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