Mod:Hunt Research Group/chelpg extract - Revision history

Irelie at 00:19, 12 January 2024

2024-01-12T00:19:53Z

Irelie: /* Python Script to Extract ESP Charges from Either opt or SP Calculations */

2024-01-12T00:12:03Z

Python Script to Extract ESP Charges from Either opt or SP Calculations

Irelie: /* Python Script to Extract ESP Charges from Either opt or SP Calculations */

2024-01-12T00:11:10Z

Python Script to Extract ESP Charges from Either opt or SP Calculations

Irelie: /* Python Script to Extract ESP Charges from Either opt or SP Calculations */

2024-01-12T00:03:18Z

Python Script to Extract ESP Charges from Either opt or SP Calculations

Irelie: /* Python Script to Extract ESP Charges from Either opt or SP Calculations */

2024-01-11T23:54:31Z

Python Script to Extract ESP Charges from Either opt or SP Calculations

Irelie: /* Python Script to Extract ESP Charges from Either opt or SP Calculations */

2024-01-11T23:44:46Z

Python Script to Extract ESP Charges from Either opt or SP Calculations

Irelie at 23:41, 11 January 2024

2024-01-11T23:41:04Z

Irelie: /* Python Script to Extract ESP Charges from Either opt or SP Calculations */

2024-01-11T23:38:27Z

Python Script to Extract ESP Charges from Either opt or SP Calculations

Irelie: /* Python Script to Extract ESP Charges from Either opt or SP Calculations */

2024-01-11T23:37:55Z

Python Script to Extract ESP Charges from Either opt or SP Calculations

Irelie at 23:35, 11 January 2024

2024-01-11T23:35:36Z

← Older revision		Revision as of 00:19, 12 January 2024
Line 179:		Line 179:
	</pre>		</pre>

−	*Sample com file to run and test the code: [[File:Test water.~~txt~~]]	+	*Sample com file to run and test the code: [[File:Test water.log]]

@@ Line 52: / Line 52: @@
 ==Python Script to Extract ESP Charges from Either opt or SP Calculations==
 * Copy the script into a file named "extract_esp.py"
-* To execute the script, type "python extract_esp.py file_name (without extension)
+* To execute the script, type "python extract_esp.py file_name (without extension.
 *This will display the charges in the terminal and create a file named "file_name.csv" simultaneously.
 *Only the last set of ESP charges is printed into the file.
@@ Line 178: / Line 178: @@
 </pre>
 *Sample com file to run and test the code: [[File:Test water.txt]]

@@ Line 51: / Line 51: @@
 ==Python Script to Extract ESP Charges from Either opt or SP Calculations==
-*Script file to extract ESP charges: [[File:Test extract_esp.txt]]
+<pre>
 *Sample com file to run and test the code: [[File:Test water.txt]]

@@ Line 52: / Line 52: @@
 ==Python Script to Extract ESP Charges from Either opt or SP Calculations==
-*Copy the script into a file named "extract_esp.py"
+*Script file to extract ESP charges: [[File:Test extract_esp.txt]]
-*To execute the script, type "python extract_esp.py file_name (without the extension).
+*Sample com file to run and test the code: [[File:Test water.txt]]

@@ Line 51: / Line 51: @@
 ==Python Script to Extract ESP Charges from Either opt or SP Calculations==
-Script file: [[File:Test extract_esp.txt]]
 Sample log file to test the code: [[File:Test water.log]]

← Older revision		Revision as of 23:41, 11 January 2024
Line 51:		Line 51:

	==Python Script to Extract ESP Charges from Either opt or SP Calculations==		==Python Script to Extract ESP Charges from Either opt or SP Calculations==
		+	Script file: [[File:Test extract_esp.py]]
		+	Sample log file to test the code: [[File:Test water.log]]

← Older revision		Revision as of 23:38, 11 January 2024
Line 51:		Line 51:

	==Python Script to Extract ESP Charges from Either opt or SP Calculations==		==Python Script to Extract ESP Charges from Either opt or SP Calculations==
−
−
−	~~#!/usr/bin/env python3~~
−	#
−	~~# extract_chelpg.py~~
−	#
−	~~# python script to extract and print ESP charges from a NBO=ChelpG, dipole, atomdipole job data from a gaussian log file~~
−	~~# to run the script type python extract_ESP.py input_file_name (without extension)~~
−	#
−	~~import sys~~
−	~~import os~~
−	~~dir=os.getcwd()~~
−	~~if len(sys.argv) == 1:~~
−	~~print('to run the script please type: python extract_ESP.py input_file_name \(without extension\)')~~
−	~~sys.exit()~~
−	~~else:~~
−	~~base=str(sys.argv[1])~~
−	~~file=base+'.log'~~
−	~~out=base+'.csv'~~
−	~~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~~
−	#
−	~~col_num=[]~~
−	~~col_atom=[]~~
−	~~col_charge=[]~~
−	~~col_pd1=[]~~
−	~~col_pd2=[]~~
−	~~col_pd3=[]~~
−	~~rep=0~~
−	~~go=False~~
−
−	~~# open file and read lines one by one in read-only mode~~
−	~~f=open(file,"r")~~
−
−	~~#reading lines from the file one by one until the end of the file is reached.~~
−	~~line = f.readline()~~
−	~~while line :~~
−	~~line = f.readline()~~
−
−	~~# check for the presence of ESP text and sets go as True 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 found: '~~
−	~~if rep == 0 : print('{0:}{1:}'.format(s,line[22:-1]))~~
−	~~c=open(out,"w")~~
−	~~c.write('{0:}{1:} \n'.format(s,line[22:-1]))~~
−	~~# if rep == 0 : print('{0:}'.format(s))~~
−	~~n=1~~
−	~~rep=rep+1~~
−	~~count=0~~
−	~~# close if~~
−	#
−	~~# inside the first while loop, if go is on or True, the script extracts ESP and stores in the defined variables~~
−	~~# only extract if you have not got to a line containing ' Tot ' and 'Sum of ESP charges'~~
−	~~while go:~~
−	~~n = n+1~~
−	~~m = 0~~
−	~~line =f.readline()~~
−	~~if ' Tot ' in line : m=-1~~
−	~~if 'Sum of ESP charges' in line : m=-1~~
−	~~if n > 3 and m == 0 :~~
−	~~count=count+1~~
−	~~#unpack the values from splitting the line into 6 variables~~
−	~~values=line.rstrip().split()~~
−	~~# appends the value, a1 into col_atom list after converting it to a string~~
−	~~if len(values) == 6:~~
−	~~a1, b1, c1, d1, e1, f1 = values~~
−	~~col_num.append(int(a1))~~
−	~~col_atom.append(str(b1))~~
−	~~col_charge.append(float(c1))~~
−	~~col_pd1.append(float(d1))~~
−	~~col_pd2.append(float(e1))~~
−	~~col_pd3.append(float(f1))~~
−	~~if len(values) == 3:~~
−	~~g1, h1, i1 = values~~
−	~~col_num.append(int(g1))~~
−	~~col_atom.append(str(h1))~~
−	~~col_charge.append(float(i1))~~
−	~~if m == -1 : go=False~~
−	~~# close while~~
−	~~#close while~~
−
−	~~#opens the output file in write mode, we can now write to the .csv file~~
−	~~c=open(out,"w")~~
−	~~# number of atoms~~
−	~~c.write('{0:} \n'.format(count))~~
−	~~s='comment'~~
−	~~c.write('{0:} \n'.format(s))~~
−	#
−
−	~~n=0~~
−	~~#adjusts the value of n to start from a position that corresponds to the beginning of the last set of ESP data.~~
−	~~if rep != 1 :~~
−	~~n=len(col_num)-count~~
−	~~count=count*rep~~
−	~~s=' sets of charges found only the last is saved'~~
−	~~print('{0:}{1:}'.format(rep,s))~~
−	~~# endif~~
−
−	~~#Write data to csv file#~~
−	~~header= ["No.", "Atom", "ESP Charges"]~~
−	~~c.write(' '.join(header) + '\n')~~
−	~~print(' '.join(header))~~
−	~~while n < count:~~
−	~~c.write('{0:3d} {1: >3s} {2: >09.6f} \n'.format(col_num[n],col_atom[n],col_charge[n]))~~
−	~~print('{0:3d} {1: >3s} {2: >09.6f}'.format(col_num[n],col_atom[n],col_charge[n]))~~
−	~~n=n + 1~~
−	~~#close while~~
−
−	~~# close all open files~~
−	~~f.close()~~
−	~~c.close()~~
−	#

← Older revision		Revision as of 23:37, 11 January 2024
Line 51:		Line 51:

	==Python Script to Extract ESP Charges from Either opt or SP Calculations==		==Python Script to Extract ESP Charges from Either opt or SP Calculations==
		+
		+
		+	#!/usr/bin/env python3
		+	#
		+	# extract_chelpg.py
		+	#
		+	# python script to extract and print ESP charges from a NBO=ChelpG, dipole, atomdipole job data from a gaussian log file
		+	# to run the script type python extract_ESP.py input_file_name (without extension)
		+	#
		+	import sys
		+	import os
		+	dir=os.getcwd()
		+	if len(sys.argv) == 1:
		+	print('to run the script please type: python extract_ESP.py input_file_name \(without extension\)')
		+	sys.exit()
		+	else:
		+	base=str(sys.argv[1])
		+	file=base+'.log'
		+	out=base+'.csv'
		+	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
		+	#
		+	col_num=[]
		+	col_atom=[]
		+	col_charge=[]
		+	col_pd1=[]
		+	col_pd2=[]
		+	col_pd3=[]
		+	rep=0
		+	go=False
		+
		+	# open file and read lines one by one in read-only mode
		+	f=open(file,"r")
		+
		+	#reading lines from the file one by one until the end of the file is reached.
		+	line = f.readline()
		+	while line :
		+	line = f.readline()
		+
		+	# check for the presence of ESP text and sets go as True 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 found: '
		+	if rep == 0 : print('{0:}{1:}'.format(s,line[22:-1]))
		+	c=open(out,"w")
		+	c.write('{0:}{1:} \n'.format(s,line[22:-1]))
		+	# if rep == 0 : print('{0:}'.format(s))
		+	n=1
		+	rep=rep+1
		+	count=0
		+	# close if
		+	#
		+	# inside the first while loop, if go is on or True, the script extracts ESP and stores in the defined variables
		+	# only extract if you have not got to a line containing ' Tot ' and 'Sum of ESP charges'
		+	while go:
		+	n = n+1
		+	m = 0
		+	line =f.readline()
		+	if ' Tot ' in line : m=-1
		+	if 'Sum of ESP charges' in line : m=-1
		+	if n > 3 and m == 0 :
		+	count=count+1
		+	#unpack the values from splitting the line into 6 variables
		+	values=line.rstrip().split()
		+	# appends the value, a1 into col_atom list after converting it to a string
		+	if len(values) == 6:
		+	a1, b1, c1, d1, e1, f1 = values
		+	col_num.append(int(a1))
		+	col_atom.append(str(b1))
		+	col_charge.append(float(c1))
		+	col_pd1.append(float(d1))
		+	col_pd2.append(float(e1))
		+	col_pd3.append(float(f1))
		+	if len(values) == 3:
		+	g1, h1, i1 = values
		+	col_num.append(int(g1))
		+	col_atom.append(str(h1))
		+	col_charge.append(float(i1))
		+	if m == -1 : go=False
		+	# close while
		+	#close while
		+
		+	#opens the output file in write mode, we can now write to the .csv file
		+	c=open(out,"w")
		+	# number of atoms
		+	c.write('{0:} \n'.format(count))
		+	s='comment'
		+	c.write('{0:} \n'.format(s))
		+	#
		+
		+	n=0
		+	#adjusts the value of n to start from a position that corresponds to the beginning of the last set of ESP data.
		+	if rep != 1 :
		+	n=len(col_num)-count
		+	count=count*rep
		+	s=' sets of charges found only the last is saved'
		+	print('{0:}{1:}'.format(rep,s))
		+	# endif
		+
		+	#Write data to csv file#
		+	header= ["No.", "Atom", "ESP Charges"]
		+	c.write(' '.join(header) + '\n')
		+	print(' '.join(header))
		+	while n < count:
		+	c.write('{0:3d} {1: >3s} {2: >09.6f} \n'.format(col_num[n],col_atom[n],col_charge[n]))
		+	print('{0:3d} {1: >3s} {2: >09.6f}'.format(col_num[n],col_atom[n],col_charge[n]))
		+	n=n + 1
		+	#close while
		+
		+	# close all open files
		+	f.close()
		+	c.close()
		+	#

← Older revision		Revision as of 23:35, 11 January 2024
Line 49:		Line 49:
	or		or
	chelpg_charge		chelpg_charge
		+
		+	==Python Script to Extract ESP Charges from Either opt or SP Calculations==