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https://github.com/rdkit/rdkit.git
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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%)
103 lines
3.5 KiB
C++
103 lines
3.5 KiB
C++
// $Id$
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//
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// Copyright (c) 2014, 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 <GraphMol/ChemReactions/Reaction.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/ChemReactions/ReactionParser.h>
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namespace{
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bool testForSameRXNRoleOfAllMoleculeAtoms(const RDKit::ROMol &mol, int role)
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{
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RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
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while(atItP.first != atItP.second ){
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const RDKit::Atom *oAtom=mol[*(atItP.first++)].get();
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int current_role;
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if(oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole, current_role) &&
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current_role!=role){
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return false;
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}
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}
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return true;
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}
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int getRXNRoleOfMolecule(const RDKit::ROMol &mol)
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{
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RDKit::ROMol::ATOM_ITER_PAIR atItP = mol.getVertices();
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while(atItP.first != atItP.second ){
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const RDKit::Atom *oAtom=mol[*(atItP.first++)].get();
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int molRxnRole;
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if(oAtom->getPropIfPresent(RDKit::common_properties::molRxnRole, molRxnRole)){
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return molRxnRole;
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}
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}
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return -1;
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}
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}
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namespace RDKit {
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ChemicalReaction * RxnMolToChemicalReaction(const ROMol &mol)
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{
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ChemicalReaction *rxn=new ChemicalReaction();
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MOL_SPTR_VECT fragments = MolOps::getMolFrags(mol);
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unsigned countFragments = 0;
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for(MOL_SPTR_VECT::iterator iter = fragments.begin();
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iter != fragments.end(); ++iter, countFragments++){
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int role = getRXNRoleOfMolecule(*iter->get());
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if(!testForSameRXNRoleOfAllMoleculeAtoms(*iter->get(), role)){
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BOOST_LOG(rdWarningLog)<<">> Atoms within one molecule have different RXN roles.\n";
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continue;
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}
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switch(role){
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case 1:
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rxn->addReactantTemplate(*iter);
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break;
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case 2:
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rxn->addProductTemplate(*iter);
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break;
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case 3:
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rxn->addAgentTemplate(*iter);
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break;
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default:
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BOOST_LOG(rdWarningLog)<<">> Fragment "<< countFragments <<" not included in the reaction, atoms do not have a correct RXN role.\n";
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}
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}
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return rxn;
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}
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}
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