def startgen(argv,flag,gui):
emsg = False
# check for configuration file
homedir = os.path.expanduser("~")
#configfile = False if not glob.glob(homedir+'/.molSimplify') else True
#if not configfile:
# print "It looks like the configuration file '~/.molSimplify' does not exist!Please follow the next steps to configure the file."
# instdir = raw_input("Please select the full path of the top installation directory for the program: ")
# cdbdir = raw_input("Please specify the full path of the directory containing chemical databases:")
# mwfn = raw_input("Specify the full path to the Multiwfn executable (for post-processing):")
# f = open(homedir+'/.molSimplify','w')
# if len(instdir) > 1:
# f.write("INSTALLDIR="+instdir+'\n')
# if len(cdbdir) > 1:
# f.write("CHEMDBDIR="+cdbdir+'\n')
# if len(mwfn) > 1 :
# f.write("MULTIWFN="+mwfn[0]+'\n')
# f.close()
### end set-up configuration file ###
############ GLOBALS DEFINITION ############
globs = globalvars()
#installdir = globs.installdir
rundir = globs.rundir
PROGRAM = globs.PROGRAM
###### END GLOBALS DEFINITION ##############
# correct installdir
#if installdir[-1]!='/':
# installdir+='/'
# print welcome message
ss = "\n************************************************************"
ss += "\n******** Welcome to "+PROGRAM+"! Let's get started. ********\n"
ss += "************************************************************\n\n"
if not flag:
print ss
sys.argv = argv
parser = argparse.ArgumentParser()
args = parseall(parser)
# check if input file exists
if not glob.glob(args.i):
emsg = 'Input file '+args.i+' does not exist. Please specify a valid input file.\n'
print emsg
return emsg
args.gui = gui # add gui flag
# parse input file
if args.i:
parseinputfile(args)
if args.cdxml:
print 'converting cdxml file into xyz'
cdxml = args.cdxml[0]
fname, msg = loadcdxml(cdxml)
print(msg)
if 'two' in msg:
core = fname + '_cat.xyz'
sub = fname + '_sub.xyz'
args.core = [core]
args.substrate = [sub]
args.tsgen = True
# if not args.postp and not args.dbsearch and not args.dbfinger and not args.drawmode and not (args.slab_gen or args.place_on_slab) and not (args.chain) and not (args.correlate): # check input arguments
if not args.postp and not args.dbsearch and not args.dbfinger and not (args.slab_gen or args.place_on_slab) and not (args.chain) and not (args.correlate): # check input arguments
# check input arguments
print 'Checking input...'
if args.tsgen:
emsg = checkinput(args,calctype="tsgen")
elif args.ligadd:
emsg = checkinput(args,calctype="dbadd")
else:
emsg = checkinput(args)
# check before cleaning input arguments and clean only if checked
cleaninput(args)
args.gui = False # deepcopy will give error
if emsg:
del args
return emsg
# check for jobs directory
rundir = args.rundir+'/' if (args.rundir) else rundir
if not os.path.isdir(rundir):
os.mkdir(rundir)
################### START MAIN ####################
args0 = copy.deepcopy(args) # save initial arguments
# add gui flag
args.gui = gui
# postprocessing run?
if (args.postp):
postproc(rundir,args,globs)
# database search?
elif (args.dbsearch or args.dbfinger):
emsg = dbsearch(rundir,args,globs)
if emsg:
del args
return emsg
else:
print 'Successful database search!\n'
# random generation?
elif (args.rgen): # check if random generation was requested
if args.charge:
args.charge = args.charge[0]
if args.spin:
args.spin = args.spin[0]
corests=args.core
for cc in corests:
args = copy.deepcopy(args0)
# add gui flag
args.gui = gui
args.core = cc
if (args.lig or args.coord or args.lignum or args.ligocc): # constraints given?
args, emsg = constrgen(rundir,args,globs)
if emsg:
del args
return emsg
else:
emsg = 'For random generation specify at least a ligand, coordination or ligand types.\n'
print emsg
del args
return emsg
#elif args.drawmode:
# emsg = draw_supervisor(args,rundir)
# slab/place on slab?
elif (args.slab_gen or args.place_on_slab):
emsg = slab_module_supervisor(args,rundir)
# chain builder
elif (args.chain):
print('chain on')
emsg = chain_builder_supervisor(args,rundir)
# correlation analysis
elif (args.correlate):
print('analysis is looking for correlations')
analysis_supervisor(args,rundir)
# add ligand to list
elif (args.ligadd):
print('adding ' +str(args.ligadd) + ' to ligand database with name ' + args.ligname + ' and connection atom(s) ' + str(args.ligcon))
addtoldb(smimol=args.ligadd.decode('utf-8'),sminame=args.ligname.decode('utf-8'),smident = len(args.ligcon),smicat=str(args.ligcon).strip('[]').decode('utf-8'),smigrps ="custom",smictg="custom",ffopt=args.ligffopt)
# normal structure generation or transition state building
else:
args = copy.deepcopy(args0)
# add gui flag
args.gui = gui
corests=args.core
# if args.tsgen: # goes through multigenruns for maximum interoperability
# print('building a transition state')
if args.tsgen: # goes through multigenruns for maximum interoperability
print('building a transition state')
else:
print('building an equilibrium complex')
for cc in corests:
args.core = cc
emsg = multigenruns(rundir,args,globs)
if emsg:
print emsg
del args
return emsg
ss = "\n**************************************************************"
ss += "\n***** Thank you for using "+PROGRAM+". Have a nice day! ******\n"
ss += "**************************************************************"
ss += globs.about
if not flag:
print ss
del args
return emsg
def startgen(argv, flag, gui):
emsg = False
### check for configuration file ##
homedir = os.path.expanduser("~")
#configfile = False if not glob.glob(homedir+'/.molSimplify') else True
#if not configfile:
# print "It looks like the configuration file '~/.molSimplify' does not exist!Please follow the next steps to configure the file."
# instdir = raw_input("Please select the full path of the top installation directory for the program: ")
# cdbdir = raw_input("Please specify the full path of the directory containing chemical databases:")
# mwfn = raw_input("Specify the full path to the Multiwfn executable (for post-processing):")
# f = open(homedir+'/.molSimplify','w')
# if len(instdir) > 1:
# f.write("INSTALLDIR="+instdir+'\n')
# if len(cdbdir) > 1:
# f.write("CHEMDBDIR="+cdbdir+'\n')
# if len(mwfn) > 1 :
# f.write("MULTIWFN="+mwfn[0]+'\n')
# f.close()
### end set-up configuration file ###
############ GLOBALS DEFINITION ############
globs = globalvars()
#installdir = globs.installdir
rundir = globs.rundir
PROGRAM = globs.PROGRAM
###### END GLOBALS DEFINITION ##############
# correct installdir
#if installdir[-1]!='/':
# installdir+='/'
# print welcome message
ss = "\n************************************************************"
ss += "\n******** Welcome to " + PROGRAM + "! Let's get started. ********\n"
ss += "************************************************************\n\n"
if not flag:
print ss
sys.argv = argv
parser = argparse.ArgumentParser()
args = parseall(parser)
# check if input file exists
if not glob.glob(args.i):
emsg = 'Input file ' + args.i + ' does not exist. Please specify a valid input file.\n'
print emsg
return emsg
args.gui = gui # add gui flag
# parse input file
if args.i:
parseinputfile(args)
if not args.postp and not args.dbsearch and not args.dbfinger and not (
args.slab_gen or args.place_on_slab) and not (args.chain) and not (
args.correlate): # check input arguments
# check input arguments
print 'Checking input...'
emsg = checkinput(args)
# check before cleaning input arguments and clean only if checked
cleaninput(args)
args.gui = False # deepcopy will give error
if emsg:
del args
return emsg
# check for jobs directory
rundir = args.rundir + '/' if (args.rundir) else rundir
if not os.path.isdir(rundir):
os.mkdir(rundir)
################### START MAIN ####################
args0 = copy.deepcopy(args) # save initial arguments
# add gui flag
args.gui = gui
# postprocessing run?
if (args.postp):
postproc(rundir, args, globs)
# database search?
elif (args.dbsearch or args.dbfinger):
emsg = dbsearch(rundir, args, globs)
if emsg:
del args
return emsg
else:
print 'Successful database search!\n'
# random generation?
elif (args.rgen): # check if random generation was requested
if args.charge:
args.charge = args.charge[0]
if args.spin:
args.spin = args.spin[0]
corests = args.core
for cc in corests:
args = copy.deepcopy(args0)
# add gui flag
args.gui = gui
args.core = cc
if (args.lig or args.coord or args.lignum
or args.ligocc): # constraints given?
args, emsg = constrgen(rundir, args, globs)
if emsg:
del args
return emsg
else:
emsg = 'For random generation specify at least a ligand, coordination or ligand types.\n'
print emsg
del args
return emsg
# slab/place on slab?
elif (args.slab_gen or args.place_on_slab):
emsg = slab_module_supervisor(args, rundir)
# chain builder
elif (args.chain):
print('chain on')
emsg = chain_builder_supervisor(args, rundir)
# correlation analysis
elif (args.correlate):
print('analysis is looking for correlations')
analysis_supervisor(args, rundir)
# normal structure generation
else:
args = copy.deepcopy(args0)
# add gui flag
args.gui = gui
corests = args.core
for cc in corests:
args.core = cc
emsg = multigenruns(rundir, args, globs)
if emsg:
print emsg
del args
return emsg
ss = "\n**************************************************************"
ss += "\n***** Thank you for using " + PROGRAM + ". Have a nice day! ******\n"
ss += "**************************************************************"
ss += globs.about
if not flag:
print ss
del args
return emsg
def startgen(argv, flag, gui):
emsg = False
# check for configuration file
homedir = os.path.expanduser("~")
#configfile = False if not glob.glob(homedir+'/.molSimplify') else True
#if not configfile:
# print "It looks like the configuration file '~/.molSimplify' does not exist!Please follow the next steps to configure the file."
# instdir = raw_input("Please select the full path of the top installation directory for the program: ")
# cdbdir = raw_input("Please specify the full path of the directory containing chemical databases:")
# mwfn = raw_input("Specify the full path to the Multiwfn executable (for post-processing):")
# f = open(homedir+'/.molSimplify','w')
# if len(instdir) > 1:
# f.write("INSTALLDIR="+instdir+'\n')
# if len(cdbdir) > 1:
# f.write("CHEMDBDIR="+cdbdir+'\n')
# if len(mwfn) > 1 :
# f.write("MULTIWFN="+mwfn[0]+'\n')
# f.close()
### end set-up configuration file ###
############ GLOBALS DEFINITION ############
globs = globalvars()
#installdir = globs.installdir
rundir = globs.rundir
PROGRAM = globs.PROGRAM
###### END GLOBALS DEFINITION ##############
# correct installdir
#if installdir[-1]!='/':
# installdir+='/'
# print welcome message
ss = "\n************************************************************"
ss += "\n******** Welcome to " + PROGRAM + "! Let's get started. ********\n"
ss += "************************************************************\n\n"
if not flag:
print ss
sys.argv = argv
parser = argparse.ArgumentParser()
args = parseall(parser)
# check if input file exists
if not glob.glob(args.i):
emsg = 'Input file ' + args.i + ' does not exist. Please specify a valid input file.\n'
print emsg
return emsg
args.gui = gui # add gui flag
# parse input file
if args.i:
parseinputfile(args)
if args.cdxml:
print 'converting cdxml file into xyz'
cdxml = args.cdxml[0]
fname, msg = loadcdxml(cdxml)
print(msg)
if 'two' in msg:
core = fname + '_cat.xyz'
sub = fname + '_sub.xyz'
args.core = [core]
args.substrate = [sub]
args.tsgen = True
# if not args.postp and not args.dbsearch and not args.dbfinger and not args.drawmode and not (args.slab_gen or args.place_on_slab) and not (args.chain) and not (args.correlate): # check input arguments
if not args.postp and not args.dbsearch and not args.dbfinger and not (
args.slab_gen or args.place_on_slab) and not (args.chain) and not (
args.correlate): # check input arguments
# check input arguments
print 'Checking input...'
if args.tsgen:
emsg = checkinput(args, calctype="tsgen")
elif args.ligadd:
emsg = checkinput(args, calctype="dbadd")
else:
emsg = checkinput(args)
# check before cleaning input arguments and clean only if checked
cleaninput(args)
args.gui = False # deepcopy will give error
if emsg:
del args
return emsg
# check for jobs directory
rundir = args.rundir + '/' if (args.rundir) else rundir
if not os.path.isdir(rundir):
os.mkdir(rundir)
################### START MAIN ####################
args0 = copy.deepcopy(args) # save initial arguments
# add gui flag
args.gui = gui
# postprocessing run?
if (args.postp):
postproc(rundir, args, globs)
# database search?
elif (args.dbsearch or args.dbfinger):
emsg = dbsearch(rundir, args, globs)
if emsg:
del args
return emsg
else:
print 'Successful database search!\n'
# random generation?
elif (args.rgen): # check if random generation was requested
if args.charge:
args.charge = args.charge[0]
if args.spin:
args.spin = args.spin[0]
corests = args.core
for cc in corests:
args = copy.deepcopy(args0)
# add gui flag
args.gui = gui
args.core = cc
if (args.lig or args.coord or args.lignum
or args.ligocc): # constraints given?
args, emsg = constrgen(rundir, args, globs)
if emsg:
del args
return emsg
else:
emsg = 'For random generation specify at least a ligand, coordination or ligand types.\n'
print emsg
del args
return emsg
#elif args.drawmode:
# emsg = draw_supervisor(args,rundir)
# slab/place on slab?
elif (args.slab_gen or args.place_on_slab):
emsg = slab_module_supervisor(args, rundir)
# chain builder
elif (args.chain):
print('chain on')
emsg = chain_builder_supervisor(args, rundir)
# correlation analysis
elif (args.correlate):
print('analysis is looking for correlations')
analysis_supervisor(args, rundir)
# add ligand to list
elif (args.ligadd):
print('adding ' + str(args.ligadd) +
' to ligand database with name ' + args.ligname +
' and connection atom(s) ' + str(args.ligcon))
addtoldb(smimol=args.ligadd.decode('utf-8'),
sminame=args.ligname.decode('utf-8'),
smident=len(args.ligcon),
smicat=str(args.ligcon).strip('[]').decode('utf-8'),
smigrps="custom",
smictg="custom",
ffopt=args.ligffopt)
# normal structure generation or transition state building
else:
args = copy.deepcopy(args0)
# add gui flag
args.gui = gui
corests = args.core
# if args.tsgen: # goes through multigenruns for maximum interoperability
# print('building a transition state')
if args.tsgen: # goes through multigenruns for maximum interoperability
print('building a transition state')
else:
print('building an equilibrium complex')
for cc in corests:
args.core = cc
emsg = multigenruns(rundir, args, globs)
if emsg:
print emsg
del args
return emsg
ss = "\n**************************************************************"
ss += "\n***** Thank you for using " + PROGRAM + ". Have a nice day! ******\n"
ss += "**************************************************************"
ss += globs.about
if not flag:
print ss
del args
return emsg