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94 lines
2.9 KiB
Python
94 lines
2.9 KiB
Python
#
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# Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
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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 Novartis Institutes for BioMedical Research Inc.
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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 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 Nadine Schneider, July 2016
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import copy
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from collections import defaultdict
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from rdkit import Chem
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from rdkit.Chem import AllChem
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def transferAgentsToReactants(rxn):
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for a in range(rxn.GetNumAgentTemplates()):
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agent = rxn.GetAgentTemplate(a)
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rxn.AddReactantTemplate(agent)
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def removeAgentsAndTransferToReactants(rxn):
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tmp = []
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rxn.RemoveAgentTemplates(tmp)
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for a in tmp:
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rxn.AddReactantTemplate(a)
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def getNumPositiveCounts(fp):
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count = 0
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for k, v in fp.GetNonzeroElements().items():
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if v > 0:
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count += v
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return count
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def getNumNegativeCounts(fp):
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count = 0
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for k, v in fp.GetNonzeroElements().items():
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if v < 0:
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count += abs(v)
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return count
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def getNumPositiveBitCountsOfRadius0(fp, bitinfo):
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count = 0
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bitsUnmappedAtoms = []
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for k in bitinfo:
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if bitinfo[k][0][1] == 0:
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v = fp[k]
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if v > 0:
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count += 1
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bitsUnmappedAtoms.append((k, v))
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return count, bitsUnmappedAtoms
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def getSumFps(fps):
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summedFP = copy.deepcopy(fps[0])
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for fp in fps[1:]:
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summedFP += fp
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return summedFP
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def uniqueMolecules(mols):
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smiles = [Chem.MolToSmiles(mol) for mol in mols]
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uniqueMolecules = defaultdict(int)
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for n, smi in enumerate(smiles):
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uniqueMolecules[n] = smiles.index(smi)
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return uniqueMolecules, smiles
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