diff mol2gspan.py @ 0:18eb78773d87 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mol2gspan.py	Tue Oct 29 11:15:59 2013 -0400
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+
+"""
+    Converts a SD-file to a GSPAN file.
+"""
+
+
+import os, sys
+import argparse
+
+def main( args ):
+
+    begin = False
+    iid = 0
+    graph_counter = 1
+
+    for line in args.infile:
+        if line.rstrip():
+            if line.strip().endswith('END'):
+                begin = False
+            elif line.strip() == '$$$$':
+                graph_counter += 1
+                iid = 0
+            else:
+                # found header line, like:  21 21  0  0  0  0  0  0  0  0999 V2000
+                if len(line.split()) >= 5 and line.split()[-1] == 'V2000':
+                    args.outfile.write('t # id %s\n' % graph_counter)
+                    begin=True
+                    continue
+                # connection or coordinate/atom table
+                if len(line.split()) >= 4 and begin:
+                    # coordinate/atom table
+                    if not line.startswith('M'):
+                        if line.split()[3].isalpha() or line.split()[3] == '*':
+                            args.outfile.write( 'v %s %s \n' % (iid, line.split()[3]) )
+                            iid += 1
+                        else:
+                            #connection table
+                            id, node, edge, trash = line.split(None, 3)
+                            args.outfile.write( 'e %s %s %s\n' % ( int(id) - 1 , int(node) -1, edge ) )
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--infile', nargs='?', type=argparse.FileType('r'),
+        default=sys.stdin, help="Specify one or more input files")
+    parser.add_argument('--outfile', type=argparse.FileType('w'),
+        default=sys.stdout, help="Specify one output file")
+    args = parser.parse_args()
+    main( args )