def rungen(rundir,args,chspfname,globs):
try:
from Classes.mWidgets import qBoxFolder
from Classes.mWidgets import mQDialogInf
from Classes.mWidgets import mQDialogErr
except ImportError:
args.gui = False
emsg = False
globs.nosmiles = 0 # reset smiles ligands for each run
# check for specified ligands/functionalization
ligocc = []
# check for files specified for multiple ligands
mligs,catoms = [False],[False]
if args.lig is not None:
if '.smi' in args.lig[0]:
ligfilename = args.lig[0].split('.')[0]
if args.lig:
mligs,catoms,multidx = checkmultilig(args.lig)
if args.debug:
print('after checking for mulitple ligs, we found ' + str(multidx) + ' ligands' )
# save initial
smicat0 = [ss for ss in args.smicat] if args.smicat else False
# loop over ligands
for mcount, mlig in enumerate(mligs):
args.smicat = [ss for ss in smicat0] if smicat0 else False
args.checkdir, skip = False, False # initialize flags
if len(mligs) > 0 and mligs[0]:
args.lig = mlig # get combination
if multidx!=-1:
if catoms[multidx][mcount]:
ssatoms = catoms[multidx][mcount].split(',')
lloc = [int(scat)-1 for scat in ssatoms]
# append connection atoms if specified in smiles
if args.smicat and len(args.smicat) > 0:
for i in range(len(args.smicat),multidx):
args.smicat.append([])
else:
args.smicat = [lloc]
args.smicat[multidx] = lloc
if (args.lig):
ligands = args.lig
if (args.ligocc):
ligocc = args.ligocc
else:
ligocc = ['1']
for i in range(len(ligocc),len(ligands)):
ligocc.append('1')
lig = ''
for i,l in enumerate(ligands):
ligentry,emsg = lig_load(l)
# update ligand
if ligentry:
ligands[i] = ligentry.name
args.lig[i] = ligentry.name
if emsg:
skip = True
break
if ligentry.ident == 'smi':
ligentry.ident += str(globs.nosmiles)
globs.nosmiles += 1
if args.sminame:
if len(args.sminame) > int(ligentry.ident[-1]):
ligentry.ident = args.sminame[globs.nosmiles-1][0:3]
lig += ''.join("%s%s" % (ligentry.ident,ligocc[i]))
else:
ligands =[]
lig = ''
ligocc = ''
##### fetch smart name
fname = name_complex(rundir,args.core,args.geometry,ligands,ligocc,mcount,args,nconf=False,sanity=False,bind=args.bind,bsmi=args.nambsmi)
if args.tsgen:
substrate = args.substrate
subcatoms = ['multiple']
if args.subcatoms:
subcatoms = args.subcatoms
mlig = args.mlig
mligcatoms = args.mligcatoms
fname = name_ts_complex(rundir,args.core,args.geometry,ligands,ligocc,substrate,subcatoms,mlig,mligcatoms,mcount,args,nconf=False,sanity=False,bind=args.bind,bsmi=args.nambsmi)
if globs.debug:
print('fname is ' + str(fname))
rootdir = fname
# check for charges/spin
rootcheck = False
if (chspfname):
rootcheck = rootdir
rootdir = rootdir + '/'+chspfname
if (args.suff):
rootdir += args.suff
# check for mannual overwrite of
# directory name
if args.jobdir:
rootdir = rundir + args.jobdir
# check for top directory
if rootcheck and os.path.isdir(rootcheck) and not args.checkdirt and not skip:
args.checkdirt = True
if not args.rprompt:
flagdir=raw_input('\nDirectory '+rootcheck +' already exists. Keep both (k), replace (r) or skip (s) k/r/s: ')
if 'k' in flagdir.lower():
flagdir = 'keep'
elif 's' in flagdir.lower():
flagdir = 'skip'
else:
flagdir = 'replace'
else:
#qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootcheck+' already exists. What do you want to do?')
#flagdir = qqb.getaction()
flagdir = 'replace'
# replace existing directory
if (flagdir=='replace'):
shutil.rmtree(rootcheck)
os.mkdir(rootcheck)
# skip existing directory
elif flagdir=='skip':
skip = True
# keep both (default)
else:
ifold = 1
while glob.glob(rootdir+'_'+str(ifold)):
ifold += 1
rootcheck += '_'+str(ifold)
os.mkdir(rootcheck)
elif rootcheck and (not os.path.isdir(rootcheck) or not args.checkdirt) and not skip:
if globs.debug:
print('rootcheck is ' + str(rootcheck))
args.checkdirt = True
try:
os.mkdir(rootcheck)
except:
print 'Directory '+rootcheck+' can not be created. Exiting..\n'
return
# check for actual directory
if os.path.isdir(rootdir) and not args.checkdirb and not skip and not args.jobdir:
args.checkdirb = True
if not args.rprompt:
flagdir=raw_input('\nDirectory '+rootdir +' already exists. Keep both (k), replace (r) or skip (s) k/r/s: ')
if 'k' in flagdir.lower():
flagdir = 'keep'
elif 's' in flagdir.lower():
flagdir = 'skip'
else:
flagdir = 'replace'
else:
#qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootdir+' already exists. What do you want to do?')
#flagdir = qqb.getaction()
flagdir = 'replace'
# replace existing directory
if (flagdir=='replace'):
shutil.rmtree(rootdir)
os.mkdir(rootdir)
# skip existing directory
elif flagdir=='skip':
skip = True
# keep both (default)
else:
ifold = 1
while glob.glob(rootdir+'_'+str(ifold)):
ifold += 1
rootdir += '_'+str(ifold)
os.mkdir(rootdir)
elif not os.path.isdir(rootdir) or not args.checkdirb and not skip:
if not os.path.isdir(rootdir):
args.checkdirb = True
os.mkdir(rootdir)
####################################
############ GENERATION ############
####################################
if not skip:
# check for generate all
if args.genall:
tstrfiles = []
# generate xyz with FF and trained ML
args.ff = 'mmff94'
args.ffoption = 'ba'
args.MLbonds = False
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
for strf in strfiles:
tstrfiles.append(strf+'FFML')
os.rename(strf+'.xyz',strf+'FFML.xyz')
# generate xyz with FF and covalent
args.MLbonds = ['c' for i in range(0,len(args.lig))]
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
for strf in strfiles:
tstrfiles.append(strf+'FFc')
os.rename(strf+'.xyz',strf+'FFc.xyz')
args.ff = False
args.ffoption = False
args.MLbonds = False
# generate xyz without FF and trained ML
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
for strf in strfiles:
tstrfiles.append(strf+'ML')
os.rename(strf+'.xyz',strf+'ML.xyz')
args.MLbonds = ['c' for i in range(0,len(args.lig))]
# generate xyz without FF and covalent ML
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
for strf in strfiles:
tstrfiles.append(strf+'c')
os.rename(strf+'.xyz',strf+'c.xyz')
strfiles = tstrfiles
else:
# generate xyz files
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
# generate QC input files
if args.qccode and not emsg:
if args.charge and (isinstance(args.charge, list)):
args.charge = args.charge[0]
if args.spin and (isinstance(args.spin, list)):
args.spin = args.spin[0]
if args.qccode.lower() in 'terachem tc Terachem TeraChem TERACHEM TC':
jobdirs = multitcgen(args,strfiles)
print 'TeraChem input files generated!'
elif 'gam' in args.qccode.lower():
jobdirs = multigamgen(args,strfiles)
print 'GAMESS input files generated!'
elif 'qch' in args.qccode.lower():
jobdirs = multiqgen(args,strfiles)
print 'QChem input files generated!'
elif 'orc' in args.qccode.lower():
jobdirs = multiogen(args,strfiles)
print 'ORCA input files generated!'
elif 'molc' in args.qccode.lower():
jobdirs = multimolcgen(args,strfiles)
print 'MOLCAS input files generated!'
else:
print 'Only TeraChem, GAMESS, QChem, ORCA, MOLCAS are supported right now.\n'
# check molpac
if args.mopac and not emsg:
print('Generating MOPAC input')
if globs.debug:
print(strfiles)
jobdirs = mlpgen(args,strfiles,rootdir)
# generate jobscripts
if args.jsched and not emsg:
if args.jsched in 'SBATCH SLURM slurm sbatch':
slurmjobgen(args,jobdirs)
print 'SLURM jobscripts generated!'
elif args.jsched in 'SGE Sungrid sge':
sgejobgen(args,jobdirs)
print 'SGE jobscripts generated!'
elif multidx != -1: # if ligand input was a list of smiles strings, write good smiles strings to separate list
try:
f = open(ligfilename+'-good.smi','a')
f.write(args.lig[0])
f.close()
except:
0
elif not emsg:
if args.gui:
qq = mQDialogInf('Folder skipped','Folder '+rootdir+' was skipped.')
qq.setParent(args.gui.wmain)
else:
print 'Folder '+rootdir+' was skipped..\n'
return emsg
# ## Transition state generation
# # @param rundir Run directory
# # @param args Namespace of arguments
# # @param chspfname Folder name for charges and spins
# # @param globs Global variables
# # @return Error messages
# def tsgen_supervisor(rundir,args,chspfname,globs):
# emsg = False
# # load specified core into a mol3D object
# cc, emsg = core_load(args.core)
# if emsg:
# return emsg
# cc.convert2mol3D()
# subcores = getsubcores()
# # load substrate molecule into a mol3D object
# if len(args.substrate) > 1:
# print('Currently only one substrate molecule is supported. Exiting...')
# return
# else:
# substr, emsg = substr_load(args.substrate[0],subcores)
# if emsg:
# return emsg
# substr.convert2mol3D()
# ##### fetch smart name
# fname = name_TS(rundir,args.core,substr,args,bind=args.bind,bsmi=args.nambsmi)
# if globs.debug:
# print('fname is ' + str(fname))
# rootdir = fname
# # check for charges/spin
# rootcheck = False
# if (chspfname):
# rootcheck = rootdir
# rootdir = rootdir + '/'+chspfname
# if (args.suff):
# rootdir += args.suff
# # check for mannual overwrite of
# # directory name
# if args.jobdir:
# rootdir = rundir + args.jobdir
# # check for top directory
# skip = False
# if rootcheck and os.path.isdir(rootcheck) and not args.checkdirt and not skip:
# args.checkdirt = True
# if not args.rprompt:
# flagdir=raw_input('\nDirectory '+rootcheck +' already exists. Keep both (k), replace (r) or skip (s) k/r/s: ')
# if 'k' in flagdir.lower():
# flagdir = 'keep'
# elif 's' in flagdir.lower():
# flagdir = 'skip'
# else:
# flagdir = 'replace'
# else:
# flagdir = 'replace'
# # replace existing directory
# if (flagdir=='replace'):
# shutil.rmtree(rootcheck)
# os.mkdir(rootcheck)
# # skip existing directory
# elif flagdir=='skip':
# skip = True
# # keep both (default)
# else:
# ifold = 1
# while glob.glob(rootdir+'_'+str(ifold)):
# ifold += 1
# rootcheck += '_'+str(ifold)
# os.mkdir(rootcheck)
# elif rootcheck and (not os.path.isdir(rootcheck) or not args.checkdirt) and not skip:
# if globs.debug:
# print('rootcheck is ' + str(rootcheck))
# args.checkdirt = True
# try:
# os.mkdir(rootcheck)
# except:
# print 'Directory '+rootcheck+' can not be created. Exiting..\n'
# return
# # check for actual directory
# if os.path.isdir(rootdir) and not args.checkdirb and not skip and not args.jobdir:
# args.checkdirb = True
# if not args.rprompt:
# flagdir=raw_input('\nDirectory '+rootdir +' already exists. Keep both (k), replace (r) or skip (s) k/r/s: ')
# if 'k' in flagdir.lower():
# flagdir = 'keep'
# elif 's' in flagdir.lower():
# flagdir = 'skip'
# else:
# flagdir = 'replace'
# else:
# #qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootdir+' already exists. What do you want to do?')
# #flagdir = qqb.getaction()
# flagdir = 'replace'
# # replace existing directory
# if (flagdir=='replace'):
# shutil.rmtree(rootdir)
# os.mkdir(rootdir)
# # skip existing directory
# elif flagdir=='skip':
# skip = True
# # keep both (default)
# else:
# ifold = 1
# while glob.glob(rootdir+'_'+str(ifold)):
# ifold += 1
# rootdir += '_'+str(ifold)
# os.mkdir(rootdir)
# elif not os.path.isdir(rootdir) or not args.checkdirb and not skip:
# if not os.path.isdir(rootdir):
# args.checkdirb = True
# os.mkdir(rootdir)
# ####################################
# ############ GENERATION ############
# ####################################
# # determine TS generation mode/reaction type
# # 1: oxidative addition of a single group to an unsaturated complex (e.g., Fe(II) + O2 -> Fe(III)-O-O)
# # 2: oxidative addition of two groups to an unsaturated complex (e.g., Pd + CH4 -> Pd(H)(CH3))
# # 3: abstraction (ligand only reaction) (e.g., Fe(IV)=O + CH4 -> Fe(III)-OH + CH3)
# # 1: compreact is the metal center, substreact is one atom
# # 2: compreact is the metal center, substreact is two bonded atoms
# # 3: compreact is not the metal center and bonded to only one atom, substreact is one atom
# if len(args.compreact) == 1:
# compreact = int(args.compreact[0]) - 1 # one-indexed in input
# else:
# print('Error: Currently only one complex reacting atom is supported. Exiting...')
# return
# if cc.getAtom(compreact).ismetal():
# if len(args.substreact) == 1:
# substreact = int(args.substreact[0]) - 1 # one-indexed in input
# if len(substr.getBondedAtoms(substreact)) == 1:
# if len(cc.getBondedAtomsOct(compreact)) < 6:
# mode = 1
# print('Mode 1: oxidative addition of a single group')
# else:
# print('Error: You have specified oxidative addition of a single group, but the metal atom is not unsaturated. Please check your input. Exiting...')
# return
# else:
# print('Error: You have specified oxidative addition of a single group, but the substrate atom is not terminal. Please check your input. Exiting...')
# return
# elif len(args.substreact) == 2:
# if int(args.substreact[1]) in substr.getBondedAtoms(int(args.substreact[0])):
# if len(cc.getBondedAtomsOct(compreact)) < 5:
# substreact = [int(i) - 1 for i in args.substreact] # one-indexed in input
# mode = 2
# print('Mode 2: oxidative addition of two groups')
# else:
# print('Error: You have specified oxidative addition of two groups, but the metal atom does not have two available empty sites. Please check your input. Exiting...')
# return
# else:
# print('Error: You have specified oxidative addition of two groups, but the two substrate groups are not bonded. Please check your input. Exiting...')
# return
# elif len(cc.getBondedAtoms(compreact)) == 1:
# if len(args.substreact) == 1:
# substreact = int(args.substreact[0]) - 1 # one-indexed in input
# else:
# print('Error: You have specified abstraction, but specified more than one substrate atom. Please check your input. Exiting...')
# return
# if len(substr.getBondedAtoms(substreact)) == 1:
# mode = 3
# print('Mode 3: Abstraction')
# else:
# print('Error: You have specified abstraction, but the substrate atom is not terminal. Please check your input. Exiting...')
# return
# else:
# print('Error: You have specified abstraction, but the abstracting atom is not terminal. Please check your input. Exiting...')
# return
# if not skip:
# # generate xyz files
# strfiles,emsg,this_diag = tsgen(mode,args,rootdir,cc,substr,compreact,substreact,globs)
# # generate QC input files
# if args.qccode and not emsg:
# args.runtyp = 'ts'
# if args.charge and (isinstance(args.charge, list)):
# args.charge = args.charge[0]
# if args.spin and (isinstance(args.spin, list)):
# args.spin = args.spin[0]
# if args.qccode.lower() in 'terachem tc Terachem TeraChem TERACHEM TC':
# jobdirs = multitcgen(args,strfiles)
# print 'TeraChem input files generated!'
# elif 'gam' in args.qccode.lower():
# jobdirs = multigamgen(args,strfiles)
# print 'GAMESS input files generated!'
# elif 'qch' in args.qccode.lower():
# jobdirs = multiqgen(args,strfiles)
# print 'QChem input files generated!'
# else:
# print 'Only TeraChem, GAMESS and QChem are supported right now.\n'
# # generate jobscripts
# if args.jsched and not emsg:
# if args.jsched in 'SBATCH SLURM slurm sbatch':
# slurmjobgen(args,jobdirs)
# print 'SLURM jobscripts generated!'
# elif args.jsched in 'SGE Sungrid sge':
# sgejobgen(args,jobdirs)
# print 'SGE jobscripts generated!'
# if this_diag.sanity: # move to separate subdirectory if generated structure was bad
# fname = rootdir.rsplit('/',1)[-1]
# shutil.move(rootdir,rundir+'/badjobs/'+fname)
# elif not emsg:
# print 'Folder '+rootdir+' was skipped..\n'
# return emsg
def rungen(rundir,args,chspfname,globs):
try:
from Classes.mWidgets import qBoxFolder
from Classes.mWidgets import mQDialogInf
from Classes.mWidgets import mQDialogErr
except ImportError:
args.gui = False
emsg = False
globs.nosmiles = 0 # reset smiles ligands for each run
# check for specified ligands/functionalization
ligocc = []
# check for files specified for multiple ligands
mligs,catoms = [False],[False]
if args.lig is not None:
if '.smi' in args.lig[0]:
ligfilename = args.lig[0].split('.')[0]
if args.lig:
mligs,catoms,multidx = checkmultilig(args.lig)
if args.debug:
print('after checking for mulitple ligs, we found ' + str(multidx) + ' ligands' )
# save initial
smicat0 = [ss for ss in args.smicat] if args.smicat else False
# loop over ligands
for mcount, mlig in enumerate(mligs):
args.smicat = [ss for ss in smicat0] if smicat0 else False
args.checkdir, skip = False, False # initialize flags
if len(mligs) > 0 and mligs[0]:
args.lig = mlig # get combination
if multidx!=-1:
if catoms[multidx][mcount]:
ssatoms = catoms[multidx][mcount].split(',')
lloc = [int(scat)-1 for scat in ssatoms]
# append connection atoms if specified in smiles
if args.smicat and len(args.smicat) > 0:
for i in range(len(args.smicat),multidx):
args.smicat.append([])
else:
args.smicat = [lloc]
args.smicat[multidx] = lloc
if (args.lig):
ligands = args.lig
if (args.ligocc):
ligocc = args.ligocc
else:
ligocc = ['1']
for i in range(len(ligocc),len(ligands)):
ligocc.append('1')
lig = ''
for i,l in enumerate(ligands):
ligentry,emsg = lig_load(l)
# update ligand
if ligentry:
ligands[i] = ligentry.name
args.lig[i] = ligentry.name
if emsg:
skip = True
break
if ligentry.ident == 'smi':
ligentry.ident += str(globs.nosmiles)
globs.nosmiles += 1
if args.sminame:
if len(args.sminame) > int(ligentry.ident[-1]):
ligentry.ident = args.sminame[globs.nosmiles-1][0:3]
lig += ''.join("%s%s" % (ligentry.ident,ligocc[i]))
else:
ligands =[]
lig = ''
ligocc = ''
##### fetch smart name
fname = name_complex(rundir,args.core,args.geometry,ligands,ligocc,mcount,args,nconf=False,sanity=False,bind=args.bind,bsmi=args.nambsmi)
if args.tsgen:
substrate = args.substrate
subcatoms = ['multiple']
if args.subcatoms:
subcatoms = args.subcatoms
mlig = args.mlig
mligcatoms = args.mligcatoms
fname = name_ts_complex(rundir,args.core,args.geometry,ligands,ligocc,substrate,subcatoms,mlig,mligcatoms,mcount,args,nconf=False,sanity=False,bind=args.bind,bsmi=args.nambsmi)
if globs.debug:
print('fname is ' + str(fname))
rootdir = fname
# check for charges/spin
rootcheck = False
if (chspfname):
rootcheck = rootdir
rootdir = rootdir + '/'+chspfname
if (args.suff):
rootdir += args.suff
# check for mannual overwrite of
# directory name
if args.jobdir:
rootdir = rundir + args.jobdir
# check for top directory
if rootcheck and os.path.isdir(rootcheck) and not args.checkdirt and not skip:
args.checkdirt = True
if not args.rprompt:
flagdir=raw_input('\nDirectory '+rootcheck +' already exists. Keep both (k), replace (r) or skip (s) k/r/s: ')
if 'k' in flagdir.lower():
flagdir = 'keep'
elif 's' in flagdir.lower():
flagdir = 'skip'
else:
flagdir = 'replace'
else:
#qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootcheck+' already exists. What do you want to do?')
#flagdir = qqb.getaction()
flagdir = 'replace'
# replace existing directory
if (flagdir=='replace'):
shutil.rmtree(rootcheck)
os.mkdir(rootcheck)
# skip existing directory
elif flagdir=='skip':
skip = True
# keep both (default)
else:
ifold = 1
while glob.glob(rootdir+'_'+str(ifold)):
ifold += 1
rootcheck += '_'+str(ifold)
os.mkdir(rootcheck)
elif rootcheck and (not os.path.isdir(rootcheck) or not args.checkdirt) and not skip:
if globs.debug:
print('rootcheck is ' + str(rootcheck))
args.checkdirt = True
try:
os.mkdir(rootcheck)
except:
print 'Directory '+rootcheck+' can not be created. Exiting..\n'
return
# check for actual directory
if os.path.isdir(rootdir) and not args.checkdirb and not skip and not args.jobdir:
args.checkdirb = True
if not args.rprompt:
flagdir=raw_input('\nDirectory '+rootdir +' already exists. Keep both (k), replace (r) or skip (s) k/r/s: ')
if 'k' in flagdir.lower():
flagdir = 'keep'
elif 's' in flagdir.lower():
flagdir = 'skip'
else:
flagdir = 'replace'
else:
#qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootdir+' already exists. What do you want to do?')
#flagdir = qqb.getaction()
flagdir = 'replace'
# replace existing directory
if (flagdir=='replace'):
shutil.rmtree(rootdir)
os.mkdir(rootdir)
# skip existing directory
elif flagdir=='skip':
skip = True
# keep both (default)
else:
ifold = 1
while glob.glob(rootdir+'_'+str(ifold)):
ifold += 1
rootdir += '_'+str(ifold)
os.mkdir(rootdir)
elif not os.path.isdir(rootdir) or not args.checkdirb and not skip:
if not os.path.isdir(rootdir):
args.checkdirb = True
os.mkdir(rootdir)
####################################
############ GENERATION ############
####################################
if not skip:
# check for generate all
if args.genall:
tstrfiles = []
# generate xyz with FF and trained ML
args.ff = 'mmff94'
args.ffoption = 'ba'
args.MLbonds = False
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
for strf in strfiles:
tstrfiles.append(strf+'FFML')
os.rename(strf+'.xyz',strf+'FFML.xyz')
# generate xyz with FF and covalent
args.MLbonds = ['c' for i in range(0,len(args.lig))]
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
for strf in strfiles:
tstrfiles.append(strf+'FFc')
os.rename(strf+'.xyz',strf+'FFc.xyz')
args.ff = False
args.ffoption = False
args.MLbonds = False
# generate xyz without FF and trained ML
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
for strf in strfiles:
tstrfiles.append(strf+'ML')
os.rename(strf+'.xyz',strf+'ML.xyz')
args.MLbonds = ['c' for i in range(0,len(args.lig))]
# generate xyz without FF and covalent ML
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
for strf in strfiles:
tstrfiles.append(strf+'c')
os.rename(strf+'.xyz',strf+'c.xyz')
strfiles = tstrfiles
else:
# generate xyz files
strfiles,emsg,this_diag = structgen(args,rootdir,ligands,ligocc,globs,mcount)
# generate QC input files
if args.qccode and not emsg:
if args.charge and (isinstance(args.charge, list)):
args.charge = args.charge[0]
if args.spin and (isinstance(args.spin, list)):
args.spin = args.spin[0]
if args.qccode.lower() in 'terachem tc Terachem TeraChem TERACHEM TC':
jobdirs = multitcgen(args,strfiles)
print 'TeraChem input files generated!'
elif 'gam' in args.qccode.lower():
jobdirs = multigamgen(args,strfiles)
print 'GAMESS input files generated!'
elif 'qch' in args.qccode.lower():
jobdirs = multiqgen(args,strfiles)
print 'QChem input files generated!'
elif 'orc' in args.qccode.lower():
jobdirs = multiogen(args,strfiles)
print 'ORCA input files generated!'
elif 'molc' in args.qccode.lower():
jobdirs = multimolcgen(args,strfiles)
print 'MOLCAS input files generated!'
else:
print 'Only TeraChem, GAMESS, QChem, ORCA, MOLCAS are supported right now.\n'
# check molpac
if args.mopac and not emsg:
print('Generating MOPAC input')
if globs.debug:
print(strfiles)
jobdirs = mlpgen(args,strfiles,rootdir)
# generate jobscripts
if args.jsched and not emsg:
if args.jsched in 'SBATCH SLURM slurm sbatch':
slurmjobgen(args,jobdirs)
print 'SLURM jobscripts generated!'
elif args.jsched in 'SGE Sungrid sge':
sgejobgen(args,jobdirs)
print 'SGE jobscripts generated!'
elif multidx != -1: # if ligand input was a list of smiles strings, write good smiles strings to separate list
try:
f = open(ligfilename+'-good.smi','a')
f.write(args.lig[0])
f.close()
except:
0
elif not emsg:
if args.gui:
qq = mQDialogInf('Folder skipped','Folder '+rootdir+' was skipped.')
qq.setParent(args.gui.wmain)
else:
print 'Folder '+rootdir+' was skipped..\n'
return emsg
def rungen(rundir, args, chspfname, globs):
try:
from Classes.mWidgets import qBoxFolder
from Classes.mWidgets import mQDialogInf
from Classes.mWidgets import mQDialogErr
except ImportError:
args.gui = False
emsg = False
globs.nosmiles = 0 # reset smiles ligands for each run
# check for specified ligands/functionalization
ligocc = []
# check for files specified for multiple ligands
mligs, catoms = [False], [False]
if '.smi' in args.lig[0]:
ligfilename = args.lig[0].split('.')[0]
if args.lig:
mligs, catoms, multidx = checkmultilig(args.lig)
if args.debug:
print('after checking for mulitple ligs, we found ' + str(multidx) +
' ligands')
# save initial
smicat0 = [ss for ss in args.smicat] if args.smicat else False
# loop over ligands
for mcount, mlig in enumerate(mligs):
args.smicat = [ss for ss in smicat0] if smicat0 else False
args.checkdir, skip = False, False # initialize flags
if len(mligs) > 0 and mligs[0]:
args.lig = mlig # get combination
if multidx != -1:
if catoms[multidx][mcount]:
ssatoms = catoms[multidx][mcount].split(',')
lloc = [int(scat) - 1 for scat in ssatoms]
# append connection atoms if specified in smiles
if args.smicat and len(args.smicat) > 0:
for i in range(len(args.smicat), multidx):
args.smicat.append([])
else:
args.smicat = [lloc]
args.smicat[multidx] = lloc
if (args.lig):
ligands = args.lig
if (args.ligocc):
ligocc = args.ligocc
else:
ligocc = ['1']
for i in range(len(ligocc), len(ligands)):
ligocc.append('1')
lig = ''
for i, l in enumerate(ligands):
ligentry, emsg = lig_load(l)
# update ligand
if ligentry:
ligands[i] = ligentry.name
args.lig[i] = ligentry.name
if emsg:
skip = True
break
if ligentry.ident == 'smi':
ligentry.ident += str(globs.nosmiles)
globs.nosmiles += 1
if args.sminame:
if len(args.sminame) > int(ligentry.ident[-1]):
ligentry.ident = args.sminame[globs.nosmiles -
1][0:3]
lig += ''.join("%s%s" % (ligentry.ident, ligocc[i]))
else:
ligands = []
lig = ''
ligocc = ''
##### fetch smart name
fname = name_complex(rundir,
args.core,
ligands,
ligocc,
mcount,
args,
nconf=False,
sanity=False,
bind=args.bind,
bsmi=args.nambsmi)
if globs.debug:
print('fname is ' + str(fname))
rootdir = fname
# check for charges/spin
rootcheck = False
if (chspfname):
rootcheck = rootdir
rootdir = rootdir + '/' + chspfname
if (args.suff):
rootdir += args.suff
# check for mannual overwrite of
# directory name
if args.jobdir:
rootdir = rundir + args.jobdir
# check for top directory
if rootcheck and os.path.isdir(
rootcheck) and not args.checkdirt and not skip:
args.checkdirt = True
if not args.rprompt:
flagdir = raw_input(
'\nDirectory ' + rootcheck +
' already exists. Keep both (k), replace (r) or skip (s) k/r/s: '
)
if 'k' in flagdir.lower():
flagdir = 'keep'
elif 's' in flagdir.lower():
flagdir = 'skip'
else:
flagdir = 'replace'
else:
#qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootcheck+' already exists. What do you want to do?')
#flagdir = qqb.getaction()
flagdir = 'replace'
# replace existing directory
if (flagdir == 'replace'):
shutil.rmtree(rootcheck)
os.mkdir(rootcheck)
# skip existing directory
elif flagdir == 'skip':
skip = True
# keep both (default)
else:
ifold = 1
while glob.glob(rootdir + '_' + str(ifold)):
ifold += 1
rootcheck += '_' + str(ifold)
os.mkdir(rootcheck)
elif rootcheck and (not os.path.isdir(rootcheck)
or not args.checkdirt) and not skip:
if globs.debug:
print('rootcheck is ' + str(rootcheck))
args.checkdirt = True
try:
os.mkdir(rootcheck)
except:
print 'Directory ' + rootcheck + ' can not be created. Exiting..\n'
return
# check for actual directory
if os.path.isdir(
rootdir
) and not args.checkdirb and not skip and not args.jobdir:
args.checkdirb = True
if not args.rprompt:
flagdir = raw_input(
'\nDirectory ' + rootdir +
' already exists. Keep both (k), replace (r) or skip (s) k/r/s: '
)
if 'k' in flagdir.lower():
flagdir = 'keep'
elif 's' in flagdir.lower():
flagdir = 'skip'
else:
flagdir = 'replace'
else:
#qqb = qBoxFolder(args.gui.wmain,'Folder exists','Directory '+rootdir+' already exists. What do you want to do?')
#flagdir = qqb.getaction()
flagdir = 'replace'
# replace existing directory
if (flagdir == 'replace'):
shutil.rmtree(rootdir)
os.mkdir(rootdir)
# skip existing directory
elif flagdir == 'skip':
skip = True
# keep both (default)
else:
ifold = 1
while glob.glob(rootdir + '_' + str(ifold)):
ifold += 1
rootdir += '_' + str(ifold)
os.mkdir(rootdir)
elif not os.path.isdir(rootdir) or not args.checkdirb and not skip:
if not os.path.isdir(rootdir):
args.checkdirb = True
os.mkdir(rootdir)
####################################
############ GENERATION ############
####################################
if not skip:
# check for generate all
if args.genall:
tstrfiles = []
# generate xyz with FF and trained ML
args.ff = 'mmff94'
args.ffoption = 'ba'
args.MLbonds = False
strfiles, emsg, this_diag = structgen(args, rootdir, ligands,
ligocc, globs, mcount)
for strf in strfiles:
tstrfiles.append(strf + 'FFML')
os.rename(strf + '.xyz', strf + 'FFML.xyz')
# generate xyz with FF and covalent
args.MLbonds = ['c' for i in range(0, len(args.lig))]
strfiles, emsg, this_diag = structgen(args, rootdir, ligands,
ligocc, globs, mcount)
for strf in strfiles:
tstrfiles.append(strf + 'FFc')
os.rename(strf + '.xyz', strf + 'FFc.xyz')
args.ff = False
args.ffoption = False
args.MLbonds = False
# generate xyz without FF and trained ML
strfiles, emsg, this_diag = structgen(args, rootdir, ligands,
ligocc, globs, mcount)
for strf in strfiles:
tstrfiles.append(strf + 'ML')
os.rename(strf + '.xyz', strf + 'ML.xyz')
args.MLbonds = ['c' for i in range(0, len(args.lig))]
# generate xyz without FF and covalent ML
strfiles, emsg, this_diag = structgen(args, rootdir, ligands,
ligocc, globs, mcount)
for strf in strfiles:
tstrfiles.append(strf + 'c')
os.rename(strf + '.xyz', strf + 'c.xyz')
strfiles = tstrfiles
else:
# generate xyz files
strfiles, emsg, this_diag = structgen(args, rootdir, ligands,
ligocc, globs, mcount)
# generate QC input files
if args.qccode and not emsg:
if args.charge and (isinstance(args.charge, list)):
args.charge = args.charge[0]
if args.spin and (isinstance(args.spin, list)):
args.spin = args.spin[0]
if args.qccode.lower(
) in 'terachem tc Terachem TeraChem TERACHEM TC':
jobdirs = multitcgen(args, strfiles)
print 'TeraChem input files generated!'
elif 'gam' in args.qccode.lower():
jobdirs = multigamgen(args, strfiles)
print 'GAMESS input files generated!'
elif 'qch' in args.qccode.lower():
jobdirs = multiqgen(args, strfiles)
print 'QChem input files generated!'
else:
print 'Only TeraChem, GAMESS and QChem are supported right now.\n'
# check molpac
if args.mopac and not emsg:
print('Generating MOPAC input')
if globs.debug:
print(strfiles)
jobdirs = mlpgen(args, strfiles, rootdir)
# generate jobscripts
if args.jsched and not emsg:
if args.jsched in 'SBATCH SLURM slurm sbatch':
slurmjobgen(args, jobdirs)
print 'SLURM jobscripts generated!'
elif args.jsched in 'SGE Sungrid sge':
sgejobgen(args, jobdirs)
print 'SGE jobscripts generated!'
elif multidx != -1: # if ligand input was a list of smiles strings, write good smiles strings to separate list
try:
f = open(ligfilename + '-good.smi', 'a')
f.write(args.lig[0])
f.close()
except:
0
elif not emsg:
if args.gui:
qq = mQDialogInf('Folder skipped',
'Folder ' + rootdir + ' was skipped.')
qq.setParent(args.gui.wmain)
else:
print 'Folder ' + rootdir + ' was skipped..\n'
return emsg
def postproc(rundir, args, globs):
globs = globalvars()
if args.gui:
from Classes.mWidgets import mQDialogErr
from Classes.mWidgets import mQDialogInf
choice = mQDialogInf(
'Post processing',
'Parsing the results will take a while..Please be patient. Start?')
choice.setParent(args.gui.pWindow)
# locate output files
pdir = args.postdir if args.postdir else globs.rundir
cmd = "find '" + pdir + "' -name *out"
t = mybash(cmd)
resf = t.splitlines()
logfile = pdir + "/post.log"
if not os.path.isdir(pdir):
print '\nSpecified directory ' + pdir + ' does not exist..\n\n'
if args.gui:
args.gui.iWtxt.setText('\nSpecified directory ' + pdir +
' does not exist.\n\n' +
args.gui.iWtxt.toPlainText())
return
flog = open(logfile, 'a')
flog.write('\n\n\n##### Date: ' + time.strftime('%m/%d/%Y %H:%M') +
'#####\n\n')
# run summary report
if args.pres:
print '\nGetting runs summary..\n\n'
flog.write('\nGetting runs summary..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nGetting runs summary..\n\n' +
args.gui.iWtxt.toPlainText())
terapost(resf, pdir, args.gui, flog)
gampost(resf, pdir, args.gui, flog)
# run nbo analysis
if args.pnbo:
print '\nGetting NBO summary..\n\n'
flog.write('\nGetting NBO summary..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nGetting NBO summary..\n\n' +
args.gui.iWtxt.toPlainText())
nbopost(resf, pdir, args.gui, flog)
# locate molden files
cmd = "find " + "'" + pdir + "'" + " -name *molden"
t = mybash(cmd)
molf = t.splitlines()
# parse molecular orbitals
if args.porbinfo:
print '\nGetting MO information..\n\n'
flog.write('\nGetting MO information..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nGetting MO information..\n\n' +
args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir + '/MO_files'):
os.mkdir(pdir + '/MO_files')
moldpost(molf, pdir, args.gui, flog)
# calculate delocalization indices
if args.pdeloc:
print '\nCalculating delocalization indices..\n\n'
flog.write('\nCalculating delocalization indices..\n\n')
if args.gui:
args.gui.iWtxt.setText(
'\nCalculating delocalization indices..\n\n' +
args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir + '/Deloc_files'):
os.mkdir(pdir + '/Deloc_files')
deloc(molf, pdir, args.gui, flog)
# calculate charges
if args.pcharge:
print '\nCalculating charges..\n\n'
flog.write('\nCalculating charges..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nCalculating charges..\n\n' +
args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir + '/Charge_files'):
os.mkdir(pdir + '/Charge_files')
getcharges(molf, pdir, args.gui, flog)
# parse wavefunction
if args.pwfninfo:
print '\nCalculating wavefunction properties..\n\n'
flog.write('\nCalculating wavefunction properties..\n\n')
if args.gui:
args.gui.iWtxt.setText(
'\nCalculating wavefunction properties..\n\n' +
args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir + '/Wfn_files'):
os.mkdir(pdir + '/Wfn_files')
if not os.path.isdir(pdir + '/Cube_files'):
os.mkdir(pdir + '/Cube_files')
getcubes(molf, pdir, args.gui, flog)
getwfnprops(molf, pdir, args.gui, flog)
if not args.pgencubes and os.path.isdir(pdir + '/Cube_files'):
shutil.rmtree(pdir + '/Cube_files')
# generate cube files
if args.pgencubes:
print '\nGenerating cube files..\n\n'
flog.write('\nGenerating cube files..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nGenerating cube files..\n\n' +
args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir + '/Cube_files'):
os.mkdir(pdir + '/Cube_files')
getcubes(molf, pdir, args.gui, flog)
flog.close()
def postproc(rundir,args,globs):
globs = globalvars()
if args.gui:
from Classes.mWidgets import mQDialogErr
from Classes.mWidgets import mQDialogInf
choice = mQDialogInf('Post processing','Parsing the results will take a while..Please be patient. Start?')
choice.setParent(args.gui.pWindow)
# locate output files
pdir = args.postdir if args.postdir else globs.rundir
cmd = "find '"+pdir+"' -name *out"
t = mybash(cmd)
resf = t.splitlines()
logfile = pdir+"/post.log"
if not os.path.isdir(pdir):
print '\nSpecified directory '+pdir+' does not exist..\n\n'
if args.gui:
args.gui.iWtxt.setText('\nSpecified directory '+pdir+' does not exist.\n\n'+args.gui.iWtxt.toPlainText())
return
flog = open(logfile,'a')
flog.write('\n\n\n##### Date: '+time.strftime('%m/%d/%Y %H:%M')+'#####\n\n')
# run summary report
if args.pres:
print '\nGetting runs summary..\n\n'
flog.write('\nGetting runs summary..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nGetting runs summary..\n\n'+args.gui.iWtxt.toPlainText())
terapost(resf,pdir,args.gui,flog)
gampost(resf,pdir,args.gui,flog)
# run nbo analysis
if args.pnbo:
print '\nGetting NBO summary..\n\n'
flog.write('\nGetting NBO summary..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nGetting NBO summary..\n\n'+args.gui.iWtxt.toPlainText())
nbopost(resf,pdir,args.gui,flog)
# locate molden files
cmd = "find "+"'"+pdir+"'"+" -name *molden"
t = mybash(cmd)
molf = t.splitlines()
# parse molecular orbitals
if args.porbinfo:
print '\nGetting MO information..\n\n'
flog.write('\nGetting MO information..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nGetting MO information..\n\n'+args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir+'/MO_files'):
os.mkdir(pdir+'/MO_files')
moldpost(molf,pdir,args.gui,flog)
# calculate delocalization indices
if args.pdeloc:
print '\nCalculating delocalization indices..\n\n'
flog.write('\nCalculating delocalization indices..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nCalculating delocalization indices..\n\n'+args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir+'/Deloc_files'):
os.mkdir(pdir+'/Deloc_files')
deloc(molf,pdir,args.gui,flog)
# calculate charges
if args.pcharge:
print '\nCalculating charges..\n\n'
flog.write('\nCalculating charges..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nCalculating charges..\n\n'+args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir+'/Charge_files'):
os.mkdir(pdir+'/Charge_files')
getcharges(molf,pdir,args.gui,flog)
# parse wavefunction
if args.pwfninfo:
print '\nCalculating wavefunction properties..\n\n'
flog.write('\nCalculating wavefunction properties..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nCalculating wavefunction properties..\n\n'+args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir+'/Wfn_files'):
os.mkdir(pdir+'/Wfn_files')
if not os.path.isdir(pdir+'/Cube_files'):
os.mkdir(pdir+'/Cube_files')
getcubes(molf,pdir,args.gui,flog)
getwfnprops(molf,pdir,args.gui,flog)
if not args.pgencubes and os.path.isdir(pdir+'/Cube_files'):
shutil.rmtree(pdir+'/Cube_files')
# generate cube files
if args.pgencubes:
print '\nGenerating cube files..\n\n'
flog.write('\nGenerating cube files..\n\n')
if args.gui:
args.gui.iWtxt.setText('\nGenerating cube files..\n\n'+args.gui.iWtxt.toPlainText())
if not os.path.isdir(pdir+'/Cube_files'):
os.mkdir(pdir+'/Cube_files')
getcubes(molf,pdir,args.gui,flog)
flog.close()