mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +08:00
8aac978f1b
- Module to generate reaction fingerprints: structural FP for screening, difference FP for similarity search - Add some utility functions to simplify handling of reactions - Add new functionality to include agents in the reactions, some adaptions to parsers and writers had to be done - Supports intra-bond breaks in products now - Molecules with rxn role (atom property) can be parse as reaction now
360 lines
11 KiB
C++
360 lines
11 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/ChemReactions/ReactionUtils.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/Descriptors/MolDescriptors.h>
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namespace RDKit {
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MOL_SPTR_VECT::const_iterator getStartIterator(
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const ChemicalReaction &rxn,
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ReactionMoleculeType t)
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{
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MOL_SPTR_VECT::const_iterator begin;
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if(t == Reactant){
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begin = rxn.beginReactantTemplates();
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}
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if(t == Product){
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begin = rxn.beginProductTemplates();;
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}
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if(t == Agent){
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begin = rxn.beginAgentTemplates();
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}
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return begin;
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}
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MOL_SPTR_VECT::const_iterator getEndIterator(
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const ChemicalReaction &rxn,
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ReactionMoleculeType t)
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{
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MOL_SPTR_VECT::const_iterator end;
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if(t == Reactant){
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end = rxn.endReactantTemplates();
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}
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if(t == Product){
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end = rxn.endProductTemplates();;
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}
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if(t == Agent){
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end = rxn.endAgentTemplates();
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}
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return end;
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}
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namespace {
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unsigned getReactionMoleculeTemplatesNumAtoms(
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const RDKit::ChemicalReaction &rxn,
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RDKit::ReactionMoleculeType t,
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bool onlyHeavy)
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{
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unsigned numAtoms=0;
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RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, t);
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RDKit::MOL_SPTR_VECT::const_iterator end = getEndIterator(rxn, t);
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for(; begin != end; ++begin){
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if(onlyHeavy){
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numAtoms += begin->get()->getNumHeavyAtoms();
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}
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else{
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numAtoms += begin->get()->getNumAtoms();
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}
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}
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return numAtoms;
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}
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unsigned getReactionMoleculeTemplatesNumBonds(
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const RDKit::ChemicalReaction &rxn,
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RDKit::ReactionMoleculeType t,
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bool onlyHeavy)
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{
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unsigned numBonds=0;
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RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, t);
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RDKit::MOL_SPTR_VECT::const_iterator end = getEndIterator(rxn, t);
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for(; begin != end; ++begin){
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numBonds += begin->get()->getNumBonds(onlyHeavy);
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}
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return numBonds;
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}
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double getReactionMoleculeTemplatesMW(
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const RDKit::ChemicalReaction &rxn,
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RDKit::ReactionMoleculeType t,
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bool onlyHeavy)
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{
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double mw=0.0;
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RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, t);
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RDKit::MOL_SPTR_VECT::const_iterator end = getEndIterator(rxn, t);
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for(; begin != end; ++begin){
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mw += RDKit::Descriptors::calcAMW(*begin->get(),onlyHeavy);
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}
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return mw;
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}
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unsigned getReactionMoleculeTemplatesNumRings(
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const RDKit::ChemicalReaction &rxn,
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RDKit::ReactionMoleculeType t)
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{
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unsigned numRings=0;
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RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, t);
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RDKit::MOL_SPTR_VECT::const_iterator end = getEndIterator(rxn, t);
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for(; begin != end; ++begin){
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if(begin->get()->getRingInfo()->isInitialized()){
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numRings += begin->get()->getRingInfo()->numRings();
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}
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else{
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begin->get()->updatePropertyCache();
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RDKit::MolOps::findSSSR(*begin->get());
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numRings += begin->get()->getRingInfo()->numRings();
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}
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}
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return numRings;
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}
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bool hasReactionMoleculeTemplateSubstructMatch(
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const RDKit::ChemicalReaction &rxn,
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const RDKit::ChemicalReaction &query_rxn,
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RDKit::ReactionMoleculeType t)
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{
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for(RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, t);
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begin != getEndIterator(rxn, t); ++begin){
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for(RDKit::MOL_SPTR_VECT::const_iterator begin_query = getStartIterator(query_rxn, t);
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begin_query != getEndIterator(query_rxn, t); ++begin_query){
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MatchVectType tvect;
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if(SubstructMatch(*begin->get(), *begin_query->get(),tvect )){
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return true;
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}
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}
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}
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return false;
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}
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}
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unsigned getReactantTemplatesNumAtoms(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesNumAtoms(rxn, Reactant, onlyHeavy);
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}
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unsigned getProductTemplatesNumAtoms(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesNumAtoms(rxn, Product, onlyHeavy);
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}
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unsigned getAgentTemplatesNumAtoms(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesNumAtoms(rxn, Agent, onlyHeavy);
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}
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unsigned getReactionNumAtoms(const ChemicalReaction &rxn, bool onlyHeavy, bool includeAgents)
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{
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if(includeAgents){
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return (getReactantTemplatesNumAtoms(rxn, onlyHeavy) +
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getProductTemplatesNumAtoms(rxn, onlyHeavy) +
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getAgentTemplatesNumAtoms(rxn, onlyHeavy));
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}
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return (getReactantTemplatesNumAtoms(rxn, onlyHeavy) +
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getProductTemplatesNumAtoms(rxn, onlyHeavy));
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}
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unsigned getReactantTemplatesNumBonds(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesNumBonds(rxn, Reactant, onlyHeavy);
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}
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unsigned getProductTemplatesNumBonds(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesNumBonds(rxn, Product, onlyHeavy);
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}
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unsigned getAgentTemplatesNumBonds(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesNumBonds(rxn, Agent, onlyHeavy);
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}
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unsigned getReactionNumBonds(const ChemicalReaction &rxn, bool onlyHeavy, bool includeAgents)
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{
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if(includeAgents){
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return (getReactantTemplatesNumBonds(rxn, onlyHeavy) +
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getProductTemplatesNumBonds(rxn, onlyHeavy) +
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getAgentTemplatesNumBonds(rxn, onlyHeavy));
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}
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return (getReactantTemplatesNumBonds(rxn, onlyHeavy) +
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getProductTemplatesNumBonds(rxn, onlyHeavy));
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}
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double calcReactantTemplatesMW(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesMW(rxn, Reactant, onlyHeavy);
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}
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double calcProductTemplatesMW(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesMW(rxn, Product, onlyHeavy);
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}
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double calcAgentTemplatesMW(const ChemicalReaction &rxn, bool onlyHeavy)
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{
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return getReactionMoleculeTemplatesMW(rxn, Agent, onlyHeavy);
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}
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double calcReactionMW(const ChemicalReaction &rxn, bool onlyHeavy, bool includeAgents)
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{
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if(includeAgents){
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return(calcReactantTemplatesMW(rxn, onlyHeavy) +
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calcProductTemplatesMW(rxn, onlyHeavy) +
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calcAgentTemplatesMW(rxn, onlyHeavy));
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}
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return(calcReactantTemplatesMW(rxn, onlyHeavy) +
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calcProductTemplatesMW(rxn, onlyHeavy));
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}
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unsigned getReactantTemplatesNumRings(const ChemicalReaction &rxn)
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{
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return getReactionMoleculeTemplatesNumRings(rxn, Reactant);
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}
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unsigned getProductTemplatesNumRings(const ChemicalReaction &rxn)
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{
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return getReactionMoleculeTemplatesNumRings(rxn, Product);
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}
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unsigned getAgentTemplatesNumRings(const ChemicalReaction &rxn)
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{
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return getReactionMoleculeTemplatesNumRings(rxn, Agent);
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}
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unsigned getReactionNumRings(const ChemicalReaction &rxn, bool includeAgents)
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{
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if(includeAgents){
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return(getReactantTemplatesNumRings(rxn) +
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getProductTemplatesNumRings(rxn) +
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getAgentTemplatesNumRings(rxn));
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}
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return(getReactantTemplatesNumRings(rxn) +
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getProductTemplatesNumRings(rxn));
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}
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bool hasReactantTemplateSubstructMatch(
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const ChemicalReaction &rxn,
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const ChemicalReaction &query_rxn)
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{
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if(rxn.getNumReactantTemplates() < query_rxn.getNumReactantTemplates()){
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return false;
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}
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if(query_rxn.getNumReactantTemplates() == 0){
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return true;
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}
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return hasReactionMoleculeTemplateSubstructMatch(rxn, query_rxn, Reactant);
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}
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bool hasProductTemplateSubstructMatch(
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const ChemicalReaction &rxn,
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const ChemicalReaction &query_rxn)
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{
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if(rxn.getNumProductTemplates() < query_rxn.getNumProductTemplates()){
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return false;
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}
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if(query_rxn.getNumProductTemplates() == 0){
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return true;
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}
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return hasReactionMoleculeTemplateSubstructMatch(rxn, query_rxn, Product);
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}
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bool hasAgentTemplateSubstructMatch(
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const ChemicalReaction &rxn,
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const ChemicalReaction &query_rxn)
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{
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if(rxn.getNumAgentTemplates() < query_rxn.getNumAgentTemplates()){
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return false;
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}
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if(query_rxn.getNumAgentTemplates() == 0){
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return true;
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}
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return hasReactionMoleculeTemplateSubstructMatch(rxn, query_rxn, Agent);
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}
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bool hasReactionSubstructMatch(
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const ChemicalReaction &rxn,
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const ChemicalReaction &query_rxn, bool includeAgents)
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{
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if(includeAgents){
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return (hasReactantTemplateSubstructMatch(rxn, query_rxn) &&
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hasProductTemplateSubstructMatch(rxn, query_rxn) &&
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hasAgentTemplateSubstructMatch(rxn, query_rxn));
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}
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return (hasReactantTemplateSubstructMatch(rxn, query_rxn) &&
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hasProductTemplateSubstructMatch(rxn, query_rxn));
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}
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bool hasReactionAtomMapping(const ChemicalReaction &rxn)
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{
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RDKit::MOL_SPTR_VECT::const_iterator begin = getStartIterator(rxn, Reactant);
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RDKit::MOL_SPTR_VECT::const_iterator end = getEndIterator(rxn, Reactant);
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for(; begin != end; ++begin){
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const ROMol &reactant = *begin->get();
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if(MolOps::getNumAtomsWithDistinctProperty(reactant, "molAtomMapNumber")){
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return true;
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}
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}
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begin = getStartIterator(rxn, Product);
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end = getEndIterator(rxn, Product);
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for(; begin != end; ++begin){
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const ROMol &reactant = *begin->get();
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if(MolOps::getNumAtomsWithDistinctProperty(reactant, "molAtomMapNumber")){
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return true;
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}
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}
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return false;
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}
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bool isReactionTemplateMoleculeAgent(const ROMol &mol, double agentThreshold)
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{
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unsigned numMappedAtoms = MolOps::getNumAtomsWithDistinctProperty(mol, "molAtomMapNumber");
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unsigned numAtoms = mol.getNumHeavyAtoms();
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if(numAtoms > 0 &&
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static_cast<double>(numMappedAtoms)/static_cast<double>(numAtoms) >= agentThreshold){
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return false;
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}
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return true;
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}
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} // end of RDKit namespace
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