def add_molecule_from_punfile(self,filename): """ Adds a molecule to MolPop from a punfile""" a = mtp_tools.molecule() a.readfrompunfile(filename) a.Calc_locMTP() self.molecules.append(a) self.nmols += 1
"Error: the script will generate a .lpun file, please rename current file."
)
exit(1)
# Read prmfile if given
prms = {}
if parmfile != '':
import numpy
f = open(parmfile, 'r')
a = f.readlines()
f.close()
for line in a:
b = line.split()
prms[(b[0][2:-2], b[1][1:-2])] = numpy.array(
[float(b[i + 3]) for i in range(len(b) - 3)])
mol = mtp_tools.molecule()
mol.readfrompunfile(punfile)
mol.Calc_locMTP()
if parmfile != '':
for atom in mol.atoms:
atom.chrg = prms[(atom.atype, 'chrg')]
atom.dloc = prms[(atom.atype, 'dloc')]
atom.Qloc = prms[(atom.atype, 'Qloc')]
mol.Calc_gloMTP()
mol.adjust_charge()
mol.write_localized_mtp_file(punfile[:punfile.rindex('.')] + '.lpun')
import copy, os, string
import rdkit
import numpy, math
from rdkit import Chem
if basename[-4:] in ['.sdf','.log','.pun','.out']: basename = basename[:-4]
##############
# Get coordinates from the gaussian output file or the punfile
# The Gaussian output file is supposed to end on .log
# If no Gaussian output file that ends on .log is found, a gaussian output file
# that ends on .out is searched. If both are not found, the program is exited.
if punxyz == True:
import mtp_tools, numpy
mo = mtp_tools.molecule()
mo.readfromrawpunfile(punchfile)
xyzblock = []
for atom in mo.atoms: xyzblock.append([atom.atype, float(atom.coords[0]), float(atom.coords[1]), float(atom.coords[2])])
else:
outfiles = []
outfile = ''
if os.path.exists(basename+'.log'):
outfiles.append(basename+'.log')
elif os.path.exists(basename+'.out'):
outfiles.append(basename+'.out')
for fi in outfiles:
f = open(fi,'r')
lines = f.readlines()
for line in lines:
elif sys.argv[i] == '-pun':
pun = sys.argv[i+1]
elif sys.argv[i] == '-out':
out = sys.argv[i+1]
elif sys.argv[i] == '-chg':
chg = int(sys.argv[i+1])
assert mtp[-4:] == '.txt'
assert pun[-3:] == 'pun'
#############
# Load molecule
import mtp_tools
mol = mtp_tools.molecule()
if pun[-4:] == '.pun':
mol.readfrompunfile(pun)
mol.Calc_locMTP()
elif pun [-5:] == '.lpun':
mol.readfromlpunfile(pun)
mol.Calc_gloMTP()
else:
print "Error. Punfile extension not recognized."
exit(1)
#############
# Parse MTP parameter file
mtp_coef = {}
# Are there bond increments?
binc = False
import copy, os, string
import rdkit
from rdkit import Chem
if basename[-4:] in ['.sdf','.log','.pun','.out']: basename = basename[:-4]
##############
# Get coordinates from the gaussian output file or the punfile
# The Gaussian output file is supposed to end on .log
# If no Gaussian output file that ends on .log is found, a gaussian output file
# that ends on .out is searched. If both are not found, the program is exited.
if punxyz == True:
import mtp_tools, numpy
mo = mtp_tools.molecule()
mo.readfromrawpunfile(basename+'.pun')
xyzblock = []
for atom in mo.atoms: xyzblock.append([atom.atype, float(atom.coords[0]), float(atom.coords[1]), float(atom.coords[2])])
else:
outfiles = []
outfile = ''
if os.path.exists(basename+'.log'):
outfiles.append(basename+'.log')
elif os.path.exists(basename+'.out'):
outfiles.append(basename+'.out')
for fi in outfiles:
f = open(fi,'r')
lines = f.readlines()
for line in lines: