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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 import os
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8 import sys
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9 import argparse
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10 import openbabel
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11 import pybel
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12
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13 def main( args ):
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14
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1
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15 for infile in args.infile:
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16 file_extension = args.format or os.path.splitext( infile )[-1].lstrip('.')
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17
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18 if not args.format and file_extension not in ['smi', 'sdf', 'inchi', 'mol']:
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19 sys.exit('Could not guess the format from the file extension please specify with the --format option.')
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20
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21 molecules = pybel.readfile(file_extension, infile)
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22 for mol in molecules:
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23 args.outfile.write( 't # id %s\n' % mol.title.strip() )
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24 for atom in openbabel.OBMolAtomIter( mol.OBMol):
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25 label = atom.GetAtomicNum()
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26 vertex_index = atom.GetIdx()
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27 args.outfile.write('v %s %s\n' % (vertex_index, label))
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28
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29 for bond in openbabel.OBMolBondIter( mol.OBMol):
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30 src_index = bond.GetBeginAtomIdx()
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31 dest_index = bond.GetEndAtomIdx()
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32 assert(src_index > 0)
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33 assert(dest_index > 0)
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34 if bond.IsAromatic():
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35 label = 'a'
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36 elif bond.IsSingle():
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37 label = 's'
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38 elif bond.IsDouble():
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39 label = 'd'
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40 elif bond.IsTriple():
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41 label = 't'
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42 atom1 = bond.GetBeginAtom()
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43 atom2 = bond.GetEndAtom()
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44 args.outfile.write('e %s %s %s\n' % (src_index, dest_index, label))
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45
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46
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47
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48 if __name__ == "__main__":
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49 parser = argparse.ArgumentParser()
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50 parser.add_argument('-i', '--infile', nargs='*',
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51 help="Specify one or more input files")
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52 parser.add_argument('-f', '--format',
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53 help="Format of the input file.")
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54 parser.add_argument('--outfile', type=argparse.FileType('w'),
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55 default=sys.stdout, help="Specify one output file")
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56 args = parser.parse_args()
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57 main( args )
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