mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
ba12d98ad0
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers * Actually delete atoms and bonds... * RWMol::clear now calls destroy to handle atom/bond deletion * Changes broken Atom lookup for windows/gcc * Adds tests for running with valgrind * Adds test designed for valgrind and molecule deletions * Removes RNG, actually tests bond deletions * update swig wrappers * deal with most recent changes on the main branch
452 lines
18 KiB
OpenEdge ABL
452 lines
18 KiB
OpenEdge ABL
/*
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* $Id$
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*
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* Copyright (c) 2010, 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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%include "std_pair.i"
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%include "std_string.i"
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%include "std_vector.i"
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%{
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#include <RDGeneral/types.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/Conformer.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <GraphMol/ChemTransforms/ChemTransforms.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/SequenceWriters.h>
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#include <GraphMol/Bond.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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#include <GraphMol/Descriptors/Crippen.h>
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#include <GraphMol/Depictor/RDDepictor.h>
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#include <GraphMol/Descriptors/MolDescriptors.h>
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#include <GraphMol/Depictor/RDDepictor.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <GraphMol/MolPickler.h>
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#include <DistGeom/BoundsMatrix.h>
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#include <GraphMol/DistGeomHelpers/Embedder.h>
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#include <GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/MolAlign/O3AAlignMolecules.h>
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#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
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#include <GraphMol/PartialCharges/GasteigerCharges.h>
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#include <sstream>
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%}
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%template(ROMol_Vect) std::vector< boost::shared_ptr<RDKit::ROMol> >;
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%template(ROMol_Vect_Vect) std::vector< std::vector< boost::shared_ptr<RDKit::ROMol> > >;
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%template(Atom_Vect) std::vector<RDKit::Atom*>;
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// These prevent duplicate definitions in Java code
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%ignore RDKit::ROMol::hasProp(std::string const) const ;
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%ignore RDKit::ROMol::clearProp(std::string const) const ;
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%ignore RDKit::ROMol::getAtomWithIdx(unsigned int) const ;
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%ignore RDKit::ROMol::getBondWithIdx(unsigned int) const ;
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%ignore RDKit::ROMol::getBondBetweenAtoms(unsigned int,unsigned int) const ;
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%ignore RDKit::ROMol::getAtomNeighbors(Atom const *at) const;
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%ignore RDKit::ROMol::getAtomBonds(Atom const *at) const;
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%ignore RDKit::ROMol::getVertices() ;
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%ignore RDKit::ROMol::getVertices() const ;
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%ignore RDKit::ROMol::getEdges() ;
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%ignore RDKit::ROMol::getEdges() const ;
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%ignore RDKit::ROMol::getTopology() const ;
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/*
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* Special handling for Conformer objects which should not be GCed until the molecule is destroyed
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* We want to modify the behavior of the Conformer coming into the addConformer method without
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* impacting Conformer objects that are arguments to other methods. Therefore we define a pattern
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* that will trigger special handling of the Conformer input (the addConf method match this pattern).
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* Then add the necessary Java code to modify the Conformer object to no longer be the owner of the
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* underlying C++ object.
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*/
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%ignore addConformer(Conformer * conf, bool assignId=false);
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%rename(addConformer) RDKit::ROMol::addConf;
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%typemap(javain) RDKit::Conformer * ownedConf "getCPtrAndReleaseControl($javainput)"
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%typemap(javacode) RDKit::ROMol %{
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// Ensure that the GC doesn't collect this item,
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// as the underlying C++ class stores a shallow copy
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private long getCPtrAndReleaseControl(Conformer conf) {
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conf.setSwigCMemOwn(false);
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return Conformer.getCPtr(conf);
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}
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%}
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%include <GraphMol/ROMol.h>
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%newobject removeHs;
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%newobject addHs;
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%newobject mergeQueryHs;
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%newobject replaceCore;
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%newobject replaceSidechains;
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%newobject deleteSubstructs;
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%newobject getAtoms;
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%extend RDKit::ROMol {
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std::string getProp(const std::string key){
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std::string res;
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self->getProp(key, res);
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return res;
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}
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/* Used in the addConformer modifications described above */
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unsigned int RDKit::ROMol::addConf(RDKit::Conformer * ownedConf, bool assignId=false) {
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return self->addConformer(ownedConf, assignId);
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}
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std::string MolToSmiles(bool doIsomericSmiles=false,bool doKekule=false, int rootedAtAtom=-1){
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return RDKit::MolToSmiles(*($self),doIsomericSmiles,doKekule,rootedAtAtom);
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}
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std::string MolToMolBlock(bool includeStereo=true, int confId=-1) {
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return RDKit::MolToMolBlock(*($self),includeStereo,confId);
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}
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void MolToMolFile(std::string fName,bool includeStereo=true, int confId=-1,bool kekulize=true) {
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RDKit::MolToMolFile(*($self), fName, includeStereo, confId, kekulize);
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}
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std::string MolToTPLText(std::string partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false) {
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return RDKit::MolToTPLText(*($self), partialChargeProp, writeFirstConfTwice);
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}
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void MolToTPLFile(std::string fName,
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std::string partialChargeProp="_GasteigerCharge",
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bool writeFirstConfTwice=false) {
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RDKit::MolToTPLFile(*($self), fName, partialChargeProp, writeFirstConfTwice);
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}
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std::string MolToPDBBlock(int confId=-1,unsigned int flavor=0) {
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return RDKit::MolToPDBBlock(*($self),confId,flavor);
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}
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void MolToPDBFile(std::string fName,int confId=-1,unsigned int flavor=0) {
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RDKit::MolToPDBFile(*($self), fName, confId, flavor);
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}
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std::string MolToSequence() {
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return RDKit::MolToSequence(*($self));
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}
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std::string MolToFASTA() {
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return RDKit::MolToFASTA(*($self));
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}
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std::string MolToHELM() {
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return RDKit::MolToHELM(*($self));
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}
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bool hasSubstructMatch(RDKit::ROMol &query,bool useChirality=false){
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RDKit::MatchVectType mv;
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return SubstructMatch(*($self),query,mv,true,useChirality);
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};
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/* From MolOps, Substruct/SubstructMatch */
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std::vector<std::pair<int, int> > getSubstructMatch(RDKit::ROMol &query,bool useChirality=false){
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RDKit::MatchVectType mv;
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SubstructMatch(*($self),query,mv,true,useChirality);
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return mv;
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};
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std::vector< std::vector<std::pair<int, int> > > getSubstructMatches(RDKit::ROMol &query,bool uniquify=true, bool useChirality=false){
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std::vector<RDKit::MatchVectType> mv;
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SubstructMatch(*($self),query,mv,uniquify,true,useChirality);
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return mv;
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};
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RDKit::ROMol *deleteSubstructs(const RDKit::ROMol &query, bool replaceAll) {
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return RDKit::deleteSubstructs(*($self), query, replaceAll);
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};
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std::vector<RDKit::ROMOL_SPTR> replaceSubstructs(const RDKit::ROMol &query,
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const RDKit::ROMol &replacement,
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bool replaceAll=false) {
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return RDKit::replaceSubstructs(*($self), query, replacement, replaceAll);
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};
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RDKit::ROMol *replaceSidechains(const RDKit::ROMol &coreQuery) {
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return RDKit::replaceSidechains(*($self), coreQuery);
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};
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RDKit::ROMol *replaceCore(const RDKit::ROMol &coreQuery, bool replaceDummies=true,bool labelByIndex=false) {
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return RDKit::replaceCore(*($self), coreQuery, replaceDummies, labelByIndex);
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};
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/* Methods from MolFileStereoChem.h */
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void DetectBondStereoChemistry(const RDKit::Conformer *conf) {
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RDKit::DetectBondStereoChemistry(*($self), conf);
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};
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void WedgeMolBonds(const RDKit::Conformer *conf) {
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RDKit::WedgeMolBonds(*($self), conf);
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};
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void pickBondsToWedge() {
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RDKit::pickBondsToWedge(*($self));
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};
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void ClearSingleBondDirFlags() {
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RDKit::ClearSingleBondDirFlags(*($self));
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};
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/* Methods from ConjugHybrid.cpp */
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void setConjugation() {
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RDKit::MolOps::setConjugation(*($self));
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}
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void setHybridization() {
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RDKit::MolOps::setHybridization(*($self));
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}
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/* From GraphMol/Depictor/RDDepictor.h */
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unsigned int compute2DCoords(const RDGeom::INT_POINT2D_MAP *coordMap=0,
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bool canonOrient=false,
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bool clearConfs=true,
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unsigned int nFlipsPerSample=0,
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unsigned int nSamples=0,
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int sampleSeed=0,
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bool permuteDeg4Nodes=false) {
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return RDDepict::compute2DCoords(*($self),
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coordMap,
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canonOrient,
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clearConfs,
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nFlipsPerSample,
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nSamples,
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sampleSeed,
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permuteDeg4Nodes);
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}
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unsigned int compute2DCoords(RDKit::ROMol &templ){
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RDKit::MatchVectType matchVect;
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if(templ.getNumConformers() && SubstructMatch(*($self),templ,matchVect)){
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RDGeom::INT_POINT2D_MAP coordMap;
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RDKit::Conformer conf=templ.getConformer();
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for(RDKit::MatchVectType::const_iterator iter=matchVect.begin();
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iter!=matchVect.end();++iter){
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RDGeom::Point2D pt;
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pt.x = conf.getAtomPos(iter->first).x;
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pt.y = conf.getAtomPos(iter->first).y;
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coordMap[iter->second]=pt;
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}
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return RDDepict::compute2DCoords(*($self),&coordMap);
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} else {
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return RDDepict::compute2DCoords(*($self),0);
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}
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}
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unsigned int compute2DCoordsMimicDistMat(const RDDepict::DOUBLE_SMART_PTR *dmat=0,
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bool canonOrient=true,
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bool clearConfs=true,
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double weightDistMat=0.5,
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unsigned int nFlipsPerSample=3,
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unsigned int nSamples=100,
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int sampleSeed=25,
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bool permuteDeg4Nodes=true) {
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return RDDepict::compute2DCoordsMimicDistMat(*($self),
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dmat,
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canonOrient,
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clearConfs,
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weightDistMat,
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nFlipsPerSample,
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nSamples,
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sampleSeed,
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permuteDeg4Nodes);
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}
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/* From FindRings.cpp, MolOps.h */
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int findSSSR(RDKit::VECT_INT_VECT &res) {
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return RDKit::MolOps::findSSSR(*($self), res);
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};
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int findSSSR() {
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return RDKit::MolOps::findSSSR(*($self));
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};
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int symmetrizeSSSR(RDKit::VECT_INT_VECT &res) {
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return RDKit::MolOps::symmetrizeSSSR(*($self), res);
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}
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int symmetrizeSSSR() {
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return RDKit::MolOps::symmetrizeSSSR(*($self));
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}
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/* From Matrices.cpp, MolOps.h */
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double *getDistanceMat(bool useBO=false,
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bool useAtomWts=false,
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bool force=false,
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const char *propNamePrefix=0) {
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return RDKit::MolOps::getDistanceMat(*($self), useBO, useAtomWts, force, propNamePrefix);
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}
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double *getDistanceMat(const std::vector<int> &activeAtoms,
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const std::vector<const Bond *> &bonds,
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bool useBO=false,
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bool useAtomWts=false) {
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return RDKit::MolOps::getDistanceMat(*($self), activeAtoms, bonds, useBO, useAtomWts);
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}
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double *getAdjacencyMatrix(bool useBO=false,
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int emptyVal=0,
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bool force=false,
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const char *propNamePrefix=0) {
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return RDKit::MolOps::getAdjacencyMatrix(*($self), useBO, emptyVal, force, propNamePrefix);
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}
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RDKit::INT_LIST getShortestPath(int aid1, int aid2) {
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return RDKit::MolOps::getShortestPath(*($self), aid1, aid2);
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}
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/* From MolTransforms.h */
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void transformMolsAtoms(RDGeom::Transform3D &tform) {
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MolTransforms::transformMolsAtoms(($self), tform);
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}
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void canonicalizeMol(bool normalizeCovar=false, bool ignoreHs=true) {
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MolTransforms::canonicalizeMol(*($self), normalizeCovar, ignoreHs);
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}
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/* From Python wrappers -- implied functionality */
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std::vector<RDKit::Atom*> *getAtoms() {
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int c = ($self)->getNumAtoms();
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std::vector<RDKit::Atom*> *atoms = new std::vector<RDKit::Atom*>;
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for (int i = 0; i < c; i++) {
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RDKit::Atom* a = ($self)->getAtomWithIdx(i);
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atoms->push_back(a);
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}
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return atoms;
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}
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/* From MolPickler.h */
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std::vector<int> ToBinary(){
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std::string sres;
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RDKit::MolPickler::pickleMol(*($self),sres);
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std::vector<int> res(sres.length());
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std::copy(sres.begin(),sres.end(),res.begin());
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return res;
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};
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static RDKit::ROMOL_SPTR MolFromBinary(std::vector<int> pkl){
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std::string sres;
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sres.resize(pkl.size());
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std::copy(pkl.begin(),pkl.end(),sres.begin());
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RDKit::ROMol *res=new RDKit::ROMol(sres);
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return RDKit::ROMOL_SPTR(res);
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}
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/* From AddHs.cpp */
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RDKit::ROMol *addHs(bool explicitOnly,bool addCoords=false){
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return RDKit::MolOps::addHs(*($self), explicitOnly, addCoords);
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}
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RDKit::ROMol *removeHs(bool implicitOnly,bool updateExplicitCount=false,bool sanitize=false) {
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return RDKit::MolOps::removeHs(*($self), implicitOnly, updateExplicitCount, sanitize);
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}
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RDKit::ROMol *mergeQueryHs() {
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return RDKit::MolOps::mergeQueryHs(*($self));
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}
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/* From GraphMol/MolAlign/AlignMolecules */
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double alignMol(const RDKit::ROMol &refMol,
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int prbCid=-1, int refCid=-1,
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const std::vector<std::pair<int,int> > *atomMap=0,
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const RDNumeric::DoubleVector *weights=0,
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bool reflect=false, unsigned int maxIters=50) {
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return RDKit::MolAlign::alignMol(*($self), refMol, prbCid, refCid, atomMap, weights, reflect, maxIters);
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}
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void alignMolConformers(ROMol &mol, const std::vector<unsigned int> *atomIds=0,
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const std::vector<unsigned int> *confIds=0,
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const RDNumeric::DoubleVector *weights=0,
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bool reflect=false, unsigned int maxIters=50) {
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RDKit::MolAlign::alignMolConformers(*($self), atomIds, confIds, weights, reflect, maxIters);
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}
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/* From GraphMol/MolAlign/AlignMolecules */
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double getAlignmentTransform(const RDKit::ROMol &refMol,
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RDGeom::Transform3D &trans, int prbCid = -1,
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int refCid = -1, const std::vector<std::pair<int,int> > *atomMap = 0,
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const RDNumeric::DoubleVector *weights = 0,
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bool reflect = false, unsigned int maxIters = 50){
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return RDKit::MolAlign::getAlignmentTransform(*($self), refMol, trans, prbCid, refCid, atomMap, weights, reflect, maxIters);
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}
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/* From GraphMol/MolAlign/AlignMolecules */
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std::pair<double,double> O3AAlignMol(RDKit::ROMol &refMol,
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int prbCid=-1, int refCid=-1,
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bool reflect=false, unsigned int maxIters=50,
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unsigned int accuracy=0) {
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RDKit::MMFF::MMFFMolProperties prbMP(*($self));
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RDKit::MMFF::MMFFMolProperties refMP(refMol);
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RDKit::MolAlign::O3A o3a(*($self), refMol, &prbMP, &refMP, RDKit::MolAlign::O3A::MMFF94,
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prbCid, refCid,
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reflect,maxIters,accuracy);
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double rmsd=o3a.align();
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double score = o3a.score();
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return std::make_pair(rmsd,score);
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}
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void computeGasteigerCharges(const RDKit::ROMol *mol,int nIter=12,bool throwOnParamFailure=false){
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RDKit::computeGasteigerCharges(*mol,nIter,throwOnParamFailure);
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}
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void computeGasteigerCharges(const RDKit::ROMol *mol,
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std::vector<double> &charges,
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int nIter=12,bool throwOnParamFailure=false){
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RDKit::computeGasteigerCharges(*mol,charges,nIter,throwOnParamFailure);
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}
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}
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%extend RDKit::ROMol {
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std::string ToSVG(const std::vector<int> &highlightAtoms,
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int lineWidthMult=2,int fontSize=50){
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// FIX: not sure any more what these are for
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if(fontSize<0) fontSize*=2;
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if(lineWidthMult<0) lineWidthMult *=2;
|
|
std::stringstream outs;
|
|
RDKit::MolDraw2DSVG drawer(300,300,outs);
|
|
//drawer.setFontSize(static_cast<float>(fontSize)*drawer.fontSize()/50);
|
|
drawer.drawMolecule(*($self),&highlightAtoms);
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
|
|
return outs.str();
|
|
}
|
|
std::string ToSVG(int lineWidthMult=2,int fontSize=50){
|
|
// FIX: not sure any more what these are for
|
|
if(fontSize<0) fontSize*=2;
|
|
if(lineWidthMult<0) lineWidthMult *=2;
|
|
std::stringstream outs;
|
|
RDKit::MolDraw2DSVG drawer(300,300,outs);
|
|
//drawer.setFontSize(static_cast<float>(fontSize)*drawer.fontSize()/50);
|
|
drawer.drawMolecule(*($self));
|
|
drawer.finishDrawing();
|
|
outs.flush();
|
|
|
|
return outs.str();
|
|
|
|
}
|
|
}
|