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cf9ea71384
* First pass at MolZip (sans bond stereo) * Add support for bond stereo zipping * Add molzip swig wrappers * Add simple python wrapper/tests * Remove smiles round tripping now that fragmentOnBonds is fixed * Responses to review * AtomMaps and Isotopes must explicitly be set * Add molzip single molecule api isotope test * Add missing %newobject * Add better python docs, label test * fix docs add a test for molzip * Update Code/GraphMol/ChemTransforms/MolFragmenter.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Add missing case breaks * Add more preconditions, move mark and restore to private functions * Remove unused and redunddant code * optimize get_other_atom * Add single arg molzip test * Update Code/GraphMol/Wrap/rough_test.py Co-authored-by: Greg Landrum <greg.landrum@gmail.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
112 lines
4.5 KiB
OpenEdge ABL
112 lines
4.5 KiB
OpenEdge ABL
/*
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* $Id$
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*
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* Copyright (c) 2011, 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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%{
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#include <GraphMol/ChemTransforms/ChemTransforms.h>
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#include <GraphMol/ChemTransforms/MolFragmenter.h>
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#include <GraphMol/Bond.h>
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// Fixes annoying compilation namespace issue
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typedef RDKit::MatchVectType MatchVectType;
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// Partial binding to one overload of RDKit::fragmentOnBonds
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RDKit::ROMol *fragmentMolOnBonds(
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const RDKit::ROMol &mol, const std::vector<int> &bondIndices,
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bool addDummies = true,
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const std::vector<std::pair<unsigned int, unsigned int>> *dummyLabels = nullptr,
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std::vector<int> *nCutsPerAtom = nullptr) {
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// The c# wrapper is unable to wrap vector<unsigned int> so pass in vector<int> and convert
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std::vector<unsigned int> uBondIndices(bondIndices.begin(), bondIndices.end());
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std::vector<unsigned int> uNCutsPerAtom;
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if (nCutsPerAtom) {
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uNCutsPerAtom.insert(uNCutsPerAtom.begin(), nCutsPerAtom->begin(), nCutsPerAtom->end());
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}
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auto cutsPerAtomPtr = nCutsPerAtom ? &uNCutsPerAtom : nullptr;
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// Can't handle the 5th argument of vector<BondType> as swig will not wrap vector of enum
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return RDKit::MolFragmenter::fragmentOnBonds(mol, uBondIndices, addDummies, dummyLabels, nullptr, cutsPerAtomPtr);
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}
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// Fix std::unique_ptr issue
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RDKit::ROMol * new_molzip(
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const RDKit::ROMol &a, const RDKit::ROMol &b,
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const RDKit::MolzipParams ¶ms=RDKit::MolzipParams()) {
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return RDKit::molzip(a, b, params).release();;
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}
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RDKit::ROMol * new_molzip(
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const RDKit::ROMol &a,
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const RDKit::MolzipParams ¶ms=RDKit::MolzipParams()) {
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return RDKit::molzip(a, params).release();
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}
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%}
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%newobject deleteSubstructs;
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%newobject replaceSidechains;
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%newobject replaceCores;
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%newobject MurckoDecompose;
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%template(StringMolMap) std::map<std::string,boost::shared_ptr<RDKit::ROMol> >;
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%include <GraphMol/Bond.h>
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%include <GraphMol/ChemTransforms/ChemTransforms.h>
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%newobject fragmentMolOnBonds;
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%newobject new_molzip;
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%ignore fragmentOnBonds;
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%ignore molzip;
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%rename("fragmentOnBonds") fragmentMolOnBonds;
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%rename("molzip") new_molzip;
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RDKit::ROMol *fragmentMolOnBonds(
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const RDKit::ROMol &mol, const std::vector<int> &bondIndices,
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bool addDummies = true,
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const std::vector<std::pair<unsigned int, unsigned int>> *dummyLabels = nullptr,
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std::vector<int> *nCutsPerAtom = nullptr);
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RDKit::ROMol * new_molzip(
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const RDKit::ROMol &a, const RDKit::ROMol &b,
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const RDKit::MolzipParams ¶ms=RDKit::MolzipParams());
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RDKit::ROMol * new_molzip(
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const RDKit::ROMol &a,
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const RDKit::MolzipParams ¶ms=RDKit::MolzipParams());
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%ignore fragmentOnSomeBonds;
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%ignore constructFragmenterAtomTypes;
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%ignore constructBRICSAtomTypes;
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%ignore constructFragmenterBondTypes;
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%ignore constructBRICSBondTypes;
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%newobject fragmentOnBRICSBonds;
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%template(UIntMolMap) std::map<unsigned int,boost::shared_ptr<RDKit::ROMol> >;
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%include <GraphMol/ChemTransforms/MolFragmenter.h>
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