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1 #!/usr/bin/env python
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2 # -*- coding: UTF-8 -*-
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3
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4 """
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5 Change the title from a molecule file to metadata
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6 value of a given-id of the same molecule file.
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7 """
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8
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9 import os, sys
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10 import argparse
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11 import openbabel
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12 openbabel.obErrorLog.StopLogging()
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13 import pybel
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14
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15
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16 def main():
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17 parser = argparse.ArgumentParser(
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18 description="Change the title from a molecule file to metadata \
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19 value of a given-id of the same molecule file.",
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20 )
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21 parser.add_argument('--infile', '-i',
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22 required=True, help="path to the input file")
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23 parser.add_argument('--outfile', '-o',
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24 required=True, help="path to the output file")
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25 parser.add_argument('--key', '-k',
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26 required=True, help="the metadata key from the sdf file which should inlcude the new title")
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27
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28 args = parser.parse_args()
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29
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30 output = pybel.Outputfile("sdf", args.outfile, overwrite=True)
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31
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32 for mol in pybel.readfile("sdf", args.infile):
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33 if args.key in mol.data:
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34 mol.title = mol.data[args.key]
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35 output.write( mol )
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36
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37 output.close()
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38
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39
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40 if __name__ == "__main__":
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41 main()
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42
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