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Commit ffb87277 authored by James Graham's avatar James Graham
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Fixed sanitize.py

Added brief info on output to documentation
Added Python 3.5 to tests
parent fcbb23a1
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......@@ -3,6 +3,7 @@ python:
- "3.2"
- "3.3"
- "3.4"
- "3.5"
cache:
directories:
- $HOME/.cache/pip
......
......@@ -48,6 +48,8 @@ The program is called by:
Example mapping and bond definition files are present in the ``test/data`` directory. Their format is explained below.
After running PyCGTOOL two files, ``out.gro`` and ``out.itp`` will be created. The gro file contains the mapped coarse-grain coordinates with every molecule for which a mapping was provided. The itp file contains the parameters for each molecule type. **NB**: charges are not currently set by PyCGTOOL as MARTINI only allows charges on certain bead types.
Mapping / Bond Definition Files
-------------------------------
The mapping and bond definition input files use a format similar to the GROMACS itp/top format.
......
......@@ -29,6 +29,7 @@ def main(args):
for c_line in constr_lines:
print(c_line, file=outfile)
print(file=outfile)
has_constr = True
print(line, file=outfile)
continue
......@@ -48,12 +49,9 @@ def main(args):
constr_lines.append(line[:line.rindex(line.split()[4]) - 1])
continue
if args.fc is not None and section == "constraints":
print(line, file=outfile)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Sanitize PDB2GMX output topology.")
parser.add_argument('-i', type=str, required=True, help="Input topology file")
......
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