From ffb872770f6393ae834e385ca746d6166b0a8b14 Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Mon, 9 May 2016 11:50:38 +0100
Subject: [PATCH] Fixed sanitize.py Added brief info on output to documentation
Added Python 3.5 to tests
---
.travis.yml | 1 +
doc/source/index.rst | 2 ++
sanitize.py | 4 +---
3 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index a726df7..de518da 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 58f0cb6..bbac12b 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 c0e33c8..05846d0 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")
--
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