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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
124 lines
4.2 KiB
Python
124 lines
4.2 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, July 2013
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import sys
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import re
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from optparse import OptionParser
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from rdkit import Chem
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from rdkit.Chem import AllChem
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def smiles_to_smarts(smi):
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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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return None
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#change the isotope to 42
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for atom in mol.GetAtoms():
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atom.SetIsotope(42)
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#preint out the smiles - all the atom attributes will be fully specified
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smarts = Chem.MolToSmiles(mol, isomericSmiles=True)
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#remove the 42 isotope labels
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smarts = re.sub(r'\[42', "[", smarts)
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#now have a fully specified SMARTS - simples!
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return smarts
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if __name__ == '__main__':
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parser = OptionParser(
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description="Program to apply transformations to a set of input molecules",
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epilog="Example command: mol_transform.py -t TRANSFORM_FILE <SMILES_FILE\t\t"
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"Format of smiles file: SMILES ID <space or comma separated>\t\t\t"
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"Format of transform file: transform <one per line>\t\t\t"
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"Output: SMILES,ID,Transfrom,Modified_SMILES")
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parser.add_option('-f', '--file', action='store', dest='transform_file', type='string',
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help='The file containing the transforms to apply to your input SMILES')
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(options, args) = parser.parse_args()
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#print options.transform_file
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if (options.transform_file == None):
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print("Please specify the transform file.")
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sys.exit(1)
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smiles = []
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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 smiles,id
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smiles.append((smi, id))
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#read the transform file
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#all the transform must come from BioDig to guarantee they have been cansmirk'ed
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infile = open(options.transform_file, 'r')
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print("Input_SMILES,ID,RG-Transform,RG-transformedSMILES")
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for transform in infile:
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transform = transform.rstrip()
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#need to conver the smiles to smart to get rid of any potential issues
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lhs, rhs = transform.split(">>")
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if (lhs == "[*:1][H]"):
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lhs = "[*;!H0:1]"
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else:
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lhs = smiles_to_smarts(lhs)
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if (rhs == "[*:1][H]"):
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rhs = "[*:1]"
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else:
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rhs = smiles_to_smarts(rhs)
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rdkit_transform = "%s>>%s" % (lhs, rhs)
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rxn = AllChem.ReactionFromSmarts(rdkit_transform)
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#rxn = AllChem.ReactionFromSmarts(transform)
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for x in smiles:
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mol = Chem.MolFromSmiles(x[0])
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ps = rxn.RunReactants([mol])
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products = set()
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for y in range(len(ps)):
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for z in range(len(ps[y])):
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p = ps[y][z]
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Chem.SanitizeMol(p)
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products.add(Chem.MolToSmiles(p, isomericSmiles=True))
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for p in products:
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print("%s,%s,%s,%s" % (x[0], x[1], transform, p))
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