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/*
* $Id: Atom.i 2519 2013-05-17 03:01:18Z glandrum $
*
* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
%include "std_string.i"
%include "std_vector.i"
%include "std_map.i"
%include "std_pair.i"
%{
#include <Query/QueryObjects.h>
#include <RDGeneral/types.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/PeriodicTable.h>
#include <GraphMol/SanitException.h>
#include <GraphMol/Atom.h>
#include <GraphMol/ConjugHybrid.cpp>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <Geometry/point.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
// from Python wrapper
std::string describeQueryHelper(const RDKit::Atom::QUERYATOM_QUERY *q, unsigned int depth) {
std::string res;
if (q) {
for (unsigned int i = 0; i < depth; ++i) {
res += " ";
}
res += q->getFullDescription() + "\n";
for (const auto &child :
boost::make_iterator_range(q->beginChildren(), q->endChildren())) {
res += describeQueryHelper(child.get(), depth + 1);
}
}
return res;
}
%}
%ignore RDKit::Atom::Match(const Atom *) const;
%ignore RDKit::Atom::expandQuery;
%template(Bond_Vect) std::vector<RDKit::Bond*>;
%include "enums.swg"
#if swifjava
%javaconst(1);
#endif
%include <GraphMol/Atom.h>
%newobject RDKit::Atom::getProp;
%newobject RDKit::Atom::getBonds;
%extend RDKit::Atom {
std::string getProp(const std::string key){
std::string res;
($self)->getProp(key, res);
return res;
}
/* Methods from ConjugHybrid.cpp */
void markConjAtomBonds() {
RDKit::markConjAtomBonds(($self));
}
int numBondsPlusLonePairs() {
return RDKit::numBondsPlusLonePairs(($self));
}
bool atomHasConjugatedBond() {
return RDKit::MolOps::atomHasConjugatedBond(($self));
}
/* From MolTransforms.h */
void transformAtom(RDGeom::Transform3D &tform) {
MolTransforms::transformAtom(($self), tform);
}
/* Based on Python wrappers and unit tests */
bool IsInRing(){
if(!($self)->getOwningMol().getRingInfo()->isInitialized()){
RDKit::MolOps::findSSSR(($self)->getOwningMol());
}
return ($self)->getOwningMol().getRingInfo()->numAtomRings(($self)->getIdx())!=0;
}
bool IsInRingSize(int size){
if(!($self)->getOwningMol().getRingInfo()->isInitialized()){
RDKit::MolOps::findSSSR(($self)->getOwningMol());
}
return ($self)->getOwningMol().getRingInfo()->isAtomInRingOfSize(($self)->getIdx(),size);
}
std::vector<RDKit::Bond*> *getBonds() {
std::vector<RDKit::Bond*> *bonds = new std::vector<RDKit::Bond*>;
RDKit::ROMol *parent = &($self)->getOwningMol();
RDKit::ROMol::OEDGE_ITER begin,end;
boost::tie(begin,end) = parent->getAtomBonds(($self));
while(begin!=end){
RDKit::Bond *tmpB = (*parent)[*begin];
bonds->push_back(tmpB);
begin++;
}
return bonds;
}
// also matches ATOM_NULL_QUERY
void setQuery(RDKit::ATOM_OR_QUERY *query) {
$self->setQuery(query);
}
void setQuery(RDKit::ATOM_EQUALS_QUERY *query) {
$self->setQuery(query);
}
// From Python Wrapper
std::string AtomGetSmarts(bool doKekule=false, bool allHsExplicit=false,
bool isomericSmiles=true) {
std::string res;
if (($self)->hasQuery()) {
res = RDKit::SmartsWrite::GetAtomSmarts(static_cast<const RDKit::QueryAtom *>(($self)));
} else {
// FIX: this should not be necessary
res = RDKit::SmilesWrite::GetAtomSmiles(($self), doKekule, nullptr, allHsExplicit,
isomericSmiles);
}
return res;
}
// from Python Wrapper
std::string describeQuery() {
std::string res = "";
res = describeQueryHelper(($self)->getQuery(), 0);
return res;
}
}
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