From fcbb23a1d7bbd6720104b7350ee1720bf99e52ca Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Fri, 6 May 2016 12:00:33 +0100
Subject: [PATCH] Add optional constraint conversion to sanitize.py
---
sanitize.py | 33 ++++++++++++++++++++++++++++++++-
1 file changed, 32 insertions(+), 1 deletion(-)
diff --git a/sanitize.py b/sanitize.py
index 192e603..c0e33c8 100755
--- a/sanitize.py
+++ b/sanitize.py
@@ -10,24 +10,55 @@ def main(args):
"dihedrals": 8,
"constraints": 4,
"pairs": -1}
+ has_constr = False
+ constr_lines = []
+
for line in infile:
line = line.strip("\n")
if line.startswith("["):
section = line.strip("[ ]")
+ if args.fc is not None and section == "constraints":
+ print(line, file=outfile)
+ has_constr = True
+ for c_line in constr_lines:
+ print(c_line, file=outfile)
+ continue
+
+ if section == "system" and not has_constr and constr_lines:
+ print("[ constraints ]", file=outfile)
+ for c_line in constr_lines:
+ print(c_line, file=outfile)
+ print(file=outfile)
+
+ print(line, file=outfile)
+ continue
+
elif line.startswith("#") or line.startswith(";") or line == "":
- pass
+ print(line, file=outfile)
+ continue
+
elif len(line.split()) < expected_toks.get(section, 0):
continue
+
elif expected_toks.get(section, 0) < 0:
continue
+ # Convert high force constants to constraints
+ if args.fc is not None and section == "bonds" and float(line.split()[4]) >= args.fc:
+ 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")
parser.add_argument('-o', type=str, required=True, help="Output topology file")
+ parser.add_argument('-fc', type=float, default=None, help="Convert high force constants to constraints")
args = parser.parse_args()
--
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