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/*
* $Id$
*
* 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 <GraphMol/RDKitBase.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <vector>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionRunner.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/ChemReactions/ReactionPickler.h>
%}
%include <GraphMol/ChemReactions/Reaction.h>
%include <GraphMol/ChemReactions/ReactionParser.h>
%ignore RDKit::ChemicalReaction::validate(unsigned int &,unsigned int &,bool);
%ignore RDKit::ChemicalReaction::validate(unsigned int &,unsigned int &);
%ignore RDKit::isMoleculeReactantOfReaction(const ChemicalReaction &r,const ROMol &,
unsigned int &);
%ignore RDKit::isMoleculeProductOfReaction(const ChemicalReaction &r,const ROMol &,
unsigned int &);
%newobject ReactionFromSmarts;
%newobject ReactionFromRxnBlock;
%newobject ReactionFromRxnFile;
%newobject ReduceProductToSideChains;
%extend RDKit::ChemicalReaction {
static RDKit::ChemicalReaction *ReactionFromSmarts(std::string sma,bool useSmiles=false){
RDKit::ChemicalReaction *res=RDKit::RxnSmartsToChemicalReaction(sma,0,useSmiles);
if(res) res->initReactantMatchers();
return res;
};
static RDKit::ChemicalReaction *ReactionFromRxnBlock(std::string block){
RDKit::ChemicalReaction *res=RDKit::RxnBlockToChemicalReaction(block);
if(res) res->initReactantMatchers();
return res;
};
static RDKit::ChemicalReaction *ReactionFromRxnFile(std::string filename){
RDKit::ChemicalReaction *res=RDKit::RxnFileToChemicalReaction(filename);
if(res) res->initReactantMatchers();
return res;
};
static std::string ReactionToSmarts(ChemicalReaction &rxn) {
return RDKit::ChemicalReactionToRxnSmarts(rxn);
}
static std::string ReactionToRxnBlock (const ChemicalReaction &rxn) {
return RDKit::ChemicalReactionToRxnBlock(rxn);
};
/*
static RDKit::ROMol *ReduceProductToSideChains(RDKit::ROMOL_SPTR product,
bool addDummyAtoms=true) {
return RDKit::reduceProductToSideChains(product, addDummyAtoms);
};
*/
static RDKit::ROMol *ReduceProductToSideChains(RDKit::ROMol *product,
bool addDummyAtoms=true) {
RDKit::ROMOL_SPTR mol(new RDKit::ROMol(*product));
return RDKit::reduceProductToSideChains(mol, addDummyAtoms);
};
void compute2DCoordsForReaction(double spacing,
bool updateProps,
bool canonOrient,
unsigned int nFlipsPerSample,
unsigned int nSamples,
int sampleSeed,
bool permuteDeg4Nodes){
RDDepict::compute2DCoordsForReaction(*($self),
spacing,
updateProps,
canonOrient,
nFlipsPerSample,
nSamples,
sampleSeed,
permuteDeg4Nodes);
};
std::vector<int> ToBinary(){
std::string sres;
RDKit::ReactionPickler::pickleReaction(*($self),sres);
std::vector<int> res(sres.length());
std::copy(sres.begin(),sres.end(),res.begin());
return res;
};
static RDKit::ChemicalReaction *RxnFromBinary(std::vector<int> pkl){
std::string sres;
sres.resize(pkl.size());
std::copy(pkl.begin(),pkl.end(),sres.begin());
RDKit::ChemicalReaction *res=new RDKit::ChemicalReaction(sres);
return res;
};
/* A Java-accessible validation function */
std::pair<int,int> *validateReaction(bool silent=false) {
std::pair<int,int> *res = new std::pair<int,int>();
// Use some local unsigned ints so that we don't create a new and useless type at the Java
// level.
unsigned int first;
unsigned int second;
($self)->validate(first, second, silent);
res->first = (int) first;
res->second = (int) second;
return res;
};
bool validate() {
unsigned int nErr=0,nWarn=0;
bool res=$self->validate(nErr,nWarn);
return res;
};
}
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