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95a92282d1
o rdkit gains a RDKit::common_properties namespace that contains common string value properties o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns true/false on success or failure. This is used to optimize access. o rdkit learns how to pass property keys by reference, not value. A new namespace has been added to RDKit, common_properties that contains the std::string values for commonly used properties. This helps to avoid typos in string values but also avoids a creation of std::strings from character values. All accessors (has/get/clear and getPropIfPresent) now pass the key by reference. Additionally, getPropIfPresent removes the double lookup of hasProp/getProp which can be a significant speedup in the smiles and smarts parsers (10-20%)
106 lines
3.4 KiB
C++
106 lines
3.4 KiB
C++
//
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// Copyright (C) 2013 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <GraphMol/GraphMol.h>
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#include <GraphMol/MolOps.h>
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#include <RDBoost/Exceptions.h>
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#include <GraphMol/AtomIterators.h>
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#include <GraphMol/BondIterators.h>
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#include <boost/foreach.hpp>
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namespace RDKit {
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namespace MolOps {
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ROMol *renumberAtoms(const ROMol &mol,const std::vector<unsigned int> &newOrder){
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unsigned int nAts=mol.getNumAtoms();
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PRECONDITION(newOrder.size()==nAts,"bad newOrder size");
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std::vector<unsigned int> revOrder(nAts);
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for(unsigned int nIdx=0;nIdx<nAts;++nIdx){
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unsigned int oIdx=newOrder[nIdx];
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if(oIdx>nAts){
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throw ValueErrorException("idx value exceeds numAtoms");
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}
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revOrder[oIdx]=nIdx;
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}
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// ------
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// newOrder[i] : which atom should be in position i of the new mol
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// revOrder[i] : where atom i of the original mol landed in the new mol
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RWMol *res=new RWMol();
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// copy over the atoms:
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for(unsigned int nIdx=0;nIdx<nAts;++nIdx){
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unsigned int oIdx=newOrder[nIdx];
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const Atom *oAtom=mol.getAtomWithIdx(oIdx);
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Atom *nAtom=oAtom->copy();
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res->addAtom(nAtom,false,true);
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// take care of atom-numbering-dependent properties:
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INT_VECT nAtoms;
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if(nAtom->getPropIfPresent(common_properties::_ringStereoAtoms, nAtoms)){
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// FIX: ought to be able to avoid this copy.
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BOOST_FOREACH(int &val,nAtoms){
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if(val<0){
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val=-1*(revOrder[(-val-1)]+1);
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} else {
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val=revOrder[val-1]+1;
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}
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}
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nAtom->setProp(common_properties::_ringStereoAtoms,nAtoms,true);
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}
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}
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// now the bonds:
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for(ROMol::ConstBondIterator bi=mol.beginBonds();
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bi!=mol.endBonds();++bi){
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const Bond *oBond=(*bi);
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Bond *nBond=oBond->copy();
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nBond->setBeginAtomIdx(revOrder[oBond->getBeginAtomIdx()]);
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nBond->setEndAtomIdx(revOrder[oBond->getEndAtomIdx()]);
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res->addBond(nBond,true);
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// take care of atom-numbering-dependent properties:
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BOOST_FOREACH(int &idx,nBond->getStereoAtoms()){
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idx=revOrder[idx];
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}
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}
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// Conformers:
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for(ROMol::ConstConformerIterator oConf=mol.beginConformers();
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oConf!=mol.endConformers();
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++oConf){
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Conformer *nConf=new Conformer(nAts);
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for(unsigned int i=0;i<nAts;++i){
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nConf->setAtomPos(i,(*oConf)->getAtomPos(revOrder[i]));
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}
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res->addConformer(nConf);
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}
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// update the ring info:
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const RingInfo *oRings=mol.getRingInfo();
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if(oRings){
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RingInfo *nRings=res->getRingInfo();
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nRings->reset();
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nRings->initialize();
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for(unsigned int i=0;i<oRings->numRings();++i){
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const INT_VECT &oRing=oRings->atomRings()[i];
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INT_VECT nRing(oRing.size());
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for(unsigned int j=0;j<oRing.size();++j){
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nRing[j]=revOrder[oRing[j]];
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}
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nRings->addRing(nRing,oRings->bondRings()[i]);
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}
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}
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return dynamic_cast<ROMol *>(res);
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}
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}; // end of namespace MolOps
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}; // end of namespace RDKit
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