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