def addtobdb(smimol,sminame):
globs = globalvars()
if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
print('To add to database, you need to set a custom path. Please enter a writeable file path:')
new_path = input('path=')
globs.add_custom_path(new_path)
copy_to_custom_path()
bpath = globs.custom_path + "/Bind/bind.dict"
bindcores = readdict(bpath)
bind_folder = globs.custom_path + "/Bind/"
# check if binding species exists
if sminame in bindcores.keys():
emsg = 'Molecule '+sminame+' already existing in binding species database.'
return emsg
else:
# convert to unicode
smimol = unicodedata.normalize('NFKD',smimol).encode('ascii','ignore')
sminame = unicodedata.normalize('NFKD',sminame).encode('ascii','ignore')
if '~' in smimol:
smimol = smimol.replace('~',os.expanduser('~'))
# convert ligand from smiles/file
bind,bsmi,emsg = bind_load(smimol,bindcores)
if emsg:
return emsg
bind.convert2mol3D() # convert to mol3D
# new entry for dictionary
# create shortname
if len(sminame) > 5:
shortname = sminame[0:3]+sminame[-2:]
else:
shortname = sminame
if '.mol' in smimol:
shutil.copy2(smimol,bind_folder+sminame+'.mol')
snew = sminame+':'+sminame+'.mol,'+shortname+','
elif '.xyz' in smimol:
shutil.copy2(smimol,bind_folder +sminame+'.xyz')
snew = sminame+':'+sminame+'.xyz,'+shortname+','
elif bind.OBmol:
# write smiles file in Bind species directory
bind.OBmol.write('smi',bind_folder +sminame+'.smi')
snew = sminame+':'+sminame+'.smi,'+shortname+','
else:
# write xyz file in Bind species directory
bind.writexyz(bind_folder +sminame+'.xyz') # write xyz file
snew = sminame+':'+sminame+'.xyz,'+shortname+','
# update dictionary
f = open(bpath,'r')
ss = f.read().splitlines()
f.close()
f = open(bpath,'w')
ss.append(snew)
ssort = sorted(ss[1:])
f.write(ss[0]+'\n')
for s in ssort:
f.write(s+'\n')
f.close()
return emsg
def addtocdb(smimol,sminame,smicat):
emsg = False
globs = globalvars()
if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
print('To add to database, you need to set a custom path. Please enter a writeable file path:')
new_path = input('path=')
globs.add_custom_path(new_path)
copy_to_custom_path()
cpath = globs.custom_path + "/Cores/cores.dict"
mcores = readdict(cpath)
cores_folder = globs.custom_path + "/Cores/"
# check if core exists
if sminame in mcores.keys():
emsg = 'Core '+sminame+' already existing in core database.'
return emsg
else:
# get connection atoms
ccats = filter(None,re.split(' |,|\t',smicat))
cats = [int(a)-1 for a in ccats]
if len(cats)==0:
cats=[0]
cs = [str(a) for a in cats]
css = ' '.join(cs)
# convert to unicode
smimol = unicodedata.normalize('NFKD',smimol).encode('ascii','ignore')
if '~' in smimol:
smimol = smimol.replace('~',os.expanduser('~'))
# convert ligand from smiles/file
core,emsg = core_load(smimol,mcores)
if emsg:
return emsg
core.convert2mol3D() # convert to mol3D
# write xyz file in Cores directory
# new entry for dictionary
if '.mol' in smimol:
shutil.copy2(smimol,cores_folder+sminame+'.mol')
snew = sminame+':'+sminame+'.mol,'+css+','+'1'
elif '.xyz' in smimol:
shutil.copy2(smimol,cores_folder + sminame+'.xyz')
snew = sminame+':'+sminame+'.xyz,'+css+','+'1'
else:
core.writexyz(cores_folder +sminame+'.xyz') # write xyz file
# new entry for dictionary
snew = sminame+':'+sminame+'.xyz,'+css+','+'1'
# update dictionary
f = open(cpath,'r')
ss = f.read().splitlines()
f.close()
f = open(cpath,'w')
ss.append(snew)
ssort = sorted(ss[1:])
f.write(ss[0]+'\n')
for s in ssort:
f.write(s+'\n')
f.close()
return emsg
def getslicores():
globs = globalvars()
if globs.custom_path: # test if a custom path is used:
slicores = str(
globs.custom_path).rstrip('/') + "/Ligands/simple_ligands.dict"
else:
slicores = resource_filename(
Requirement.parse("molSimplify"),
"molSimplify/Ligands/simple_ligands.dict")
slicores = readdict(slicores)
return slicores
def checkinput(args):
globs = globalvars()
emsg = False
# check core
if not args.core:
print 'WARNING: No core specified. Defaulting to Fe. Available cores are: '+getcores()
args.core = ['fe']
# check oxidation state
if not args.oxstate:
try:
print 'WARNING: No oxidation state specified. Defaulting to '+globs.defaultoxstate[args.core[0].lower()]
args.oxstate = globs.defaultoxstate[args.core[0].lower()]
except:
print 'WARNING: No oxidation state specified. Defaulting to II'
args.oxstate = 'II'
# check ligands
if not args.lig and not args.rgen:
if args.gui:
from Classes.mWidgets import mQDialogWarn
qqb = mQDialogWarn('Warning','You specified no ligands.\n')
qqb.setParent(args.gui.wmain)
else:
print 'WARNING: No ligands specified. Defaulting to water.\n'
args.lig = ['water']
# check coordination number and geometry
if not args.coord and not args.geometry:
if not args.gui:
print 'WARNING: No geometry and coordination number specified. Defaulting to octahedral (6).\n'
args.coord = 6
args.geometry = 'oct'
coords,geomnames,geomshorts,geomgroups = getgeoms()
if args.coord and (not args.geometry or (args.geometry not in geomnames and args.geometry not in geomshorts)):
print 'WARNING: No or unknown coordination geometry specified. Defaulting to '+globs.defaultgeometry[int(args.coord)][1]
args.geometry = globs.defaultgeometry[int(args.coord)][0]
if args.geometry and not args.coord:
if args.geometry not in geomnames and args.geometry not in geomshorts:
print 'You have specified an invalid geometry. Available geometries are:'
printgeoms()
print 'Defaulting to octahedral (6)'
args.geometry = 'oct'
args.coord = 6
else:
try:
args.coord = coords[geomnames.index(args.geometry)]
except:
args.coord = coords[geomshorts.index(args.geometry)]
print 'WARNING: No coordination number specified. Defaulting to '+str(args.coord)
# check number of ligands
if args.coord and not args.ligocc:
print('WARNING: No ligand numbers specified. Defaulting to '+str(args.coord)+' of the first ligand and 0 of all others.\n')
args.ligocc = [args.coord]
for lig in args.lig[1:]:
args.ligocc.append(0)
def getsimilar(smi, nmols, dbselect, finger, squery, args):
#######################################
## smi: pybel reference smiles ##
## nmols: number of similar ones ##
## dbselect: database to be searched ##
#######################################
## get database files
[dbsdf, dbfs] = setupdb(dbselect)
print('database set up :' + str(dbsdf) + ' || ' + str(dbfs))
globs = globalvars()
print('Finding results similar, comparing to ' + smi)
obab = 'babel'
if dbfs and args.dbfs:
com = obab + ' ' + dbfs + ' ' + 'simres.smi -d -xf' + finger + ' -s"' + smi + '" -al' + nmols
else:
mybash(obab + ' -isdf ' + dbsdf + ' -osdf -O tmp.sdf -d')
com = obab + ' tmp.sdf simres.smi -xf' + finger + ' -s"' + smi + '"'
## perform search using bash commandline
print('Performing substructure search:')
print('running: ' + str(com))
res = mybash(com)
print('res = ' + str(res))
print('number of SMILES returned : ' +
str(mybash('cat simres.smi | wc -l')))
if os.path.isfile('tmp.sdf'):
os.remove('tmp.sdf')
shutil.copy('simres.smi', 'initial.smi')
if args.dbmaxsmartsmatches:
print('Applying filters: inside get similar')
com = obab + " -ismi simres.smi -osmi -O simres.smi -h --filter " + squery
print('running: ' + str(com))
mybash(com)
print('number of lines in simres.smi: ' +
str(mybash('cat simres.smi | wc -l')))
# com = obab+" -ismi simres.smi -osmi -O simres.smi -d --filter 'nsmartsmatches<="+args.dbmaxsmartsmatches+"'"
# rint('running: '+ str(com))
# res = mybash(com)
# print('number of lines in simres.smi after dxbsmartmatches: '+str(mybash('cat simres.smi | wc -l')))
# print res
shutil.copy('simres.smi', 'afterfilteringsmarts.smi')
## check output and print error if nothing was found
if ('errors' in res):
ss = 'No matches were found in DB. Log info:\n' + res
print ss
return ss, True
else:
return 'simres.smi', False
def getmcores():
## this form of the functionn
## is used extensively in the GUI
## so it got it's own call. This
## is basically the same as getcores() but
## returns the full dictionary
globs = globalvars()
if globs.custom_path: # test if a custom path is used:
mcores = str(globs.custom_path).rstrip('/') + "/Cores/cores.dict"
else:
mcores = resource_filename(Requirement.parse("molSimplify"),"molSimplify/Cores/cores.dict")
mcores = readdict(mcores)
return mcores
def simple_slope_ann(slope_excitation):
globs=globalvars()
path_to_file = resource_filename(Requirement.parse("molSimplify"),"molSimplify/python_nn/" + "ms_slope")
#print('path to ANN data: ',path_to_file)
n = simple_network_builder([24,50,50],"ms_slope") ## no alpha value
#print(slope_excitation)
slope_excitation,sl_center,sl_shift = excitation_standardizer(slope_excitation,'slope')
#print(slope_excitation)
result = n.activate(slope_excitation)
# print('result is ' + str(result))
# print('center is ' + str(sl_center) + ' shift '+ str(sl_shift))
result = (result*sl_shift) + sl_center
#print('result is ' + str(result))
return result
def getlicores():
globs = globalvars()
if globs.custom_path: # test if a custom path is used:
licores = str(globs.custom_path).rstrip('/') + "/Ligands/ligands.dict"
else:
licores = resource_filename(Requirement.parse("molSimplify"),
"molSimplify/Ligands/ligands.dict")
licores = readdict(licores)
for ligand in licores.keys():
if len(licores[ligand][2]) == 2 and type(licores[ligand][2]) == list:
licores[ligand + '_flipped'] = copy.deepcopy(licores[ligand])
licores[ligand + '_flipped'][2].reverse()
return licores
def loadcoord(coord):
globs = globalvars()
# f = open(installdir+'Data/'+coord+'.dat')
if globs.custom_path:
f = globs.custom_path + "/Data/" +coord + ".dat"
else:
f = resource_filename(Requirement.parse("molSimplify"),"molSimplify/Data/" +coord + ".dat")
f = open(f)
txt = filter(None,f.read().splitlines())
f.close()
b = []
for line in txt:
l = filter(None,line.split(None))
b.append([float(l[0]),float(l[1]),float(l[2])])
return b
def simple_slope_ann(slope_excitation):
globs = globalvars()
path_to_file = resource_filename(Requirement.parse("molSimplify"),
"molSimplify/python_nn/" + "ms_slope")
#print('path to ANN data: ',path_to_file)
n = simple_network_builder([24, 50, 50], "ms_slope") ## no alpha value
#print(slope_excitation)
slope_excitation, sl_center, sl_shift = excitation_standardizer(
slope_excitation, 'slope')
#print(slope_excitation)
result = n.activate(slope_excitation)
# print('result is ' + str(result))
# print('center is ' + str(sl_center) + ' shift '+ str(sl_shift))
result = (result * sl_shift) + sl_center
#print('result is ' + str(result))
return result
def simple_splitting_ann(excitation):
globs=globalvars()
path_to_file = resource_filename(Requirement.parse("molSimplify"),"molSimplify/python_nn/" + "ms_split")
#print('path to ANN data: ',path_to_file)
n = simple_network_builder([25,50,50],"ms_split")
excitation,sp_center,sp_shift = excitation_standardizer(excitation,'split')
#print(excitation)
#print('center is ' + str(sp_center))
#print('scale is '+ str(sp_shift))
#print(excitation)
result = n.activate(excitation)
#print('result is ' + str(result))
result = (result*sp_shift) + sp_center
#print('result is ' + str(result))
return result,excitation
def getsimilar(smi, nmols, dbselect, finger, squery, args):
##get database files
[dbsdf, dbfs] = setupdb(dbselect)
print('database set up :' + str(dbsdf) + ' || ' + str(dbfs))
globs = globalvars()
print('Finding results similar, comparing to ' + smi)
obab = 'babel'
if dbfs and args.dbfs:
com = obab + ' ' + dbfs + ' ' + 'simres.smi -d -xf' + finger + ' -s"' + smi + '" -al' + nmols
else:
mybash(obab + ' -isdf ' + dbsdf + ' -osdf -O tmp.sdf -d')
com = obab + ' tmp.sdf simres.smi -xf' + finger + ' -s"' + smi + '"'
# perform search using bash commandline
print('Performing substructure search:')
print('running: ' + str(com))
res = mybash(com)
print ('res = ' + str(res))
print('number of SMILES returned : ' + str(mybash('cat simres.smi | wc -l')))
if os.path.isfile('tmp.sdf'):
os.remove('tmp.sdf')
shutil.copy('simres.smi', 'initial.smi')
if args.dbmaxsmartsmatches:
print('Applying filters: inside get similar')
com = obab + " -ismi simres.smi -osmi -O simres.smi -h --filter " + squery
print('running: ' + str(com))
mybash(com)
print('number of lines in simres.smi: ' + str(mybash('cat simres.smi | wc -l')))
# com = obab+" -ismi simres.smi -osmi -O simres.smi -d --filter 'nsmartsmatches<="+args.dbmaxsmartsmatches+"'"
# rint('running: '+ str(com))
# res = mybash(com)
# print('number of lines in simres.smi after dxbsmartmatches: '+str(mybash('cat simres.smi | wc -l')))
# print res
shutil.copy('simres.smi', 'afterfilteringsmarts.smi')
## check output and print error if nothing was found
if ('errors' in res):
ss = 'No matches were found in DB. Log info:\n' + res
print ss
return ss, True
else:
return 'simres.smi', False
def simple_splitting_ann(excitation):
globs = globalvars()
path_to_file = resource_filename(Requirement.parse("molSimplify"),
"molSimplify/python_nn/" + "ms_split")
#print('path to ANN data: ',path_to_file)
n = simple_network_builder([25, 50, 50], "ms_split")
excitation, sp_center, sp_shift = excitation_standardizer(
excitation, 'split')
# print('center is ' + str(sp_center))
# print('scale is '+ str(sp_shift))
result = n.activate(excitation)
#print(excitation)
#print('result is ' + str(result))
result = (result * sp_shift) + sp_center
#print('result is ' + str(result))
return result
def loaddata(path):
globs = globalvars()
# loads ML data from ML.dat file and
# store to dictionary
if globs.custom_path: # test if a custom path is used:
fname = str(globs.custom_path).rstrip('/') + path
else:
fname = resource_filename(Requirement.parse("molSimplify"),"molSimplify"+path)
d = dict()
f = open(fname)
txt = f.read()
lines = filter(None,txt.splitlines())
for line in lines[1:]:
if '#'!=line[0]: # skip comments
l = filter(None,line.split(None))
d[(l[0],l[1],l[2],l[3],l[4])] = l[5] # read dictionary
f.close()
return d
def copy_to_custom_path():
globs = globalvars()
if not globs.custom_path:
print('Error, custom path not set!')
raise ('')
## create folder
if not os.path.exists(globs.custom_path):
os.makedirs(globs.custom_path)
### copytree cannot overwrite, need to enusre directory does not exist already
core_dir = resource_filename(Requirement.parse("molSimplify"),
"molSimplify/Cores")
li_dir = resource_filename(Requirement.parse("molSimplify"),
"molSimplify/Ligands")
bind_dir = (resource_filename(Requirement.parse("molSimplify"),
"molSimplify/Bind"))
data_dir = (resource_filename(Requirement.parse("molSimplify"),
"molSimplify/Data"))
subs_dir = (resource_filename(Requirement.parse("molSimplify"),
"molSimplify/Substrates"))
if os.path.exists(str(globs.custom_path).rstrip("/") + "/Cores"):
print('Note: removing old molSimplify data')
shutil.rmtree(str(globs.custom_path).rstrip("/") + "/Cores")
if os.path.exists(str(globs.custom_path).rstrip("/") + "/Ligands"):
print('Note: removing old molSimplify data')
shutil.rmtree(str(globs.custom_path).rstrip("/") + "/Ligands")
if os.path.exists(str(globs.custom_path).rstrip("/") + "/Bind"):
print('Note: removing old molSimplify data')
shutil.rmtree(str(globs.custom_path).rstrip("/") + "/Bind")
if os.path.exists(str(globs.custom_path).rstrip("/") + "/Data"):
print('Note: removing old molSimplify data')
shutil.rmtree(str(globs.custom_path).rstrip("/") + "/Data")
if os.path.exists(str(globs.custom_path).rstrip("/") + "/Substrates"):
print('Note: removing old molSimplify data')
shutil.rmtree(str(globs.custom_path).rstrip("/") + "/Substrates")
shutil.copytree(core_dir, str(globs.custom_path).rstrip("/") + "/Cores")
shutil.copytree(li_dir, str(globs.custom_path).rstrip("/") + "/Ligands")
shutil.copytree(bind_dir, str(globs.custom_path).rstrip("/") + "/Bind")
shutil.copytree(data_dir, str(globs.custom_path).rstrip("/") + "/Data")
shutil.copytree(subs_dir,
str(globs.custom_path).rstrip("/") + "/Substrates")
def setupdb(dbselect):
globs = globalvars()
dbdir = os.path.relpath(globs.chemdbdir) + '/'
# get files in directory
dbfiles = os.listdir(dbdir)
# search for db files
dbmatches = [dbf for dbf in dbfiles if dbselect.lower() in dbf.lower()]
dbsdf = [dbm for dbm in dbmatches if '.sdf' in dbm]
dbfs = [dbm for dbm in dbmatches if '.fs' in dbm]
# print('thefile list' + str(dbfiles))
if len(dbsdf) == 0:
print dbselect + ' sdf database file missing from ' + dbdir + '. Please make sure file ' + dbselect + '.sdf is there..'
dbf1 = False
else:
dbf1 = dbdir + dbsdf[0]
if len(dbfs) == 0:
print dbselect + ' fastsearch database file missing from ' + dbdir + '. Please make sure file ' + dbselect + '.fs is there, it speeds up search significantly..'
dbf2 = False
else:
dbf2 = dbdir + dbfs[0]
return [dbf1, dbf2]
def setupdb(dbselect):
globs = globalvars()
dbdir = os.path.relpath(globs.chemdbdir) + '/'
# get files in directory
dbfiles = os.listdir(dbdir)
# search for db files
dbmatches = [dbf for dbf in dbfiles if dbselect.lower() in dbf.lower()]
dbsdf = [dbm for dbm in dbmatches if '.sdf' in dbm]
dbfs = [dbm for dbm in dbmatches if '.fs' in dbm]
# print('thefile list' + str(dbfiles))
if len(dbsdf) == 0:
print dbselect + ' sdf database file missing from ' + dbdir + '. Please make sure file ' + dbselect + '.sdf is there..'
dbf1 = False
else:
dbf1 = dbdir + dbsdf[0]
if len(dbfs) == 0:
print dbselect + ' fastsearch database file missing from ' + dbdir + '. Please make sure file ' + dbselect + '.fs is there, it speeds up search significantly..'
dbf2 = False
else:
dbf2 = dbdir + dbfs[0]
return [dbf1, dbf2]
def parseall(parser):
globs = globalvars()
parser.add_argument("-i", help="input file")
# hidden (non-user) arguments for GUI
parser.add_argument("-rprompt", help=argparse.SUPPRESS,action="store_true")
parser.add_argument("-gui", help=argparse.SUPPRESS,action="store_true") # gui placeholder
parser.add_argument("-checkdirb", help="CLI only: automatically ignore warning to replace existing folder", action="store_true")
parser.add_argument("-checkdirt", action="store_true") # directory removal check flag (what does this actually do?)
args=parser.parse_args()
parseinputs_basic(parser,args)
parseinputs_advanced(parser,args)
parseinputs_slabgen(parser,args)
parseinputs_autocorr(parser,args)
parseinputs_chainb(parser,args)
parseinputs_db(parser,args)
parseinputs_inputgen(parser,args)
parseinputs_postproc(parser,args)
parseinputs_random(parser,args)
parseinputs_binding(parser,args)
parseinputs_customcore(parser,args)
parseinputs_naming(parser,args)
return args
def bind_load(userbind, bindcores):
globs = globalvars()
if '~' in userbind:
homedir = os.path.expanduser("~")
userbind = userbind.replace('~', homedir)
emsg = False
bind = mol3D() # initialize binding molecule
bsmi = False # flag for smiles
### check if binding molecule exists in dictionary
if userbind in bindcores.keys():
# load bind mol file (with hydrogens)
# fbind = installdir+'Bind/'+bindcores[userbind][0]
if globs.custom_path:
fbind = globs.custom_path + "/Bind/" + bindcores[userbind][0]
else:
fbind = resource_filename(
Requirement.parse("molSimplify"),
"molSimplify/Bind/" + bindcores[userbind][0])
# check if bind xyz/mol file exists
if not glob.glob(fbind):
emsg = "We can't find the binding species structure file %s right now! Something is amiss. Exiting..\n" % fbind
print emsg
return False, False, emsg
if ('.xyz' in fbind):
bind.OBMol = bind.getOBMol(fbind, 'xyzf')
elif ('.mol' in fbind):
bind.OBMol = bind.getOBMol(fbind, 'molf')
elif ('.smi' in fbind):
bind.OBMol = bind.getOBMol(fbind, 'smif')
bind.charge = bind.OBMol.GetTotalCharge()
### load from file
elif ('.mol' in userbind or '.xyz' in userbind or '.smi' in userbind):
if glob.glob(userbind):
ftype = userbind.split('.')[-1]
# try and catch error if conversion doesn't work
try:
bind.OBMol = bind.getOBMol(userbind,
ftype + 'f') # convert from file
bind.charge = bind.OBMol.GetTotalCharge()
except IOError:
emsg = 'Failed converting file ' + userbind + ' to molecule..Check your file.\n'
return False, emsg
bind.ident = userbind.rsplit('/')[-1]
bind.ident = bind.ident.split('.' + ftype)[0]
else:
emsg = 'Binding species file ' + userbind + ' does not exist. Exiting..\n'
return False, emsg
### if not, try converting from SMILES
else:
# check for transition metals
userbind = checkTMsmiles(userbind)
# try and catch error if conversion doesn't work
try:
bind.OBMol = bind.getOBMol(userbind, 'smi') # convert from smiles
bind.charge = bind.OBMol.GetTotalCharge()
bsmi = True
bind.ident = 'smi'
except IOError:
emsg = "We tried converting the string '%s' to a molecule but it wasn't a valid SMILES string.\n" % userbind
emsg += "Furthermore, we couldn't find the binding species structure: '%s' in the binding species dictionary. Try again!\n" % userbind
print emsg
return False, False, emsg
return bind, bsmi, emsg
def lig_load(userligand, licores=None):
if licores == None:
licores = getlicores()
#@licores.pop("x", None)
globs = globalvars()
### get groups ###
groups = []
for entry in licores:
groups += licores[entry][3]
groups = sorted(list(set(groups)))
# check if user requested group
if userligand.lower() in groups:
subligs = [
key for key in licores if userligand.lower() in licores[key][3]
]
# randomly select ligand
userligand = random.choice(subligs)
if '~' in userligand:
homedir = os.path.expanduser("~")
userligand = userligand.replace('~', homedir)
emsg = False
lig = mol3D() # initialize ligand molecule
lig.needsconformer = False
### check if ligand exists in dictionary
if userligand in licores.keys():
print('loading ligand from dictionary: ' + str(userligand))
dbentry = licores[userligand]
# load lig mol file (with hydrogens)
if globs.custom_path:
flig = globs.custom_path + "/Ligands/" + dbentry[0]
else:
flig = resource_filename(Requirement.parse("molSimplify"),
"molSimplify/Ligands/" + dbentry[0])
# check if ligand xyz/mol file exists
#print('looking for '+flig)
if not glob.glob(flig):
emsg = "We can't find the ligand structure file %s right now! Something is amiss. Exiting..\n" % flig
print emsg
return False, emsg
if ('.xyz' in flig):
lig.OBMol = lig.getOBMol(flig, 'xyzf')
elif ('.mol' in flig):
lig.OBMol = lig.getOBMol(flig, 'molf')
elif ('.smi' in flig):
print('SMILES conversion')
lig.OBMol = lig.getOBMol(flig, 'smif')
lig.needsconformer = True
### modified the check for length,
### as it parsing string length instead of
### list length!
if isinstance(dbentry[2], (str, unicode)):
lig.denticity = 1
else:
lig.denticity = len(dbentry[2])
lig.ident = dbentry[1]
lig.charge = lig.OBMol.GetTotalCharge()
if 'pi' in dbentry[2]:
lig.cat = [int(l) for l in dbentry[2][:-1]]
lig.cat.append('pi')
else:
if lig.denticity == 1:
lig.cat = [int(dbentry[2])]
else:
lig.cat = [int(l) for l in dbentry[2]]
if lig.denticity > 1:
lig.grps = dbentry[3]
else:
lig.grps = []
if len(dbentry) > 3:
lig.ffopt = dbentry[4][0]
### load from file
elif ('.mol' in userligand or '.xyz' in userligand or '.smi' in userligand
or '.sdf' in userligand):
#flig = resource_filename(Requirement.parse("molSimplify"),"molSimplify/" +userligand)
if glob.glob(userligand):
ftype = userligand.split('.')[-1]
# try and catch error if conversion doesn't work
try:
print('ligand is an ' + ftype + ' file')
lig.OBMol = lig.getOBMol(userligand,
ftype + 'f') # convert from file
# generate coordinates if not existing
lig.charge = lig.OBMol.GetTotalCharge()
print('Ligand successfully converted to OBMol')
except IOError:
emsg = 'Failed converting file ' + userligand + ' to molecule..Check your file.\n'
return False, emsg
lig.ident = userligand.rsplit('/')[-1]
lig.ident = lig.ident.split('.' + ftype)[0]
else:
emsg = 'Ligand file ' + userligand + ' does not exist. Exiting..\n'
print emsg
return False, emsg
### if not, try interpreting as SMILES string
else:
try:
lig.getOBMol(userligand, 'smistring', True) # convert from smiles
lig.convert2mol3D()
assert lig.natoms
lig.charge = lig.OBMol.GetTotalCharge()
print('Ligand successfully interpreted as SMILES')
except:
emsg = "We tried converting the string '%s' to a molecule but it wasn't a valid SMILES string.\n" % userligand
emsg += "Furthermore, we couldn't find the ligand structure: '%s' in the ligands dictionary. Try again!\n" % userligand
emsg += "\nAvailable ligands are: %s\n" % getligs()
emsg += "\nAnd available groups are: %s\n" % getligroups(licores)
print emsg
return False, emsg
lig.ident = 'smi'
lig.needsconformer = True
lig.name = userligand
return lig, emsg
def substr_load(usersubstrate, sub_i, subcatoms, subcores=None):
if subcores == None:
subcores = getsubcores()
globs = globalvars()
if '~' in usersubstrate:
homedir = os.path.expanduser("~")
usersubstrate = usersubstrate.replace('~', homedir)
emsg = False
sub = mol3D() # initialize core molecule
### check if substrate exists in dictionary
if usersubstrate.lower() in [i.subname for i in subcores.keys()]:
print('loading substrate from dictionary')
# create a list for each item column in the dictionary
var_list = []
for var in [
subcores[i][0:] for i in subcores.keys()
if i.subname == usersubstrate.lower()
]:
var_list.append(var)
var_list = sorted(var_list)
var_list_sub_i = var_list[sub_i]
if globs.custom_path:
fsubst = globs.custom_path + "/Substrates/" + var_list_sub_i[0]
else:
fsubst = resource_filename(
Requirement.parse("molSimplify"),
"molSimplify/Substrates/" + var_list_sub_i[0])
# check if substrate xyz/mol file exists
if not glob.glob(fsubst):
emsg = "We can't find the substrate structure file %s right now! Something is amiss. Exiting..\n" % fcore
print emsg
return False, emsg
if ('.xyz' in fsubst):
sub.OBMol = sub.getOBMol(fsubst, 'xyzf')
elif ('.mol' in fsubst):
sub.OBMol = sub.getOBMol(fsubst, 'molf')
elif ('.smi' in fsubst):
sub.OBMol = sub.getOBMol(fsubst, 'smif')
# Parsing substrate denticity
### modified the check for length,
### as it parsing string length instead of
### list length!
if isinstance(var_list_sub_i[2], (str, unicode)):
sub.denticity = 1
else:
sub.denticity = len(var_list_sub_i[2])
# Parsing substrate identity
sub.ident = var_list_sub_i[1]
# Parsing substrate charge
sub.charge = sub.OBMol.GetTotalCharge()
# Parsing substrate connection atoms
if 'pi' in var_list_sub_i[2]:
sub.denticity = 1
sub.cat = [int(l) for l in var_list_sub_i[2][:-1]]
sub.cat.append('pi')
else:
if sub.denticity == 1:
sub.cat = [int(var_list_sub_i[2])]
else:
sub.cat = [int(l) for l in var_list_sub_i[2]]
if not subcatoms:
subcatoms = sub.cat
# Parsing substrate group
sub.grps = var_list_sub_i[3]
if len(var_list_sub_i[4]) > 0:
sub.ffopt = var_list_sub_i[4]
### load from file
elif ('.mol' in usersubstrate or '.xyz' in usersubstrate
or '.smi' in usersubstrate):
if glob.glob(usersubstrate):
ftype = usersubstrate.split('.')[-1]
print('Substrate is a ' + ftype + ' file')
# try and catch error if conversion doesn't work
try:
sub.OBMol = sub.getOBMol(usersubstrate,
ftype + 'f') # convert from file
print('Substrate successfully converted to OBMol')
except IOError:
emsg = 'Failed converting file ' + usersubstrate + ' to molecule..Check your file.\n'
print emsg
return False, emsg
sub.ident = usersubstrate.split('.')[0]
sub.ident = sub.ident.rsplit('/')[-1]
else:
emsg = 'Substrate file ' + usersubstrate + ' does not exist. Exiting..\n'
print emsg
return False, emsg
### if not, try converting from SMILES
else:
# check for transition metals
usersubstrate = checkTMsmiles(usersubstrate)
# try and catch error if conversion doesn't work
try:
sub.OBMol = sub.getOBMol(usersubstrate, 'smistring',
True) # convert from smiles
print('Substrate successfully interpreted as smiles')
except IOError:
emsg = "We tried converting the string '%s' to a molecule but it wasn't a valid SMILES string.\n" % usercore
emsg += "Furthermore, we couldn't find the substrate structure: '%s' in the substrates dictionary. Try again!\n" % usercore
emsg += "\nAvailable substrates are: %s\n" % getsubstrates()
print emsg
return False, emsg
sub.cat = [0]
sub.denticity = 1
sub.ident = 'substrate'
return sub, subcatoms, emsg
def core_load(usercore, mcores=None):
if mcores == None:
mcores = getmcores()
globs = globalvars()
if '~' in usercore:
homedir = os.path.expanduser("~")
usercore = usercore.replace('~', homedir)
emsg = False
core = mol3D() # initialize core molecule
### check if core exists in dictionary
if usercore.lower() in mcores.keys():
#print('loading core from dictionary')
dbentry = mcores[usercore.lower()]
# load core mol file (with hydrogens
if globs.custom_path:
fcore = globs.custom_path + "/Cores/" + dbentry[0]
else:
fcore = resource_filename(Requirement.parse("molSimplify"),
"molSimplify/Cores/" + dbentry[0])
# check if core xyz/mol file exists
if not glob.glob(fcore):
emsg = "We can't find the core structure file %s right now! Something is amiss. Exiting..\n" % fcore
print emsg
return False, emsg
if ('.xyz' in fcore):
core.OBMol = core.getOBMol(fcore, 'xyzf')
elif ('.mol' in fcore):
core.OBMol = core.getOBMol(fcore, 'molf')
elif ('.smi' in fcore):
core.OBMol = core.getOBMol(fcore, 'smif')
core.cat = [int(l) for l in filter(None, dbentry[1])]
core.denticity = dbentry[2]
core.ident = usercore
### load from file
elif ('.mol' in usercore or '.xyz' in usercore or '.smi' in usercore):
if glob.glob(usercore):
ftype = usercore.split('.')[-1]
print('Core is a ' + ftype + ' file')
# try and catch error if conversion doesn't work
try:
core.OBMol = core.getOBMol(usercore,
ftype + 'f') # convert from file
print('Core successfully converted to OBMol')
except IOError:
emsg = 'Failed converting file ' + usercore + ' to molecule..Check your file.\n'
print emsg
return False, emsg
core.ident = usercore.split('.')[0]
core.ident = core.ident.rsplit('/')[-1]
else:
emsg = 'Core file ' + usercore + ' does not exist. Exiting..\n'
print emsg
return False, emsg
### if not, try converting from SMILES
else:
# check for transition metals
usercore = checkTMsmiles(usercore)
# try and catch error if conversion doesn't work
try:
core.OBMol = core.getOBMol(usercore, 'smistring',
True) # convert from smiles
print('Core successfully interpreted as smiles')
except IOError:
emsg = "We tried converting the string '%s' to a molecule but it wasn't a valid SMILES string.\n" % usercore
emsg += "Furthermore, we couldn't find the core structure: '%s' in the cores dictionary. Try again!\n" % usercore
emsg += "\nAvailable cores are: %s\n" % getcores()
print emsg
return False, emsg
core.cat = [0]
core.denticity = 1
core.ident = 'core'
return core, emsg
def checkTMsmiles(smi):
g = globalvars()
for m in g.metals():
if m in smi:
smi = smi.replace(m, '[' + m + ']')
return smi
def mlpgen(args, strfiles, rootdir):
# get global variables
globs = globalvars()
jobdirs = []
coordfs = []
# Initialize the jobparams dictionary with mandatory/useful keywords.
jobparams = ['EF', 'PM7', 'XYZ', 'HESSIAN']
spin_keywords = {
1: 'SINGLET',
2: 'DOUBLET',
3: 'TRIPLET',
4: 'QUARTET',
5: 'QUINTET',
6: 'SEXTET',
7: 'SEPTET'
}
# Overwrite plus add any new dictionary keys from commandline input.
for xyzf in strfiles:
rdir = xyzf.rsplit('/', 1)[0]
xyzft = xyzf.rsplit('/', 1)[-1]
xyzf += '.xyz'
coordfs.append(xyzf.rsplit('/', 1)[-1])
coordname = xyzft
# Setting jobname for files + truncated name for queue.
nametrunc = coordname
if not os.path.exists(rdir + '/' + nametrunc) and not args.jobdir:
os.mkdir(rdir + '/' + nametrunc)
if args.jobdir:
mdir = args.jobdir
else:
mdir = rdir + '/' + nametrunc
jobdirs.append(mdir)
# shutil.copy2(xyzf,mdir)
# shutil.copy2(xyzf.replace('.xyz','.molinp'),mdir.replace('.xyz','.molinp'))
# Just carry over spin and charge keywords if they're set. Could do checks, none for now.
if args.spin:
jobparams.append(spin_keywords[int(args.spin)])
jobparams.append('UHF')
else:
jobparams.append("SINGLET")
if args.charge:
jobparams.append('CHARGE=' + str(args.charge))
# Now we're ready to start building the input file and the job script
for i, jobd in enumerate(jobdirs):
output = open(strfiles[i] + '.mop', 'w')
f = open(strfiles[i] + '.xyz')
s = f.readlines()[2:] # read coordinates
f.close()
# write rem block
for terms in jobparams:
output.write(' ' + terms)
# write additional options
if (args.remoption):
if len(args.remoption) % 2 > 0:
print('WARNING: wrong number of arguments in -remoption')
else:
for elem in range(0, int(0.5 * len(args.remoption))):
key, val = args.remoption[2 *
elem], args.remoption[2 * elem +
1]
output.write(key + '\t\t' + val + '\n')
output.write('\n' + nametrunc + '\n')
output.write('\n')
# write $molecule block
for lines in s:
ll = lines.split('\t')
for i, items in enumerate(ll):
output.write(' ' + items.strip('\n'))
if i > 0:
output.write(' 1')
if i == 3:
output.write('\n')
output.close()
return jobdirs
def qgen(args, strfiles, method):
# get global variables
globs = globalvars()
jobdirs = []
coordfs = []
# Initialize the jobparams dictionary with mandatory/useful keywords.
jobparams = {
'UNRESTRICTED': 'true',
'BASIS': 'lanl2dz',
'JOBTYPE': 'opt',
'EXCHANGE': 'b3lyp',
'CORRELATION': 'none',
'MAX_SCF_CYCLES': '500',
'GEOM_OPT_MAX_CYCLES': '1000',
'SYMMETRY': 'off',
'PRINT_ORBITALS': 'true',
'CHARGE': '1',
'SPIN': '1',
}
# Overwrite plus add any new dictionary keys from commandline input.
for xyzf in strfiles:
rdir = xyzf.rsplit('/', 1)[0]
xyzft = xyzf.rsplit('/', 1)[-1]
xyzf += '.xyz'
coordfs.append(xyzf.rsplit('/', 1)[-1])
coordname = xyzft
# Setting jobname for files + truncated name for queue.
if len(coordname) > 10:
nametrunc = coordname[0:6] + coordname[-4:]
else:
nametrunc = coordname
if not os.path.exists(rdir + '/' + nametrunc) and not args.jobdir:
os.mkdir(rdir + '/' + nametrunc)
mdir = rdir + '/' + nametrunc
if method:
mmd = '/' + method
mdir = rdir + '/' + nametrunc + mmd
if not os.path.exists(mdir):
os.mkdir(mdir)
jobdirs.append(mdir)
shutil.copy2(xyzf, mdir)
shutil.copy2(xyzf.replace('.xyz', '.molinp'),
mdir.replace('.xyz', '.molinp'))
try:
shutil.copy2(xyzf.replace('.xyz', '.report'),
mdir.replace('.xyz', '.report'))
except:
pass
# Check for existence of basis and sanitize name
if args.basis and len(args.basis) > 1:
jobparams['BASIS'] = args.basis
if args.correlation and len(args.correlation) > 1:
jobparams['CORRELATION'] = args.correlation
if method and len(method) > 1:
jobparams['EXCHANGE'] = method
if not args.unrestricted:
jobparams['UNRESTRICTED'] = 'false'
if (args.runtyp and 'en' in args.runtyp.lower()):
jobparams['run'] = 'SP'
elif (args.runtyp and 'ts' in args.runtyp.lower()):
jobparams['run'] = 'TS'
# Just carry over spin and charge keywords if they're set. Could do checks, none for now.
if args.spin:
jobparams['SPIN'] = args.spin
if args.charge:
jobparams['CHARGE'] = args.charge
# Now we're ready to start building the input file and the job script
for i, jobd in enumerate(jobdirs):
output = open(jobd + '/qch.inp', 'w')
f = open(jobd + '/' + coordfs[i])
s0 = f.readlines()[2:] # read coordinates
f.close()
# if separate split to two molecules
if args.bsep and '--' in ''.join(s0):
idxsplit = [isdx for isdx, ss in enumerate(s0) if '--' in ss][0]
s = '--\n' + jobparams['CHARGE'] + ' ' + jobparams['SPIN'] + '\n'
s += ''.join(s0[:idxsplit])
s += '--\n0 1\n'
s += ''.join(s0[idxsplit + 3:])
else:
s = s0
# write rem block
output.write('$rem\nUNRESTRICTED\t\t' + jobparams['UNRESTRICTED'])
output.write('\nBASIS\t\t' + jobparams['BASIS'] + '\nJOBTYPE\t\t' +
jobparams['JOBTYPE'])
output.write('\nEXCHANGE\t\t' + jobparams['EXCHANGE'] +
'\nCORRELATION\t\t')
output.write(jobparams['CORRELATION'] + '\nMAX_SCF_CYCLES\t\t')
output.write(jobparams['MAX_SCF_CYCLES'] + '\nGEOM_OPT_MAX_CYCLES\t\t')
output.write(jobparams['GEOM_OPT_MAX_CYCLES'] + '\nSYMMETRY\t\t' +
jobparams['SYMMETRY'])
output.write('\nPRINT_ORBITALS\t\t' + jobparams['PRINT_ORBITALS'] +
'\n')
# write additional options
if (args.remoption):
if len(args.remoption) % 2 > 0:
print('WARNING: wrong number of arguments in -remoption')
else:
for elem in range(0, int(0.5 * len(args.remoption))):
key, val = args.remoption[2 *
elem], args.remoption[2 * elem +
1]
output.write(key + '\t\t' + val + '\n')
output.write('$end\n\n')
# write $molecule block
output.write('$molecule\n' + jobparams['CHARGE'] + ' ' +
jobparams['SPIN'] + '\n')
output.write(''.join(s) + '$end')
output.close()
return jobdirs
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
''' # Written by the HJK Group # Dpt of Chemical Engineering, MIT ########################################################## ############ Main script that coordinates ############## ############# all parts of the program ################ ########################################################## import sys, argparse, os, platform, shutil from Scripts.inparse import * from Scripts.generator import * from molSimplify.Classes.globalvars import * globs = globalvars() DescString_basic = 'Welcome to molSimplify. Only basic usage is described here.\n' DescString_basic += 'For help on advanced modules, please refer to our documentation at WEBLINK or provide additional commands to -h, as below:\n' DescString_basic += '-h advanced: advanced structure generation help\n' DescString_basic += '-h slabgen: slab builder help\n' #DescString_basic += '-h chainb: chain builder help\n' DescString_basic += '-h autocorr: automated correlation analysis help\n' DescString_basic += '-h db: database search help\n' DescString_basic += '-h inputgen: quantum chemistry code input file generation help\n' DescString_basic += '-h postproc: post-processing help\n' DescString_basic += '-h random: random generation help\n' DescString_basic += '-h binding: binding species (second molecule) generation help\n' DescString_basic += '-h customcore: custom core functionalization help\n' DescString_basic += '-h naming: custom filename help\n' DescString_advanced = 'Printing advanced structure generation help.'
def removefromDB(sminame,ropt):
emsg = False
globs = globalvars()
if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
print('To database, you need to set a custom path. Please enter a writeable file path:')
new_path = input('path=')
globs.add_custom_path(new_path)
copy_to_custom_path()
li_path = globs.custom_path + "/Ligands/ligands.dict"
li_folder = globs.custom_path + "/Ligands/"
core_path = globs.custom_path + "/Cores/cores.dict"
core_dir = globs.custom_path + "/Cores/"
bind_path = globs.custom_path + "/Bind/bind.dict"
bind_folder = globs.custom_path +"/Bind/"
# convert to unicode
sminame = unicodedata.normalize('NFKD',sminame).encode('ascii','ignore')
if ropt==1:
# update dictionary
f = open(li_path,'r')
ss = f.read().splitlines()
f.close()
f = open(li_path,'w')
ssort = sorted(ss[1:])
f.write(ss[0]+'\n')
for s in ssort:
sss = s.split(':')
if sminame!=sss[0]:
f.write(s+'\n')
else:
os.remove(li_folder + sss[1].split(',')[0])
f.close()
elif ropt==0:
mcores = readdict(core_path)
# update dictionary
f = open(core_path,'r')
ss = f.read().splitlines()
f.close()
f = open(core_path,'w')
ssort = sorted(ss[1:])
f.write(ss[0]+'\n')
for s in ssort:
sss = s.split(':')
if sminame!=sss[0]:
f.write(s+'\n')
else:
os.remove(core_folder+sss[1].split(',')[0])
f.close()
elif ropt==2:
bindcores = readdict(bind_path)
# update dictionary
f = open(bind_path,'r')
ss = f.read().splitlines()
f.close()
f = open(bind_path,'w')
ssort = sorted(ss[1:])
f.write(ss[0]+'\n')
for s in ssort:
sss = s.split(':')
if sminame!=sss[0]:
f.write(s+'\n')
else:
os.remove(bind_folder+sss[1].split(',')[0])
f.close()
return emsg
def removefromDB(sminame, ropt):
emsg = False
globs = globalvars()
if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
print(
'To database, you need to set a custom path. Please enter a writeable file path:'
)
new_path = eval(input('path='))
globs.add_custom_path(new_path)
copy_to_custom_path()
li_path = globs.custom_path + "/Ligands/ligands.dict"
li_folder = globs.custom_path + "/Ligands/"
core_path = globs.custom_path + "/Cores/cores.dict"
core_dir = globs.custom_path + "/Cores/"
bind_path = globs.custom_path + "/Bind/bind.dict"
bind_folder = globs.custom_path + "/Bind/"
# convert to unicode
sminame = unicodedata.normalize('NFKD', sminame).encode('ascii',
'ignore').decode()
if ropt == 1:
# update dictionary
f = open(li_path, 'r')
ss = f.read().splitlines()
f.close()
f = open(li_path, 'w')
ssort = sorted(ss[1:])
f.write(ss[0] + '\n')
for s in ssort:
sss = s.split(':')
if sminame != sss[0]:
f.write(s + '\n')
else:
os.remove(li_folder + sss[1].split(',')[0])
f.close()
elif ropt == 0:
mcores = readdict(core_path)
# update dictionary
f = open(core_path, 'r')
ss = f.read().splitlines()
f.close()
f = open(core_path, 'w')
ssort = sorted(ss[1:])
f.write(ss[0] + '\n')
for s in ssort:
sss = s.split(':')
if sminame != sss[0]:
f.write(s + '\n')
else:
os.remove(core_folder + sss[1].split(',')[0])
f.close()
elif ropt == 2:
bindcores = readdict(bind_path)
# update dictionary
f = open(bind_path, 'r')
ss = f.read().splitlines()
f.close()
f = open(bind_path, 'w')
ssort = sorted(ss[1:])
f.write(ss[0] + '\n')
for s in ssort:
sss = s.split(':')
if sminame != sss[0]:
f.write(s + '\n')
else:
os.remove(bind_folder + sss[1].split(',')[0])
f.close()
return emsg
def molcgen(args, strfiles, method):
# global variables
globs = globalvars()
jobdirs = []
coordfs = []
# Initialize the jobparams dictionary with mandatory/useful keywords. TG: removed min_coordinates cartesian
jobparams = {
'Group': 'Nosym',
'method': 'CASSCF',
'spin': '1',
'charge': '0',
# 'nactel':'2',
# 'frozen':'0',
# 'ras2':'12',
'ciroot': '1 1 ;1',
'ITER': '1000,100',
'multistate': '1 1',
'imaginary': '0.1',
'ipeashift': '0.25',
'density': 'no',
'grid_it': 'no',
'gridtype': 'TOTAL',
'NPOINTS': '100 100 100',
}
# if multiple methods requested generate c directories
# Overwrite plus add any new dictionary keys from commandline input.
for xyzf in strfiles:
rdir = xyzf.rsplit('/', 1)[0]
xyzft = xyzf.rsplit('/', 1)[-1]
xyzf += '.xyz'
coordfs.append(xyzf.rsplit('/', 1)[-1])
coordname = xyzft
# Setting jobname for files + truncated name for queue.
if len(coordname) > 10:
nametrunc = coordname
else:
nametrunc = coordname
if not os.path.exists(rdir + '/' + nametrunc) and not args.jobdir:
os.mkdir(rdir + '/' + nametrunc)
mdir = rdir + '/' + nametrunc
if method:
if method[0] == 'U' or method[0] == 'u':
mmd = '/' + method[1:]
else:
mmd = '/' + method
mdir = rdir + '/' + nametrunc + mmd
if not os.path.exists(mdir):
try:
os.mkdirs(mdir)
except:
pass
if not args.jobdir:
jobdirs.append(mdir)
shutil.copy2(xyzf, mdir)
shutil.copy2(xyzf.replace('.xyz', '.molinp'),
mdir.replace('.xyz', '.molinp'))
try:
shutil.copy2(xyzf.replace('.xyz', '.report'),
mdir.replace('.xyz', '.report'))
except:
pass
elif args.jobdir:
jobdirs.append(rdir)
# parse extra arguments
# Method parsing, does not check if a garbage method is used here:
if method:
jobparams['method'] = method
else:
jobparams['method'] = 'CASSCF'
print((args.method, method, jobparams['method']))
# Check runtype
if (args.runtyp and 'energy' in args.runtyp.lower()):
jobparams['run'] = 'energy'
else:
print(
'''Warning! Currently MOLCAS input file generation is only supported for
single point energy. For other types of calculation requested, the input
file is generated for single point energy instead''')
# Just carry over spin and charge keywords if they're set. Could do checks, none for now.
if args.spin:
jobparams['spin'] = str(args.spin)
if args.charge:
if args.bcharge:
args.charge = int(args.charge) + int(args.bcharge)
jobparams['charge'] = str(args.charge)
# Check for existence of basis and sanitize name
# Automatically assign basis based on element
if args.basis and args.basis != 'lacvps_ecp':
jobparams['basis'] = args.basis
elif (not args.basis) or args.basis == 'lacvps_ecp':
temp = mol3D()
jobparams['basis'] = molcbasis(strfiles, 'ANO-rcc')
# Overwrite plus add any new dictionary keys from commandline input.
if args.qoption:
if len(args.qoption) % 2 != 0:
print('WARNING: wrong number of arguments in -qoption')
else:
for elem in range(0, int(0.5 * len(args.qoption))):
key, val = args.qoption[2 * elem], args.qoption[2 * elem + 1]
jobparams[key] = val
# Check which paramters are missing
# Check and automatically assign number of active electrons
if 'nactel' not in jobparams:
oxnum = 0 # oxidation state number
if args.oxstate in list(romans.keys()):
oxnum = int(romans[args.oxstate])
else:
oxnum = int(args.oxstate)
jobparams['nactel'] = molcnactels(strfiles, oxnum)
else:
nactel = int(jobparams['nactel'])
jobparams['nactel'] = [nactel for i in range(0, len(strfiles))]
# Check and automatically assign number of frozen orbitals for CASSCF
if 'frozen' not in jobparams:
jobparams['frozen'] = molcfrozens(strfiles)
else:
frozen = int(jobparams['frozen'])
jobparams['frozen'] = [frozen for i in range(0, len(strfiles))]
# Check and automatically assign number of frozen orbitals for ras2
if 'ras2' not in jobparams:
jobparams['ras2'] = molcras2s(strfiles)
else:
ras2 = int(jobparams['ras2'])
jobparams['ras2'] = [ras2 for i in range(0, len(strfiles))]
# Check key for grid_it. Overwrite the default in case
# the command line input is in different case
for key in list(jobparams.keys()):
if 'grid_it' in key.lower() and key != 'grid_it':
jobparams['grid_it'] = jobparams[key]
break
# Now we're ready to start building the input file
if not args.jobdir:
for i, jobd in enumerate(jobdirs):
output = open(jobd + '/molcas.input', 'w')
output.write('# file created with %s\n' % globs.PROGRAM)
molcwrt(output, jobparams, coordfs[i], i)
output.close()
elif args.jobdir:
for i, jobd in enumerate(jobdirs):
print(('jobd is ' + jobd))
output = open(jobd + '/molcas.input', 'w')
output.write('# file created with %s\n' % globs.PROGRAM)
molcwrt(output, jobparams, coordfs[i], i)
output.close()
return jobdirs
def plugin_defs():
globs = globalvars()
plugin_path = resource_filename(Requirement.parse("molSimplify"),
"molSimplify/plugindefines_reference.txt")
return plugin_path
def dissim(outf, n):
globs = globalvars()
obab = 'babel'
# clone hitlist file
hit_list_path = "hitlist.smi"
with open(outf) as f:
smiles_list = f.readlines()
with open(hit_list_path, 'w') as f:
f.writelines(smiles_list)
# generate fs of original hit list
mybash(obab + ' -ismi ' + hit_list_path + ' -osdf tmp.sdf')
mybash(obab + ' tmp.sdf -ofs')
# number of hits
numcpds = mybash('obabel tmp.sdf -onul')
numcpds = int(numcpds.split(None)[0])
# pick first element of list
mybash('obabel tmp.sdf -O 1.smi -f 1 -l 1')
del smiles_list[0]
with open(hit_list_path, 'w') as f:
f.writelines(smiles_list)
# recompute the fs and number of hits parameters
numcpds += -1 # decrease number of hits
mybash(obab + ' -ismi ' + hit_list_path + ' -osdf tmp.sdf')
mybash(obab + ' tmp.sdf -ofs')
print 'Performing dissimilarity search:'
mostdissim = []
if n > 1:
# find most dissimilar structure
for i in range(n - 1):
# initialize list of total similarities
simsum = [0] * numcpds
# compute total similarity of each dissimilar structure with hit list
for j in range(i + 1):
a = mybash('obabel ' + str(j + 1) + '.smi tmp.sdf -ofpt')
a = a.splitlines()
a = [s.split('= ') for s in a]
a = [item for sublist in a for item in sublist]
aa = []
for k in a:
try:
aa.append(float(k))
except:
pass
a = aa
simsum = [x + y for x, y in zip(simsum, a)]
# pick most dissimilar structure by greedily minimizing total similarity
mostdissim = simsum.index(min(simsum))
mybash('obabel tmp.sdf -O ' + str(i + 2) + '.smi -f ' + str(mostdissim + 1) + ' -l' + str(mostdissim + 1))
# remove most dissimilar from the list and re-write the smi file
del smiles_list[mostdissim]
with open(hit_list_path, 'w') as f:
f.writelines(smiles_list)
# recompute the fs and number of hits parameters
numcpds += -1 # decrease number of hits
mybash(obab + ' -ismi ' + hit_list_path + ' -osdf tmp.sdf')
mybash(obab + ' tmp.sdf -ofs')
# combine results into one file
f = open('dissimres.smi', 'w')
for i in range(n):
ff = open(str(i + 1) + '.smi', 'r')
s = ff.read().splitlines()
ff.close()
f.write(s[0] + '\n')
os.remove(str(i + 1) + '.smi')
f.close()
return 0
def gamgen(args, strfiles, method):
# get global variables
globs = globalvars()
jobdirs = []
coordfs = []
# Initialize the jobparams dictionary with mandatory/useful keywords.
jobparams = {
'RUNTYP': 'OPTIMIZE',
'GBASIS': 'N21',
'MAXIT': '500',
'DFTTYP': 'B3LYP',
'SCFTYP': 'UHF',
'ICHARG': '0',
'MULT': '1',
}
# Overwrite plus add any new dictionary keys from commandline input.
for xyzf in strfiles:
# convert to "gamess format"
xyzf = xyz2gxyz(xyzf + '.xyz')
rdir = xyzf.rsplit('/', 1)[0]
xyzft = xyzf.rsplit('/', 1)[-1]
xyzf += '.gxyz'
coordfs.append(xyzf)
coordname = xyzft
# Setting jobname for files + truncated name for queue.
if len(coordname) > 10:
nametrunc = coordname[0:6] + coordname[-4:]
else:
nametrunc = coordname
if not os.path.exists(rdir + '/' + nametrunc):
os.mkdir(rdir + '/' + nametrunc)
mdir = rdir + '/' + nametrunc
if method:
if method[0] == 'U' or method[0] == 'u':
mmd = '/' + method[1:]
else:
mmd = '/' + method
jobparams['SCFTYP'] = 'RHF'
mdir = rdir + '/' + nametrunc + mmd
if not os.path.exists(mdir):
os.mkdir(mdir)
jobdirs.append(mdir)
shutil.copy2(xyzf, mdir)
shutil.copy2(xyzf.replace('.gxyz', '.molinp'),
mdir.replace('.gxyz', '.molinp'))
try:
shutil.copy2(xyzf.replace('.xyz', '.report'),
mdir.replace('.xyz', '.report'))
except:
pass
if method:
if method[0] == 'U' or method[0] == 'u':
method = method[1:]
# Just carry over spin and charge keywords if they're set. Could do checks, none for now.
if args.spin:
jobparams['MULT'] = str(args.spin)
if args.charge:
jobparams['ICHARG'] = str(args.charge)
# Check for existence of basis and sanitize name
if args.gbasis:
jobparams['GBASIS'] = args.gbasis.upper()
if args.ngauss:
jobparams['NGAUSS'] = args.ngauss.upper()
if method:
jobparams['DFTTYP'] = method.upper()
if (args.runtyp and 'en' in args.runtyp.lower()):
jobparams['run'] = 'ENERGY'
elif (args.runtyp and 'ts' in args.runtyp.lower()):
jobparams['run'] = 'SADPOINT'
# Now we're ready to start building the input file and the job script
for i, jobd in enumerate(jobdirs):
output = open(jobd + '/gam.inp', 'w')
f = open(coordfs[i])
s = f.read() # read coordinates
f.close()
jobparams['coordinates'] = s
output.write('! File created using %s\n' % globs.PROGRAM)
# write $BASIS block
output.write(' $BASIS ')
if args.ngauss:
output.write(' GBASIS=' + jobparams['GBASIS'])
output.write(' NGAUSS=' + jobparams['NGAUSS'])
else:
output.write(' GBASIS=' + jobparams['GBASIS'])
if args.ndfunc:
output.write(' NDFUNC=' + args.ndfunc)
if args.npfunc:
output.write(' NPFUNC=' + args.npfunc)
output.write(' $END\n')
# write $SYSTEM block
output.write(' $SYSTEM ')
# check if MWORDS specified by the user
if not args.sysoption or not ('MWORDS' in args.sysoption):
output.write(' MWORDS=16')
# write additional options
if (args.sysoption):
if len(args.sysoption) % 2 > 0:
print('WARNING: wrong number of arguments in -sysoption')
else:
for elem in range(0, int(0.5 * len(args.sysoption))):
key, val = args.sysoption[2 *
elem], args.sysoption[2 * elem +
1]
output.write(' ' + key + '=' + val + ' ')
output.write(' $END\n')
# write CONTRL block
output.write(' $CONTRL SCFTYP=' + jobparams['SCFTYP'] + ' DFTTYP=')
output.write(jobparams['DFTTYP'] + ' RUNTYP=' + jobparams['RUNTYP'])
output.write('\n ICHARG=' + jobparams['ICHARG'] + ' MULT=')
# check if CC basis set specified and add spherical
if 'CC' in jobparams['GBASIS']:
output.write(jobparams['MULT'] + ' ISPHER=1\n')
else:
output.write(jobparams['MULT'] + '\n')
# write additional options
if (args.ctrloption):
if len(args.ctrloption) % 2 > 0:
print('WARNING: wrong number of arguments in -ctrloption')
else:
for elem in range(0, int(0.5 * len(args.ctrloption))):
key, val = args.ctrloption[2 *
elem], args.ctrloption[2 * elem
+ 1]
output.write(' ' + key + '=' + val + ' ')
output.write(' $END\n')
# write $SCF block
output.write(' $SCF ')
# check if options specified by the user
if not args.scfoption or not ('DIRSCF' in args.scfoption):
output.write(' DIRSCF=.TRUE.')
if not args.scfoption or not ('DIIS' in args.scfoption):
output.write(' DIIS=.TRUE.')
if not args.scfoption or not ('SHIFT' in args.scfoption):
output.write(' SHIFT=.TRUE.')
# write additional options
if (args.scfoption):
if len(args.scfoption) % 2 != 0:
print('WARNING: wrong number of arguments in -scfoption')
else:
for elem in range(0, int(0.5 * len(args.scfoption))):
key, val = args.scfoption[2 *
elem], args.scfoption[2 * elem +
1]
output.write(' ' + key + '=' + val + ' ')
output.write(' $END\n')
# write $STATPT block
output.write(' $STATPT ')
# check if NSTEP specified by the user
if not args.statoption or not ('NSTEP' in args.statoption):
output.write(' NSTEP=100')
# write additional options
if (args.statoption):
if len(args.statoption) % 2 > 0:
print('WARNING: wrong number of arguments in -statoption')
else:
for elem in range(0, int(0.5 * len(args.statoption))):
key, val = args.statoption[2 *
elem], args.statoption[2 * elem
+ 1]
output.write(' ' + key + '=' + val + ' ')
output.write(' $END\n')
# write $DATA block
output.write(' $DATA\n')
output.write(jobparams['coordinates'] + ' $END\n')
output.close()
return jobdirs
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 tcgen(args, strfiles, method):
# global variables
# print('----- args provided to tc gen --------')
# print(args)
globs = globalvars()
jobdirs = []
coordfs = []
# Initialize the jobparams dictionary with mandatory/useful keywords. TG: removed min_coordinates cartesian
jobparams = {
'run': 'minimize',
'timings': 'yes',
'maxit': '500',
'scrdir': './scr',
'method': 'b3lyp',
'basis': 'lacvps_ecp',
'spinmult': '1',
'charge': '0',
'gpus': '1',
}
# if multiple methods requested generate c directories
# Overwrite plus add any new dictionary keys from commandline input.
for xyzf in strfiles:
rdir = xyzf.rsplit('/', 1)[0]
xyzft = xyzf.rsplit('/', 1)[-1]
xyzf += '.xyz'
coordfs.append(xyzf.rsplit('/', 1)[-1])
coordname = xyzft
# Setting jobname for files + truncated name for queue.
if len(coordname) > 10:
nametrunc = coordname
else:
nametrunc = coordname
if not os.path.exists(rdir + '/' + nametrunc) and not args.jobdir:
os.mkdir(rdir + '/' + nametrunc)
mdir = rdir + '/' + nametrunc
if method:
if method[0] == 'U' or method[0] == 'u':
mmd = '/' + method[1:]
else:
mmd = '/' + method
mdir = rdir + '/' + nametrunc + mmd
if not os.path.exists(mdir):
os.mkdir(mdir)
if not args.jobdir:
jobdirs.append(mdir)
if not args.reportonly:
shutil.copy2(xyzf, mdir)
shutil.copy2(xyzf.replace('.xyz', '.molinp'),
mdir.replace('.xyz', '.molinp'))
try:
shutil.copy2(xyzf.replace('.xyz', '.report'),
mdir.replace('.xyz', '.report'))
except:
pass
elif args.jobdir:
jobdirs.append(rdir)
# if report only specified, end here
if args.reportonly:
return jobdirs
# parse extra arguments
# Method parsing, does not check if a garbage method is used here:
unrestricted = False
if method:
jobparams['method'] = method
if ('u' or 'U') in method[0]:
# Unrestricted calculation
unrestricted = True
else:
# Restricted calculation
unrestricted = False
if args.spin and int(args.spin) > 1:
jobparams['method'] = 'u' + method
unrestricted = True
else:
if args.spin and int(args.spin) >= 1:
jobparams['method'] = 'ub3lyp'
unrestricted = True
else:
jobparams['method'] = 'b3lyp'
if (args.runtyp and 'energy' in args.runtyp.lower()):
jobparams['run'] = 'energy'
elif (args.runtyp and 'ts' in args.runtyp.lower()):
jobparams['run'] = 'ts'
elif (args.runtyp and 'gradient' in args.runtyp.lower()):
jobparams['run'] = 'gradient'
if (args.gpus):
jobparams['gpus'] = args.gpus
if (args.dispersion):
jobparams['dispersion'] = args.dispersion
# Just carry over spin and charge keywords if they're set. Could do checks, none for now.
if args.spin:
jobparams['spinmult'] = args.spin
if args.charge:
if args.bcharge:
args.charge = int(args.charge) + int(args.bcharge)
jobparams['charge'] = args.charge
# Check for existence of basis and sanitize name
if args.basis:
ecp = False # Flag not currently used, for deciding gpus_ecp code or not later. Can always specify with 'extra' command
if '*' in args.basis:
jobparams['basis'] = args.basis.replace('*', 's')
else:
jobparams['basis'] = args.basis
# Overwrite plus add any new dictionary keys from commandline input.
if args.qoption:
if len(args.qoption) % 2 != 0:
print('WARNING: wrong number of arguments in -qoption')
else:
for elem in range(0, int(0.5 * len(args.qoption))):
key, val = args.qoption[2 * elem], args.qoption[2 * elem + 1]
jobparams[key] = val
# Extra keywords for unrestricted.
if unrestricted:
# If running unrestricted, assume convergence will be more difficult for now.
jobparams['scf'] = 'diis+a'
if 'levelshift' not in jobparams:
jobparams['levelshift'] = 'yes'
elif jobparams['levelshift'] != 'yes':
print((
"Warning! You're doing an unrestricted calculation but have set levelshift = %s"
% (jobparams['levelshift'])))
if 'levelshiftvala' not in jobparams:
jobparams['levelshiftvala'] = '0.25'
if 'levelshiftvalb' not in jobparams:
jobparams['levelshiftvalb'] = '0.25'
# Now we're ready to start building the input file
if not args.jobdir:
for i, jobd in enumerate(jobdirs):
output = open(jobd + '/terachem_input', 'w')
output.write('# file created with %s\n' % globs.PROGRAM)
jobparams['coordinates'] = coordfs[i]
for keys in list(jobparams.keys()):
output.write('%s %s\n' % (keys, jobparams[keys]))
if jobparams['run'] == 'minimize':
output.write('new_minimizer yes\n')
#output.write('min_coordinates cartesian\n')
if args.tc_fix_dihedral:
temp = mol3D()
temp.readfromxyz(strfiles[i])
metal_ind = temp.findMetal()
fixed_atoms = list()
fixed_atoms = temp.getBondedAtoms(metal_ind)
fixed_atoms = [str(int(i) + 1)
for i in fixed_atoms] # 1-based indices
string_to_write = 'dihedral 0 ' + '_'.join(fixed_atoms)
# print(string_to_write)
output.write('$constraint_set \n')
output.write(string_to_write + '\n')
output.write('end\n')
output.close()
elif args.jobdir:
for i, jobd in enumerate(jobdirs):
print(('jobd is ' + jobd))
if args.name:
output = open(jobd + '/' + args.name + '.in', 'w')
else:
output = open(jobd + '/terachem_input', 'w')
output.write('# file created with %s\n' % globs.PROGRAM)
jobparams['coordinates'] = coordfs[i]
for keys in list(jobparams.keys()):
output.write('%s %s\n' % (keys, jobparams[keys]))
if jobparams['run'] == 'minimize':
output.write('new_minimizer yes\n')
#output.write('min_coordinates cartesian\n')
if args.tc_fix_dihedral:
temp = mol3D()
temp.readfromxyz(strfiles[i])
metal_ind = temp.findMetal()
fixed_atoms = list()
fixed_atoms = temp.getBondedAtoms(metal_ind)
fixed_atoms = [str(int(i) + 1)
for i in fixed_atoms] # 1-based indices
string_to_write = 'dihedral 0 ' + '_'.join(fixed_atoms)
# print(string_to_write)
output.write('$constraint_set \n')
output.write(string_to_write + '\n')
output.write('end\n')
output.close()
return jobdirs
def addtoldb(smimol,sminame,smident,smicat,smigrps,smictg,ffopt):
emsg = False
globs = globalvars()
if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
print('To add to database, you need to set a custom path. Please enter a writeable file path:')
new_path = input('path=')
globs.add_custom_path(new_path)
copy_to_custom_path()
lipath = globs.custom_path + "/Ligands/ligands.dict"
licores = readdict(lipath)
ligands_folder = globs.custom_path + "/Ligands/"
print("ligands_folder is : " + str(ligands_folder))
# check if ligand exists
if sminame in licores.keys():
emsg = 'Ligand '+sminame+' already existing in ligands database.'
emsg += ' To replace, delete the existing entry first.'
return emsg
else:
# get connection atoms
ccats = filter(None,re.split(' |,|\t',smicat))
# get groups
groups = filter(None,re.split(' |,|\t',smigrps))
grp = 'all '+' '.join(groups)
grp += ' '+smictg
if smicat=='':
cats = range(0,int(smident))
else:
cats = [int(a)-1 for a in ccats]
cs = [str(a) for a in cats]
css = ' '.join(cs)
# convert to unicode
smimol = unicodedata.normalize('NFKD',smimol).encode('ascii','ignore')
sminame = unicodedata.normalize('NFKD',sminame).encode('ascii','ignore')
if '~' in smimol:
smimol = smimol.replace('~',os.expanduser('~'))
# convert ligand from smiles/file
lig,emsg = lig_load(smimol,licores)
if emsg:
return emsg
lig.convert2mol3D() # convert to mol3D
shortname = sminame
print("smimol is "+str(smimol))
print("sminame is "+str(sminame))
# sanitize ff options:
if not ffopt in ["A","B","BA"]:
print('warning: incompatible ffopt choice. Options are ' + str(["A","B","BA","N"]))
sys.exit(1)
# new entry for dictionary
if '.mol' in smimol:
shutil.copy2(smimol,ligands_folder + sminame+'.mol')
snew = sminame+':'+sminame+'.mol,'+shortname+','+css+','+grp+','+ffopt
elif '.xyz' in smimol:
shutil.copy2(smimol,ligands_folder + sminame+'.xyz')
snew = sminame+':'+sminame+'.xyz,'+shortname+','+css+','+grp+','+ffopt
elif lig.OBMol:
# write smiles file in Ligands directory
obConversion = openbabel.OBConversion()
obConversion.SetOutFormat("smi")
red = obConversion.Read(lig.OBMol)
obConversion.WriteFile(lig.OBMol,ligands_folder + sminame+'.smi')
#lig.OBMol.write('smi',ligands_folder + sminame+'.smi')
snew = sminame+':'+sminame+'.smi,'+shortname+','+css+','+grp+','+ffopt
else:
# write xyz file in Ligands directory
lig.writexyz(ligands_folder+sminame+'.xyz') # write xyz file
snew = sminame+':'+sminame+'.xyz,'+shortname+','+css+','+grp+','+ffopt
# update dictionary
f = open(lipath,'r')
ss = f.read().splitlines()
f.close()
f = open(lipath,'w')
ss.append(snew)
ssort = sorted(ss[1:])
f.write(ss[0]+'\n')
for s in ssort:
f.write(s+'\n')
f.close()
return emsg
def ogen(args, strfiles, method):
# global variables
globs = globalvars()
jobdirs = []
coordfs = []
# Initialize the jobparams dictionary with mandatory/useful keywords. TG: removed min_coordinates cartesian
jobparams = {
'run': 'Sp',
'basis': 'def2-TZVP',
'MaxIter': '500',
'method': 'B3LYP',
'spinmult': '1',
'charge': '0',
'ERI': 'NORI',
'REL': '',
'UNO': '',
'mdci_maxit': '200',
'mdci_shift': '0.2',
'HFX': False,
}
# if multiple methods requested generate c directories
# Overwrite plus add any new dictionary keys from commandline input.
for xyzf in strfiles:
rdir = xyzf.rsplit('/', 1)[0]
xyzft = xyzf.rsplit('/', 1)[-1]
xyzf += '.xyz'
coordfs.append(xyzf.rsplit('/', 1)[-1])
coordname = xyzft
# Setting jobname for files + truncated name for queue.
if len(coordname) > 10:
nametrunc = coordname
else:
nametrunc = coordname
if not os.path.exists(rdir + '/' + nametrunc) and not args.jobdir:
os.mkdir(rdir + '/' + nametrunc)
mdir = rdir + '/' + nametrunc
if method:
if method[0] == 'U' or method[0] == 'u':
mmd = '/' + method[1:]
else:
mmd = '/' + method
mdir = rdir + '/' + nametrunc + mmd
if not os.path.exists(mdir):
try:
os.mkdirs(mdir)
except:
pass
if not args.jobdir:
jobdirs.append(mdir)
shutil.copy2(xyzf, mdir)
shutil.copy2(xyzf.replace('.xyz', '.molinp'),
mdir.replace('.xyz', '.molinp'))
try:
shutil.copy2(xyzf.replace('.xyz', '.report'),
mdir.replace('.xyz', '.report'))
except:
pass
elif args.jobdir:
jobdirs.append(rdir)
# parse extra arguments
# Method parsing, does not check if a garbage method is used here:
unrestricted = False
if method:
jobparams['method'] = method
if args.spin and int(args.spin) > 1:
unrestricted = True
# For ORCA, "ro" or "u" is not needed
if ('u' or 'U') in method[0]:
jobparams['method'] = method[1:]
# Unrestricted calculation
elif ('ro' or 'RO') in method[0]:
# Restricted calculation
unrestricted = False
jobparams['method'] = method[2:]
else:
if args.spin and int(args.spin) >= 1:
jobparams['method'] = 'B3LYP'
unrestricted = True
else:
jobparams['method'] = 'B3LYP'
print((args.method, method, jobparams['method']))
# Check runtype and we accept both ORCA and terachem naming convention
if (args.runtyp and 'energy' in args.runtyp.lower()):
jobparams['run'] = 'Sp'
elif (args.runtyp and 'sp' in args.runtyp.lower()):
jobparams['run'] = 'Sp'
elif (args.runtyp and 'opt' in args.runtyp.lower()):
jobparams['run'] = 'Opt'
elif (args.runtyp and 'minimize' in args.runtyp.lower()):
jobparams['run'] = 'Opt'
elif (args.runtyp and 'gradient' in args.runtyp.lower()):
jobparams['run'] = 'EnGrad'
elif (args.runtyp and 'engrad' in args.runtyp.lower()):
jobparams['run'] = 'EnGrad'
# Special sanity check for CCSD(T)
if jobparams['run'] == 'Opt' and 'CC' in jobparams['method']:
print(
'''Warning! You requested geometry optimization with Coupled-Cluster methods,
which is NOT supported. Instead, we will geometry optimize the structure
with B3LYP and then conduct CCSD(T) energy calculation on the optimized structure'''
)
# TODO: check ORCA dispersion
if (args.dispersion):
jobparams['dispersion'] = args.dispersion
# Just carry over spin and charge keywords if they're set. Could do checks, none for now.
if args.spin:
jobparams['spinmult'] = args.spin
if args.charge:
if args.bcharge:
args.charge = int(args.charge) + int(args.bcharge)
jobparams['charge'] = args.charge
# Check for existence of basis and sanitize name
# Read in basis name from args only if it's not the default for terachem
if args.basis and args.basis != 'lacvps_ecp':
jobparams['basis'] = args.basis
if 'DIISMaxEq' not in jobparams:
jobparams['DIISMaxEq'] = 15
# Overwrite plus add any new dictionary keys from commandline input.
if args.qoption:
if len(args.qoption) % 2 != 0:
print('WARNING: wrong number of arguments in -qoption')
else:
for elem in range(0, int(0.5 * len(args.qoption))):
key, val = args.qoption[2 * elem], args.qoption[2 * elem + 1]
jobparams[key] = val
# Extra keywords for unrestricted.
if unrestricted:
# If running unrestricted, assume convergence will be more difficult for now.
jobparams['scf'] = 'SlowConv'
jobparams['UNO'] = 'UNO'
if 'levelshift' not in jobparams:
jobparams['levelshift'] = 'yes'
elif jobparams['levelshift'] != 'yes':
print((
"Warning! You're doing an unrestricted calculation but have set levelshift = %s"
% (jobparams['levelshift'])))
if 'levelshiftval' not in jobparams:
if 'levelshiftvala' in jobparams:
jobparams['levelshiftval'] = jobparams['levelshiftvala']
elif 'levelshiftvalb' in jobparams:
jobparams['levelshiftval'] = jobparams['levelshiftvalb']
else:
jobparams['levelshiftval'] = 0.25
if 'ErrOff' not in jobparams:
jobparams['ErrOff'] = 0.00001
# Now we're ready to start building the input file
if not args.jobdir:
for i, jobd in enumerate(jobdirs):
output = open(jobd + '/orca.in', 'w')
output.write('# file created with %s\n' % globs.PROGRAM)
if 'CC' in jobparams['method'] and jobparams['run'] == 'Opt':
params0 = jobparams.copy()
params0['method'] = 'B3LYP'
ogenwrt(output, params0, coordfs[i])
output.write('\n$new_job\n')
jobparams['run'] = 'Sp'
ogenwrt(output, jobparams, '')
else:
ogenwrt(output, jobparams, coordfs[i])
output.close()
elif args.jobdir:
for i, jobd in enumerate(jobdirs):
print(('jobd is ' + jobd))
output = open(jobd + '/orca.in', 'w')
output.write('# file created with %s\n' % globs.PROGRAM)
if 'CC' in jobparams['method'] and jobparams['run'] == 'Opt':
params0 = jobparams.copy()
params0['method'] = 'B3LYP'
ogenwrt(output, params0, coordfs[i])
output.write('\n$new_job\n')
jobparams['run'] = 'Sp'
ogenwrt(output, jobparams, '')
else:
ogenwrt(output, jobparams, coordfs[i])
output.close()
return jobdirs
molSimplify is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with molSimplify. If not, see http://www.gnu.org/licenses/.
'''
import sys, argparse, os, platform, shutil
from Scripts.inparse import *
from Scripts.generator import *
from molSimplify.Classes.globalvars import *
globs = globalvars()
## Basic help description string
DescString_basic = 'Welcome to molSimplify. Only basic usage is described here.\n'
DescString_basic += 'For help on advanced modules, please refer to our documentation at molsimplify.mit.edu or provide additional commands to -h, as below:\n'
DescString_basic += '-h advanced: advanced structure generation help\n'
DescString_basic += '-h slabgen: slab builder help\n'
#DescString_basic += '-h chainb: chain builder help\n'
DescString_basic += '-h autocorr: automated correlation analysis help\n'
DescString_basic += '-h db: database search help\n'
DescString_basic += '-h inputgen: quantum chemistry code input file generation help\n'
DescString_basic += '-h postproc: post-processing help\n'
DescString_basic += '-h random: random generation help\n'
DescString_basic += '-h binding: binding species (second molecule) generation help\n'
DescString_basic += '-h customcore: custom core functionalization help\n'
DescString_basic += '-h tsgen: transition state generation help\n'
DescString_basic += '-h naming: custom filename help\n'
def addtobdb(smimol, sminame):
globs = globalvars()
if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
print(
'To add to database, you need to set a custom path. Please enter a writeable file path:'
)
new_path = eval(input('path='))
globs.add_custom_path(new_path)
copy_to_custom_path()
bpath = globs.custom_path + "/Bind/bind.dict"
bindcores = readdict(bpath)
bind_folder = globs.custom_path + "/Bind/"
# check if binding species exists
if sminame in list(bindcores.keys()):
emsg = 'Molecule ' + sminame + ' already existing in binding species database.'
return emsg
else:
# convert to unicode
smimol = unicodedata.normalize('NFKD',
smimol).encode('ascii',
'ignore').decode()
sminame = unicodedata.normalize('NFKD',
sminame).encode('ascii',
'ignore').decode()
if '~' in smimol:
smimol = smimol.replace('~', os.expanduser('~'))
# convert ligand from smiles/file
bind, bsmi, emsg = bind_load(smimol, bindcores)
if emsg:
return emsg
bind.convert2mol3D() # convert to mol3D
# new entry for dictionary
# create shortname
if len(sminame) > 5:
shortname = sminame[0:3] + sminame[-2:]
else:
shortname = sminame
if '.mol' in smimol:
shutil.copy2(smimol, bind_folder + sminame + '.mol')
snew = sminame + ':' + sminame + '.mol,' + shortname + ','
elif '.xyz' in smimol:
shutil.copy2(smimol, bind_folder + sminame + '.xyz')
snew = sminame + ':' + sminame + '.xyz,' + shortname + ','
elif bind.OBmol:
# write smiles file in Bind species directory
bind.OBmol.write('smi', bind_folder + sminame + '.smi')
snew = sminame + ':' + sminame + '.smi,' + shortname + ','
else:
# write xyz file in Bind species directory
bind.writexyz(bind_folder + sminame + '.xyz') # write xyz file
snew = sminame + ':' + sminame + '.xyz,' + shortname + ','
# update dictionary
f = open(bpath, 'r')
ss = f.read().splitlines()
f.close()
f = open(bpath, 'w')
ss.append(snew)
ssort = sorted(ss[1:])
f.write(ss[0] + '\n')
for s in ssort:
f.write(s + '\n')
f.close()
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 addtoldb(smimol, sminame, smident, smicat, smigrps, smictg, ffopt):
emsg = False
globs = globalvars()
if not globs.custom_path or not os.path.exists(str(globs.custom_path)):
print(
'To add to database, you need to set a custom path. Please enter a writeable file path:'
)
new_path = eval(input('path='))
globs.add_custom_path(new_path)
copy_to_custom_path()
lipath = globs.custom_path + "/Ligands/ligands.dict"
licores = readdict(lipath)
ligands_folder = globs.custom_path + "/Ligands/"
print(("ligands_folder is : " + str(ligands_folder)))
# check if ligand exists
if sminame in list(licores.keys()):
emsg = 'Ligand ' + sminame + ' already existing in ligands database.'
emsg += ' To replace, delete the existing entry first.'
return emsg
else:
# get connection atoms
ccats = [_f for _f in re.split(' |,|\t', smicat) if _f]
# get groups
groups = [_f for _f in re.split(' |,|\t', smigrps) if _f]
grp = 'build ' + ' '.join(groups)
grp += ' ' + smictg
if smicat == '':
cats = list(range(0, int(smident)))
else:
cats = [int(a) - 1 for a in ccats]
cs = [str(a) for a in cats]
css = ' '.join(cs)
# convert to unicode
smimol = unicodedata.normalize('NFKD',
str(smimol)).encode('ascii',
'ignore').decode()
sminame = unicodedata.normalize('NFKD', str(sminame)).encode(
'ascii', 'ignore').decode()
if '~' in smimol:
smimol = smimol.replace('~', os.expanduser('~'))
# convert ligand from smiles/file
lig, emsg = lig_load(smimol, licores)
if emsg:
return emsg
lig.convert2mol3D() # convert to mol3D
shortname = sminame
print(("smimol is " + str(smimol)))
print(("sminame is " + str(sminame)))
# sanitize ff options:
if not ffopt in ["A", "B", "BA"]:
print(('warning: incompatible ffopt choice. Options are ' +
str(["A", "B", "BA", "N"])))
sys.exit(1)
# new entry for dictionary
if '.mol' in smimol:
shutil.copy2(smimol, ligands_folder + sminame + '.mol')
snew = str(sminame) + ':' + str(sminame) + '.mol,' + str(
shortname) + ',' + str(css) + ',' + str(grp) + ',' + str(
ffopt) + ',' + str(lig.charge)
elif '.xyz' in smimol:
shutil.copy2(smimol, ligands_folder + sminame + '.xyz')
snew = str(sminame) + ':' + str(sminame) + '.xyz,' + str(
shortname) + ',' + str(css) + ',' + str(grp) + ',' + str(
ffopt) + ',' + str(lig.charge)
elif lig.OBMol:
# write smiles file in Ligands directory
obConversion = openbabel.OBConversion()
obConversion.SetOutFormat("smi")
red = obConversion.Read(lig.OBMol)
obConversion.WriteFile(lig.OBMol,
ligands_folder + sminame + '.smi')
#lig.OBMol.write('smi',ligands_folder + sminame+'.smi')
snew = str(sminame) + ':' + str(sminame) + '.smi,' + str(
shortname) + ',' + str(css) + ',' + str(grp) + ',' + str(
ffopt) + ',' + str(lig.charge)
else:
# write xyz file in Ligands directory
lig.writexyz(ligands_folder + sminame + '.xyz') # write xyz file
snew = str(sminame) + ':' + str(sminame) + '.xyz,' + str(
shortname) + ',' + str(css) + ',' + str(grp) + ',' + str(
ffopt) + ',' + str(lig.charge)
# update dictionary
f = open(lipath, 'r')
ss = f.read().splitlines()
f.close()
f = open(lipath, 'w')
ss.append(snew)
ssort = sorted(ss[1:])
f.write(ss[0] + '\n')
for s in ssort:
f.write(s + '\n')
f.close()
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()
