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24f1737839
* remove all of the "from __future__" imports * remove the first batch of rdkit.six imports/uses * next step of rdkit.six removal * removing xrange, range, and some maps * next round of removals * next round of cleanups * fix inchi test * last bits of "from rdkit.six" are gone * and the last of the six stuff is gone * strange importlib problem
65 lines
2.6 KiB
Python
65 lines
2.6 KiB
Python
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are
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# met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above
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# copyright notice, this list of conditions and the following
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# disclaimer in the documentation and/or other materials provided
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# with the distribution.
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# * Neither the name of GlaxoSmithKline Research & Development Ltd.
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# nor the names of its contributors may be used to endorse or promote
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# products derived from this software without specific prior written
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# permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Created by Jameed Hussain, May 2013
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from rdkit import Chem
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from rdkit.Chem.Fraggle import FraggleSim
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if __name__ == '__main__':
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import sys, re
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if (len(sys.argv) >= 2):
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print(
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"Program to run the first part of Fraggle. Program splits the molecule\nready for the search\n")
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print("USAGE: ./fraggle.py <file_of_smiles")
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print("Format of smiles file: SMILES ID (space or comma separated)")
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print("Output: whole mol smiles,ID,fraggle split smiles\n")
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sys.exit(1)
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#read the STDIN
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for line in sys.stdin:
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line = line.rstrip()
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smi, id_ = re.split('\s|,', line)
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#print smi,id_
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mol = Chem.MolFromSmiles(smi)
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if mol is None:
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sys.stderr.write("Can't generate mol for: %s\n" % (smi))
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continue
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out_fragments = FraggleSim.generate_fraggle_fragmentation(mol)
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#print out the unique fragments
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for x in out_fragments:
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#cansmi
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temp = Chem.MolFromSmiles(x)
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print("%s,%s,%s" % (smi, id_, Chem.MolToSmiles(temp)))
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