settings)
print('\nReading conformers...')
Isomers = MacroModel.ReadConformers(MacroModelOutputs, Isomers,
settings)
print('Energy window: ' + str(settings.MaxCutoffEnergy) +
' kJ/mol')
for iso in Isomers:
print(iso.InputFile + ": " + str(len(iso.Conformers)) +
' conformers read within energy window')
else:
print('No conformational search was requested. Skipping...')
settings.ConfPrune = False
# Prune conformations, if requested.
# For each isomer, the conformers list is replaced with a smaller list of conformers
if (settings.ConfPrune) and not (settings.AssumeDone
or settings.UseExistingInputs):
print('\nPruning conformers...')
Isomers = ConfPrune.RMSDPrune(Isomers, settings)
for iso in Isomers:
print(iso.InputFile + ": " + str(len(iso.Conformers)) +
' conformers after pruning with ' + str(iso.RMSDCutoff) +
'A RMSD cutoff')
if ('n' in settings.Workflow) or ('o' in settings.Workflow) \
or ('e' in settings.Workflow) or settings.AssumeDone:
DFT = ImportDFT(settings.DFT)
else:
print('\nNo DFT calculations were requested. Skipping...')
if not (settings.AssumeDone):
# Run DFT optimizations, if requested
if ('o' in settings.Workflow):
now = datetime.datetime.now()
settings.StartTime = now.strftime('%d%b%H%M')
print('\nSetting up geometry optimization calculations...')
Isomers = DFT.SetupOptCalcs(Isomers, settings)
print('\nRunning geometry optimization calculations...')
Isomers = DFT.RunOptCalcs(Isomers, settings)
print('\nReading DFT optimized geometries...')
Isomers = DFT.ReadGeometries(Isomers, settings)
# Add convergence check here before continuing with calcs!
if (DFT.Converged(Isomers) == False) and (settings.AssumeConverged
== False):
print('Some of the conformers did not converge, quitting...')
quit()
# Run DFT single-point energy calculations, if requested
if ('e' in settings.Workflow):
now = datetime.datetime.now()
settings.StartTime = now.strftime('%d%b%H%M')
print('\nSetting up energy calculations...')
Isomers = DFT.SetupECalcs(Isomers, settings)
print('\nRunning energy calculations...')
Isomers = DFT.RunECalcs(Isomers, settings)
print('\nReading data from the output files...')
Isomers = DFT.ReadEnergies(Isomers, settings)
print("Energies: ")
for iso in Isomers:
print(iso.InputFile + ": " + str(iso.DFTEnergies))
# Run DFT NMR calculations, if requested
if ('n' in settings.Workflow):
now = datetime.datetime.now()
settings.StartTime = now.strftime('%d%b%H%M')
print('\nSetting up NMR calculations...')
Isomers = DFT.SetupNMRCalcs(Isomers, settings)
print('\nRunning NMR calculations...')
Isomers = DFT.RunNMRCalcs(Isomers, settings)
print('\nReading data from the output files...')
Isomers = DFT.ReadShieldings(Isomers)
print("Shieldings: ")
for iso in Isomers:
print(iso.InputFile + ": ")
for conf in iso.ConformerShieldings:
print(str(conf))
Isomers = DFT.ReadEnergies(Isomers, settings)
print("Energies: ")
for iso in Isomers:
print(iso.InputFile + ": " + str(iso.DFTEnergies))
else:
# Read DFT optimized geometries, if requested
if ('o' in settings.Workflow):
Isomers = DFT.GetPrerunOptCalcs(Isomers)
if ('e' in settings.Workflow):
Isomers = DFT.GetPrerunECalcs(Isomers)
if ('n' in settings.Workflow):
Isomers = DFT.GetPrerunNMRCalcs(Isomers)
Isomers = DFT.ReadGeometries(Isomers, settings)
# Read DFT NMR data, if requested
if ('n' in settings.Workflow):
Isomers = DFT.ReadShieldings(Isomers)
Isomers = DFT.ReadEnergies(Isomers, settings)
if not (NMR.NMRDataValid(Isomers)) or ('n' not in settings.Workflow):
print('\nNo NMR data calculated, quitting...')
quit()
if ('s' in settings.Workflow) or ('a' in settings.Workflow):
print('\nSetting TMS computational NMR shielding constant references')
settings.TMS_SC_C13, settings.TMS_SC_H1 = NMR.GetTMSConstants(settings)
print('\nConverting DFT data to NMR shifts...')
Isomers = NMR.CalcBoltzmannWeightedShieldings(Isomers)
Isomers = NMR.CalcNMRShifts(Isomers, settings)
print('\nReading experimental NMR data...')
NMRData = NMR.NMRData(settings)
"""
print("Conformation data:")
NMR.PrintConformationData(Isomers)
"""
if NMRData.Type == 'desc':
print('Experimental NMR description found and read.')
# performs a pairwise assignment
Isomers = NMR.PairwiseAssignment(Isomers, NMRData)
print('Cshifts: ' + str(NMRData.Cshifts))
print('Hshifts: ' + str(NMRData.Hshifts))
print('Equivalents: ' + str(NMRData.Equivalents))
print('Omits: ' + str(NMRData.Omits))
elif NMRData.Type == "fid":
for f in settings.NMRsource:
if f.name == "Proton" or f.name == "proton":
from Proton_assignment import AssignProton
from Proton_plotting import PlotProton
print('\nAssigning proton spectrum...')
Isomers = AssignProton(NMRData, Isomers, settings)
if settings.GUIRunning == False:
print('\nPlotting proton spectrum...')
PlotProton(NMRData, Isomers, settings)
elif f.name == "Carbon" or f.name == "carbon":
from Carbon_assignment import AssignCarbon
from Carbon_plotting import PlotCarbon
print('\nAssigning carbon spectrum...')
Isomers = AssignCarbon(NMRData, Isomers, settings)
if settings.GUIRunning == False:
print('\nPlotting carbon spectrum...')
PlotCarbon(NMRData, Isomers, settings)
elif NMRData.Type == "jcamp":
for f in settings.NMRsource:
if f.name == "Proton.dx" or f.name == "proton.dx":
from Proton_assignment import AssignProton
from Proton_plotting import PlotProton
print('\nAssigning proton spectrum...')
Isomers = AssignProton(NMRData, Isomers, settings)
if settings.GUIRunning == False:
print('\nPlotting proton spectrum...')
PlotProton(NMRData, Isomers, settings)
elif f.name == "Carbon.dx" or f.name == "carbon.dx":
from Carbon_assignment import AssignCarbon
from Carbon_plotting import PlotCarbon
print('\nAssigning carbon spectrum...')
Isomers = AssignCarbon(NMRData, Isomers, settings)
if settings.GUIRunning == False:
print('\nPlotting carbon spectrum...')
PlotCarbon(NMRData, Isomers, settings)
print('Raw FID NMR datafound and read.')
# print('\nProcessing experimental NMR data...')
# NMRdata = NMR.ProcessNMRData(Isomers, settings.NMRsource, settings)
if 's' in settings.Workflow:
print('\nCalculating DP4 probabilities...')
DP4data = DP4.DP4data()
DP4data = DP4.ProcessIsomers(DP4data, Isomers)
DP4data = DP4.InternalScaling(DP4data)
DP4data = DP4.CalcProbs(DP4data, settings)
DP4data = DP4.CalcDP4(DP4data)
DP4data = DP4.MakeOutput(DP4data, Isomers, settings)
# print(DP4.FormatData(DP4data))
else:
print('\nNo DP4 analysis requested.')
NMRData = []
DP4data = []
print('\nPyDP4 process completed successfully.')
return NMRData, Isomers, settings, DP4data
def main(settings):
print("==========================")
print("PyDP4 script,\nintegrating Tinker/MacroModel,")
print("Gaussian/NWChem and DP4\nv1.0")
print("\nCopyright (c) 2015-2019 Kristaps Ermanis, Alexander Howarth, Jonathan M. Goodman")
print("Distributed under MIT license")
print("==========================\n\n")
print("Initial input files: " + str(settings.InputFiles))
print("NMR file: " + str(settings.NMRsource))
print("Workflow: " + str(settings.Workflow))
# Check the number of input files, generate some if necessary
if ('g' in settings.Workflow) and len(settings.InputFiles) == 1:
import InchiGen
print("\nGenerating diastereomers...")
settings.InputFiles = InchiGen.GenDiastereomers(settings.InputFiles[0], settings.SelectedStereocentres)
print("Generated input files: " + str(settings.InputFiles) + '\n')
# Create isomer data structures
Isomers = [Isomer(f.split('.sdf')[0]) for f in settings.InputFiles]
# Run conformational search, if requested
print("assume",settings.AssumeDone )
print("Use exist",settings.UseExistingInputs)
if ('m' in settings.Workflow) and not (settings.AssumeDone or settings.UseExistingInputs):
print("in")
print(settings.MM)
if settings.MM == 't':
print('\nSetting up Tinker files...')
TinkerInputs = Tinker.SetupTinker(settings)
print('\nRunning Tinker...')
TinkerOutputs = Tinker.RunTinker(TinkerInputs, settings)
Isomers = Tinker.ReadConformers(TinkerOutputs, Isomers, settings)
elif settings.MM == 'm':
print('\nSetting up MacroModel files...')
MacroModelInputs = MacroModel.SetupMacroModel(settings)
print("MacroModel inputs: " + str(MacroModelInputs))
print('Running MacroModel...')
MacroModelOutputs = MacroModel.RunMacroModel(MacroModelInputs, settings)
print('\nReading conformers...')
Isomers = MacroModel.ReadConformers(MacroModelOutputs, Isomers, settings)
print('Energy window: ' + str(settings.MaxCutoffEnergy) + ' kJ/mol')
for iso in Isomers:
print(iso.InputFile + ": "+ str(len(iso.Conformers)) + ' conformers read within energy window' )
else:
print('No conformational search was requested. Skipping...')
settings.ConfPrune = False
# Prune conformations, if requested.
# For each isomer, the conformers list is replaced with a smaller list of conformers
if (settings.ConfPrune) and not(settings.AssumeDone or settings.UseExistingInputs):
print('\nPruning conformers...')
Isomers = ConfPrune.RMSDPrune(Isomers, settings)
for iso in Isomers:
print(iso.InputFile + ": " + str(len(iso.Conformers)) + ' conformers after pruning with ' +
str(iso.RMSDCutoff) + 'A RMSD cutoff')
if ('n' in settings.Workflow) or ('o' in settings.Workflow) \
or ('e' in settings.Workflow) or settings.AssumeDone:
DFT = ImportDFT(settings.DFT)
else:
print('\nNo DFT calculations were requested. Skipping...')
if not(settings.AssumeDone):
# Run DFT optimizations, if requested
if ('o' in settings.Workflow):
now = datetime.datetime.now()
settings.StartTime = now.strftime('%d%b%H%M')
print('\nSetting up geometry optimization calculations...')
Isomers = DFT.SetupOptCalcs(Isomers, settings)
print('\nRunning geometry optimization calculations...')
Isomers = DFT.RunOptCalcs(Isomers, settings)
print('\nReading DFT optimized geometries...')
Isomers = DFT.ReadGeometries(Isomers,settings)
#Add convergence check here before continuing with calcs!
if (DFT.Converged(Isomers) == False) and (settings.AssumeConverged == False):
print('Some of the conformers did not converge, quitting...')
quit()
# Run DFT single-point energy calculations, if requested
if ('e' in settings.Workflow):
now = datetime.datetime.now()
settings.StartTime = now.strftime('%d%b%H%M')
print('\nSetting up energy calculations...')
Isomers = DFT.SetupECalcs(Isomers, settings)
print('\nRunning energy calculations...')
Isomers = DFT.RunECalcs(Isomers, settings)
print('\nReading data from the output files...')
Isomers = DFT.ReadEnergies(Isomers, settings)
print("Energies: ")
for iso in Isomers:
print(iso.InputFile + ": " + str(iso.DFTEnergies))
# Run DFT NMR calculations, if requested
if ('n' in settings.Workflow):
now = datetime.datetime.now()
settings.StartTime = now.strftime('%d%b%H%M')
print('\nSetting up NMR calculations...')
Isomers = DFT.SetupNMRCalcs(Isomers, settings)
print('\nRunning NMR calculations...')
Isomers = DFT.RunNMRCalcs(Isomers, settings)
print('\nReading data from the output files...')
Isomers = DFT.ReadShieldings(Isomers)
print("Shieldings: ")
for iso in Isomers:
print(iso.InputFile + ": ")
for conf in iso.ConformerShieldings:
print(str(conf))
Isomers = DFT.ReadEnergies(Isomers, settings)
print("Energies: ")
for iso in Isomers:
print(iso.InputFile + ": " + str(iso.DFTEnergies))
else:
# Read DFT optimized geometries, if requested
if ('o' in settings.Workflow):
Isomers = DFT.GetPrerunOptCalcs(Isomers)
if ('e' in settings.Workflow):
Isomers = DFT.GetPrerunECalcs(Isomers)
if ('n' in settings.Workflow):
Isomers = DFT.GetPrerunNMRCalcs(Isomers)
Isomers = DFT.ReadGeometries(Isomers, settings)
# Read DFT NMR data, if requested
if ('n' in settings.Workflow):
Isomers = DFT.ReadShieldings(Isomers)
Isomers = DFT.ReadEnergies(Isomers, settings)
if not(NMR.NMRDataValid(Isomers)) or ('n' not in settings.Workflow):
print('\nNo NMR data calculated, quitting...')
quit()
if ('s' in settings.Workflow) or ('a' in settings.Workflow):
print('\nSetting TMS computational NMR shielding constant references')
settings.TMS_SC_C13, settings.TMS_SC_H1 = NMR.GetTMSConstants(settings)
print('\nConverting DFT data to NMR shifts...')
Isomers = NMR.CalcBoltzmannWeightedShieldings(Isomers)
Isomers = NMR.CalcNMRShifts(Isomers, settings)
print('\nReading experimental NMR data...')
NMRData = NMR.NMRData(settings)
"""
print("Conformation data:")
NMR.PrintConformationData(Isomers)
"""
if NMRData.Type == 'desc':
print('Experimental NMR description found and read.')
# performs a pairwise assignment
Isomers = NMR.PairwiseAssignment(Isomers,NMRData)
print('Cshifts: ' + str(NMRData.Cshifts))
print('Hshifts: ' + str(NMRData.Hshifts))
print('Equivalents: ' + str(NMRData.Equivalents))
print('Omits: ' + str(NMRData.Omits))
elif NMRData.Type == "fid":
if os.path.exists(str(settings.NMRsource) + "/Proton"):
from Proton_assignment import AssignProton
from Proton_plotting import PlotProton
print('\nAssigning proton spectrum...')
Isomers = AssignProton(NMRData,Isomers,settings)
print('\nPlotting proton spectrum...')
PlotProton(NMRData, Isomers, settings)
if os.path.exists(str(settings.NMRsource) + "/Carbon"):
from Carbon_assignment import AssignCarbon
from Carbon_plotting import PlotCarbon
print('\nAssigning carbon spectrum...')
Isomers = AssignCarbon(NMRData,Isomers,settings)
print('\nPlotting carbon spectrum...')
PlotCarbon(NMRData, Isomers, settings)
elif NMRData.Type == "jcamp":
if os.path.exists(str(settings.NMRsource) + "/Proton.dx"):
from Proton_assignment import AssignProton
from Proton_plotting import PlotProton
print('\nAssigning proton spectrum...')
Isomers = AssignProton(NMRData, Isomers, settings)
print('\nPlotting proton spectrum...')
PlotProton(NMRData, Isomers, settings)
if os.path.exists(str(settings.NMRsource) + "/Carbon.dx"):
from Carbon_assignment import AssignCarbon
from Carbon_plotting import PlotCarbon
print('\nAssigning carbon spectrum...')
Isomers = AssignCarbon(NMRData, Isomers, settings)
print('\nPlotting carbon spectrum...')
PlotCarbon(NMRData, Isomers, settings)
print('Raw FID NMR datafound and read.')
#print('\nProcessing experimental NMR data...')
#NMRdata = NMR.ProcessNMRData(Isomers, settings.NMRsource, settings)
if 's' in settings.Workflow:
print('\nCalculating DP4 probabilities...')
DP4data = DP4.DP4data()
DP4data = DP4.ProcessIsomers(DP4data,Isomers)
DP4data = DP4.InternalScaling(DP4data)
DP4data = DP4.CalcProbs(DP4data,settings)
DP4data = DP4.CalcDP4(DP4data)
DP4data = DP4.MakeOutput(DP4data,Isomers,settings)
#print(DP4.FormatData(DP4data))
else:
print('\nNo DP4 analysis requested.')
NMRData = []
DP4data = []
print('\nPyDP4 process completed successfully.')
return NMRData, Isomers, settings, DP4data