I have a file that looks like this:
; [ atomtypes ] opls_BZCG BCG1 78.113999 0.000 A 2.9310E-01 1.9173E-01 [ moleculetype ] ; Name nrexcl BZCG 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_BZCG 1 BZCG BCG1 1 0 78.113999
I am trying to use python to change the values in the second last and last field under the [ atomtypes ]
title. The deal is that I am running a code which iteratively updates this file, so I specifically want that field to be targeted, not the regular expression “2.931E-01” or “1.9173E-01”. I know we can use things like awk, but I was wondering if this is possible from python itself.
This is what I am doing so far:
flag = 0 with open("file.itp") as f: for line in f: iterable = line.strip().split() if flag: line.strip().split()[5] = sigma line.strip().split()[6]) = eps print("epsilon is {} and sigma is {}".format(eps, sigma)) if "atomtypes" in iterable: flag = 1 else: flag = 0 f.close()
I am changing the value in python, but I am not able to send that change to the file itself. How do I pull this off?
Any advice you have would be appreciated!
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Answer
Use enumerate on lines so we can access current line and next line
Code
def update_line(filenm, eps, sigma): with open(filenm, 'r') as fin: lines = fin.readlines() for idx, line in enumerate(lines): if "atomtypes" in line: # Current line has marker, so change next line (i.e. index idx + 1) # Split next line into fields # split from end so so only have three fields, namely: # 1) everything before next to last field, # 2) next to last field, # 3) last field) arr = lines[idx+1].rsplit(' ', maxsplit = 3) arr[-3], arr[-1] = f"{eps:e}", f"{sigma:e}" lines[idx+1] = ' '.join(arr) + "n" # last_val dropped the 'n' so add back break with open(filenm, 'w') as fout: # Updated lines placed back into file fout.writelines(lines)
Test
update_line('test.txt', 4.573133E-02, 8.2737123E-01)
File test.txt prior:
; [ atomtypes ] opls_BZCG BCG1 78.113999 0.000 A 2.9310E-01 1.9173E-01 [ moleculetype ] ; Name nrexcl BZCG 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_BZCG 1 BZCG BCG1 1 0 78.113999
File test.txt after
; [ atomtypes ] opls_BZCG BCG1 78.113999 0.000 A 4.573133e-02 8.273712e-01 [ moleculetype ] ; Name nrexcl BZCG 1 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_BZCG 1 BZCG BCG1 1 0 78.113999