From 11811c5ec19f5384fe7b705225eac5cc09e7ce93 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@cse.msu.edu>
Date: Thu, 30 Jun 2016 23:45:08 -0400
Subject: [PATCH] Tools: begin combining geo tools into Python code.
---
tools/geo_tool.py | 135 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 135 insertions(+)
create mode 100644 tools/geo_tool.py
diff --git a/tools/geo_tool.py b/tools/geo_tool.py
new file mode 100644
index 00000000..9f6a61ed
--- /dev/null
+++ b/tools/geo_tool.py
@@ -0,0 +1,135 @@
+#!/usr/bin/env python3
+
+import argparse
+import contextlib
+from os import linesep
+from re import match, sub
+import sys
+
+
+FORMATS=["PDB", "PUREMD", "REAXFF_FORTRAN"]
+
+
+@contextlib.contextmanager
+def smart_open(filename=None):
+ if filename and filename != '-':
+ fh = open(filename, 'w')
+ else:
+ fh = sys.stdout
+
+ try:
+ yield fh
+ finally:
+ if fh is not sys.stdout:
+ fh.close()
+
+
+def count_atoms(input_file, input_format):
+ count = 0
+ regex = lambda x: False
+ if input_format == "PDB":
+ regex = lambda l: match(r'ATOM ', l) != None
+ elif input_format == "PUREMD":
+ regex = lambda l: match(r'BOXGEO', l) == None
+ elif input_format == "REAXFF_FORTRAN":
+ regex = lambda l: match(r'HETATM', l) != None
+
+ with open(input_file, 'r') as infile:
+ for line in infile:
+ if regex(line):
+ count = count + 1
+
+ return count
+
+
+def convert(args):
+ patterns = { \
+ ("PDB", "PUREMD"): [ \
+ lambda l, **kwargs: (sub(r'^ATOM ([ 0-9]{5}) (.{4}).{14}([. 0-9]{8})([. 0-9]{8})([. 0-9]{8}).{22}([ a-zA-z]{2}).{2}$',
+ r'\1 \2 \6 \3 \4 \5', l), True) if not match(r'ATOM ', l) == None else (l, False),
+ lambda l, **kwargs: (sub(r'^CRYST1([. 0-9]{9})([. 0-9]{9})([. 0-9]{9})([. 0-9]{7})([. 0-9]{7})([. 0-9]{7}) .{15}$',
+ r'BOXGEO \1 \2 \3 \4 \5 \6', l), False) if not match(r'CRYST1', l) == None else (l, False),
+ lambda l, **kwargs: (l + str(kwargs['atom_count']) + linesep, True)
+ if not match(r'BOXGEO', l) == None else (l, False)
+ ],
+ ("PDB", "REAXFF_FORTRAN"): [ \
+ lambda l, **kwargs: ('HETATM {:5d} {:<5} {:3} {:1} {:5}{:10.5f}{:10.5f}{:10.5f} {:5}{:3d}{:2d} {:8.5f}'.format(
+ int(l[6:11].strip()), l[76:78].strip(), ' ', ' ', ' ', float(l[30:38].strip()),
+ float(l[38:46].strip()), float(l[46:54].strip()), l[76:78].strip(),
+ 1, 1, 0.0) + linesep, True)
+ if not match(r'ATOM ', l) == None else (l, False),
+ lambda l, **kwargs: (l, True),
+ ],
+ ("PUREMD", "PDB"): [ \
+ #TODO
+ ],
+ ("PUREMD", "REAXFF_FORTRAN"): [ \
+ #TODO
+ ],
+ ("REAXFF_FORTRAN", "PDB"): [ \
+ #TODO
+ ],
+ ("REAXFF_FORTRAN", "PUREMD"): [ \
+ #TODO
+ ],
+ }
+
+ ac = count_atoms(args.input_file, args.input_format)
+
+ with open(args.input_file, 'r') as infile, smart_open(args.output_file) as outfile:
+ for line in infile:
+ for p in patterns[(args.input_format, args.output_format)]:
+ try:
+ (line, matched) = p(line, atom_count=ac)
+ except Exception as exc:
+ raise RuntimeError('Invalid input format')
+ if matched:
+ break
+ else:
+ continue
+ outfile.write(line)
+
+
+def replicate(args):
+ #TODO
+ print(args)
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(description='Munge geometry file(s) for molecular dynamics simulations.')
+ subparsers = parser.add_subparsers(dest='cmd')
+ subparsers.required = True
+
+ # convert subcommand
+ parser_convert = subparsers.add_parser('convert', aliases=['c', 'co'],
+ help='Convert between geometry formats.')
+ parser_convert.add_argument('input_format', metavar='in_format',
+ choices=FORMATS, help='input format')
+ parser_convert.add_argument('input_file', metavar='in_file',
+ help='input geometry file')
+ parser_convert.add_argument('output_format', metavar='out_format',
+ choices=FORMATS, help='output format')
+ parser_convert.add_argument('output_file', metavar='out_file', nargs='?',
+ help='output geometry file')
+ parser_convert.set_defaults(func=convert)
+
+ # replicate subcommand
+ parser_replicate = subparsers.add_parser('replicate', aliases=['r', 'rep'],
+ help='Replicate geometry by prescribed factors in X, Y, and Z dimensions.')
+ parser_replicate.add_argument('input_format', metavar='in_format',
+ choices=FORMATS, help='input format')
+ parser_replicate.add_argument('input_file', metavar='in_file',
+ help='input geometry file')
+ parser_replicate.add_argument('X repl', metavar='X', type=int,
+ help='replication factor in X dimension')
+ parser_replicate.add_argument('Y repl', metavar='Y', type=int,
+ help='replication factor in Y dimension')
+ parser_replicate.add_argument('Z repl', metavar='Z', type=int,
+ help='replication factor in Z dimension')
+ parser_replicate.add_argument('output_file', metavar='out_file', nargs='?',
+ help='output geometry file')
+ parser_replicate.set_defaults(func=replicate)
+
+ # parse args and take action
+ args = parser.parse_args()
+ args.func(args)
--
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