Mercurial > repos > bgruening > eden_toolbox

comparison mol2gspan.py @ 0:99091a5d5c84 draft

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author bgruening
date Wed, 04 Sep 2013 05:10:04 -0400
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-1:000000000000 0:99091a5d5c84
1 #!/usr/bin/env python
2
3 import os, sys
4 import argparse
5
6 def main(args ):
7
8 begin = True
9 iid = 0
10 graph_counter = 1
11
12 for line in args.infile:
13 if line.rstrip():
14 if line.strip().endswith('END'):
15 begin = False
16 elif line.strip() == '$$$$':
17 graph_counter += 1
18 iid = 0
19 else:
20 # found header line, like: 21 21 0 0 0 0 0 0 0 0999 V2000
21 if len(line.split()) >= 5 and line.split()[-1] == 'V2000':
22 args.outfile.write('t # id %s\n' % graph_counter)
23 begin=True
24 continue
25 # connection or coordinate/atom table
26 if len(line.split()) >= 4 and begin:
27 # coordinate/atom table
28 if line.split()[3].isalpha():
29 args.outfile.write( 'v %s %s \n' % (iid, line.split()[3]) )
30 iid += 1
31 else:
32 #connection table
33 id, node, edge, trash = line.split(None, 3)
34 args.outfile.write( 'e %s %s %s\n' % ( int(id) - 1 , int(node) -1, edge ) )
35
36 if __name__ == "__main__":
37 parser = argparse.ArgumentParser()
38 parser.add_argument('--infile', nargs='?', type=argparse.FileType('r'),
39 default=sys.stdin, help="Specify one or more input files")
40 parser.add_argument('--outfile', type=argparse.FileType('w'),
41 default=sys.stdout, help="Specify one output file")
42 args = parser.parse_args()
43 main( args )