Limit the line length for the command in the top #314
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Martinize2 writes the command it has been invoked with in the header of the TOP file it writes. If that command is too long, then it can pass the maximum line length that grompp can read. This commit truncate the command if it passes the limit.
pckroon
requested changes
Sep 29, 2020
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| gromacs_char_limit = 4000 # the limit is actually 4095, but I play safe | ||
| command = ' '.join(sys.argv) | ||
| if len(command) > gromacs_char_limit: | ||
| command = command[:gromacs_char_limit] + ' ...' |
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Set it to 80, and linebreak properly. Keep printing the complete command, just linewrap it.
Also see: https://docs.python.org/3/library/textwrap.html
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I considered that, but:
- it is a fairly rare corner case so it should not affect the general case
- the line, once wrapped, will make a header that will be very long and push the relevant information (the topology) far bellow
- the line can be easily copy-pasted, which is not the case if it is wrapped because the comment character will pollute the text block; I am fine with if a pathologic line cannot be copied, but I'd rather not affect the legit ones.
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I individually ignore all the ligands of the PDB for which we do not have a mapping, so it seems that my command line is longer than 4094 characters... Anyway, that odd corner case should not prevent the output file from being read. |
pckroon
approved these changes
Sep 30, 2020
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Martinize2 writes the command it has been invoked with in
the header of the TOP file it writes. If that command is too
long, then it can pass the maximum line length that grompp
can read.
This commit truncate the command if it passes the limit.