mirror of
https://github.com/rdkit/rdkit.git
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2debdfde0d
* Adds RDAny (smaller generic holder) Updates all used dictionaries This is an API compliant version of the current rdany system, but uses a lot less memory in practice. * Removes code duplication * Converts CHECK_INVARIANT to TEST_ASSERT * Fixes DoubleTag issue * Adds Bool to DoubleMagic implementation * Removes reference to property pickler
114 lines
3.8 KiB
OpenEdge ABL
114 lines
3.8 KiB
OpenEdge ABL
/*
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* $Id: Atom.i 2519 2013-05-17 03:01:18Z glandrum $
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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_string.i"
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%include "std_vector.i"
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%include "std_map.i"
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%include "std_pair.i"
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%{
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#include <Query/QueryObjects.h>
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#include <RDGeneral/types.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/PeriodicTable.h>
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#include <GraphMol/SanitException.h>
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#include <GraphMol/Atom.h>
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#include <GraphMol/ConjugHybrid.cpp>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <Geometry/point.h>
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#include <GraphMol/MolOps.h>
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%}
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%ignore RDKit::Atom::Match(const Atom *) const;
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%template(Bond_Vect) std::vector<RDKit::Bond*>;
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%include "enums.swg"
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#if swifjava
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%javaconst(1);
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#endif
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%include <GraphMol/Atom.h>
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%newobject RDKit::Atom::getProp;
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%extend RDKit::Atom {
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std::string getProp(const std::string key){
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std::string res;
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($self)->getProp(key, res);
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return res;
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}
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/* Methods from ConjugHybrid.cpp */
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void markConjAtomBonds() {
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RDKit::markConjAtomBonds(($self));
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}
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int numBondsPlusLonePairs() {
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RDKit::numBondsPlusLonePairs(($self));
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}
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bool atomHasConjugatedBond() {
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return RDKit::MolOps::atomHasConjugatedBond(($self));
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}
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/* From MolTransforms.h */
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void transformAtom(RDGeom::Transform3D &tform) {
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MolTransforms::transformAtom(($self), tform);
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}
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/* Based on Python wrappers and unit tests */
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bool IsInRing(){
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if(!($self)->getOwningMol().getRingInfo()->isInitialized()){
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RDKit::MolOps::findSSSR(($self)->getOwningMol());
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}
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return ($self)->getOwningMol().getRingInfo()->numAtomRings(($self)->getIdx())!=0;
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}
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bool IsInRingSize(int size){
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if(!($self)->getOwningMol().getRingInfo()->isInitialized()){
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RDKit::MolOps::findSSSR(($self)->getOwningMol());
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}
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return ($self)->getOwningMol().getRingInfo()->isAtomInRingOfSize(($self)->getIdx(),size);
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}
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std::vector<RDKit::Bond*> *getBonds() {
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std::vector<RDKit::Bond*> *bonds = new std::vector<RDKit::Bond*>;
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const RDKit::ROMol *parent = &($self)->getOwningMol();
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RDKit::ROMol::OEDGE_ITER begin,end;
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boost::tie(begin,end) = parent->getAtomBonds(($self));
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while(begin!=end){
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RDKit::Bond *tmpB = (*parent)[*begin].get();
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bonds->push_back(tmpB);
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begin++;
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}
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return bonds;
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}
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}
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