- copy the code into a script called "extract_charges.py"
- to execute the script type "python extract_charges.py file_name (without extension)
- this will print to terminal the charges and create a file file_name.chg
- if there are multiple sets of charges only the last set are printed to the file
#!/usr/bin/python
# extract_charges.py
#
# python script to extract and print ESP and NBO charges from a gaussian log file
# to run the script type python extract_charges.py file_name (without extension)
# charges will be printed and sent to file_name.chg
#
import sys
import os
dir=os.getcwd()
#
if len(sys.argv) == 1:
print('to run the script please type: python extract_charges.py file_name (without extension)')
sys.exit()
else:
base=str(sys.argv[1])
if base.endswith('log'):
file=base
base=base[0:-4]
else:
file=base+'.log'
# endif
out=base+'.chg'
s='directory is '
print('{0:}{1:}'.format(s,dir))
s='input file is '
print('{0:}{1:}'.format(s,file))
s='output file is '
print('{0:}{1:}'.format(s,out))
#close if
#set some defaults
go=False
totalN=0
totalE=0
total=0
esp=0
nbo=0
col_Enum=[]
col_Eatom=[]
col_Eesp=[]
col_Nnum=[]
col_Natom=[]
col_Nnbo=[]
# open file and read lines one by one
f=open(file,"r")
c=open(out,"w")
line =f.readline()
while line:
# read a line from the file
line =f.readline()
#==ESP charges==
# check for key text for ESP and set go if the text appears
# print and write fit error to out file
if 'Charges from ESP fit' in line:
go=True
s='Charges from ESP fit '
print('{0:}{1:}'.format(s,line[22:-1]))
c.write('{0:}{1:} \n'.format(s,line[22:-1]))
esp=esp+1
n=0
m=0
# close if
# if go is on then read through the next section and print out the charges
# put the numbers in an array for atom number, atom type and esp value
# but also check if the charges are finished and exit if they are
# if see sum of ESP then stop
while go:
n = n+1
line =f.readline()
if 'Sum of ESP charges' in line: m=1
if n > 2 and m == 0 :
a1,b1,c1=line.rstrip().split()
col_Enum.append(int(a1))
col_Eatom.append(b1)
col_Eesp.append(float(c1))
print('{0:>3s} {1:>3s} {2:>10s}'.format(a1,b1,c1))
# close if
if m == 1 :
go=False
totalE=n-3
# close if
# close while
#
# now keep going to search for NBO charges
#==NBO charges==
# check for key text set go if the text appears
# print and write key lines to out file
if 'Summary of Natural Population Analysis:' in line:
go=True
s='Charges from NBO '
print('{0:}'.format(s))
p=0
n=0
nbo=nbo+1
# close if
# if go is on then print out the charges
# but also check if the charges are finished and exit if they are
while go:
n = n+1
line =f.readline()
if ' ======================' in line: p=1
if n > 5 and p == 0 :
a1,b1,c1,d1,e1,f1,g1=line.rstrip().split()
col_Natom.append(a1)
col_Nnum.append(int(b1))
col_Nnbo.append(float(c1))
print('{0:>3s} {1:>3s} {2:>10s}'.format(a1,b1,c1))
if p == 1 :
go=False
totalN=n-6
# close if
# close while
#now write to the .chg file
#formating decimal, total length=8 with 6 after decimal point leading zero to add space for plus
#formating the ^ means place in middle
#formating the > means right justify
#
# we could have only ESP or only NBO
# also if there has been more than one set of charges advance counter to last set of charges
if totalE > 0 and totalN == 0 :
n=0
total=totalE
if esp != 0 :
n=len(col_Enum)-total
total=total*esp
s='only printing last set of charges'
# c.write('{0:} \n'.format(s))
print('{0:}'.format(s))
# endif
# print 0 into the NBO charges
x=0
while x < total :
col_Nnbo.append(0.0)
x=x+1
# close while
c.write('{0:>4s}{1:>4s} {2:^9s} \n'.format('no.','atm','ESP'))
while n < total :
c.write('{0:>4d}{1:>4s} {2: 08.6f} \n'.format(col_Enum[n],col_Eatom[n],col_Eesp[n]))
n=n + 1
# close while
#close if
#endif
if totalE == 0 and totalN > 0 :
n=0
total=totalN
if nbo != 0 :
n=len(col_Nnum)-total
total=total*nbo
s=' sets of charges only printing last set of charges'
c.write('{0:}{0:} \n'.format(nbo,s))
print('{0:}'.format(s))
# endif
x=0
while x < total :
col_Enum[x]=col_Nnum[x]
col_Eatom[x]=col_Natom[x]
col_Eesp.append(0.0)
x=x+1
# close while
c.write('{0:>4s}{1:>4s} {2:^9s} \n'.format('no.','atm','NBO'))
while n < total :
c.write('{0:>4d}{1:>4s} {2: 08.6f} \n'.format(col_Enum[n],col_Eatom[n],col_Nnbo[n]))
n=n + 1
# close while
#close if
if totalN > 0 and totalE > 0 :
n=0
total=totalE
if esp != 0 :
n=len(col_Enum)-total
total=total*esp
s=' sets of charges only writing last set of charges'
print('{0:}{1:}'.format(nbo,s))
c.write('{0:}{1:} \n'.format(nbo,s))
# endif
#
# now write out
#
c.write('{0:>4s}{1:>4s} {2:^9s} {3:^9s} \n'.format('no.','atm','ESP','NBO'))
while n < total :
c.write('{0:>4d}{1:>4s} {2: 08.6f} {3: 08.6f} \n'.format(col_Enum[n],col_Eatom[n],col_Eesp[n],col_Nnbo[n]))
n=n + 1
# close while
#close if
# close all open files
c.close()
f.close()
#
