diff --git a/.travis.yml b/.travis.yml index a726df771f38e445722926b3c56846d79a7cbb3e..de518da3c40554b5e5c1fc00c7f4a4aa25c07095 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,6 +3,7 @@ python: - "3.2" - "3.3" - "3.4" + - "3.5" cache: directories: - $HOME/.cache/pip diff --git a/doc/source/index.rst b/doc/source/index.rst index 58f0cb63fedd9ddeb69f2f43b2fdc782ae4ac27c..bbac12bcb16cfd88ea77fc742ff44d48a3ce4834 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -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. diff --git a/sanitize.py b/sanitize.py index c0e33c844fe7ef56c284760a96cc30fbe7f245df..05846d07cd6410853bfa84fbf435bc2846c699f1 100755 --- a/sanitize.py +++ b/sanitize.py @@ -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")