mirror of
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%)
331 lines
12 KiB
C++
331 lines
12 KiB
C++
// $Id$
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//
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// Copyright (C) 2007-2011 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/RDKitBase.h>
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#include <GraphMol/Descriptors/MolDescriptors.h>
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#include <GraphMol/PartialCharges/GasteigerCharges.h>
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#include <vector>
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#include <algorithm>
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#ifndef M_PI
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#define M_PI 3.14159265358979323846
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#endif
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namespace RDKit{
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namespace Descriptors {
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double getLabuteAtomContribs(const ROMol &mol,
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std::vector<double> &Vi,
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double &hContrib,
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bool includeHs,
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bool force){
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TEST_ASSERT(Vi.size()==mol.getNumAtoms());
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if(!force && mol.hasProp(common_properties::_labuteAtomContribs)){
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mol.getProp(common_properties::_labuteAtomContribs,Vi);
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mol.getProp(common_properties::_labuteAtomHContrib,hContrib);
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double res;
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mol.getProp(common_properties::_labuteASA,res);
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return res;
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}
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unsigned int nAtoms=mol.getNumAtoms();
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std::vector<double> rads(nAtoms);
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for(unsigned int i=0;i<nAtoms;++i){
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rads[i]=PeriodicTable::getTable()->getRb0(mol.getAtomWithIdx(i)->getAtomicNum());
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Vi[i]=0.0;
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}
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for(ROMol::ConstBondIterator bondIt=mol.beginBonds();
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bondIt!=mol.endBonds();++bondIt){
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const double bondScaleFacts[4]={.1,0,.2,.3};
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double Ri=rads[(*bondIt)->getBeginAtomIdx()];
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double Rj=rads[(*bondIt)->getEndAtomIdx()];
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double bij=Ri+Rj;
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if(!(*bondIt)->getIsAromatic()){
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if((*bondIt)->getBondType()<4){
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bij -= bondScaleFacts[(*bondIt)->getBondType()];
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}
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} else {
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bij -= bondScaleFacts[0];
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}
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double dij=std::min(std::max(fabs(Ri-Rj),bij),Ri+Rj);
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Vi[(*bondIt)->getBeginAtomIdx()] += Rj*Rj-(Ri-dij)*(Ri-dij)/dij;
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Vi[(*bondIt)->getEndAtomIdx()] += Ri*Ri-(Rj-dij)*(Rj-dij)/dij;
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}
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hContrib=0.0;
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if(includeHs){
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double Rj=PeriodicTable::getTable()->getRb0(1);
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for(unsigned int i=0;i<nAtoms;++i){
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double Ri=rads[i];
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double bij=Ri+Rj;
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double dij=std::min(std::max(fabs(Ri-Rj),bij),Ri+Rj);
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Vi[i] += Rj*Rj-(Ri-dij)*(Ri-dij)/dij;
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hContrib += Ri*Ri-(Rj-dij)*(Rj-dij)/dij;
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}
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}
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double res=0.0;
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for(unsigned int i=0;i<nAtoms;++i){
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double Ri=rads[i];
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Vi[i] = M_PI*Ri*(4.*Ri-Vi[i]);
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res+=Vi[i];
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}
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if(includeHs){
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double Rj=PeriodicTable::getTable()->getRb0(1);
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hContrib = M_PI*Rj*(4.*Rj-hContrib);
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res+=hContrib;
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}
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mol.setProp(common_properties::_labuteAtomContribs,Vi,true);
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mol.setProp(common_properties::_labuteAtomHContrib,hContrib,true);
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mol.setProp(common_properties::_labuteASA,res,true);
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return res;
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}
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double calcLabuteASA(const ROMol &mol,bool includeHs,bool force){
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if(!force && mol.hasProp(common_properties::_labuteASA)){
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double res;
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mol.getProp(common_properties::_labuteASA,res);
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return res;
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}
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std::vector<double> contribs;
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contribs.resize(mol.getNumAtoms());
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double hContrib;
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double res;
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res=getLabuteAtomContribs(mol,contribs,hContrib,includeHs,force);
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return res;
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}
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double getTPSAAtomContribs(const ROMol &mol,
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std::vector<double> &Vi,
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bool force){
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TEST_ASSERT(Vi.size()>=mol.getNumAtoms());
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double res=0;
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if(!force && mol.hasProp(common_properties::_tpsaAtomContribs)){
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mol.getProp(common_properties::_tpsaAtomContribs,Vi);
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mol.getProp(common_properties::_tpsa,res);
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return res;
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}
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unsigned int nAtoms=mol.getNumAtoms();
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std::vector<int> nNbrs(nAtoms,0),nSing(nAtoms,0),nDoub(nAtoms,0),nTrip(nAtoms,0),nArom(nAtoms,0),nHs(nAtoms,0);
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for(ROMol::ConstBondIterator bIt=mol.beginBonds();bIt!=mol.endBonds();++bIt){
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const Bond *bnd=(*bIt);
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if(bnd->getBeginAtom()->getAtomicNum()==1){
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nNbrs[bnd->getEndAtomIdx()]-=1;
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nHs[bnd->getEndAtomIdx()]+=1;
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} else if(bnd->getEndAtom()->getAtomicNum()==1){
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nNbrs[bnd->getBeginAtomIdx()]-=1;
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nHs[bnd->getBeginAtomIdx()]+=1;
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} else if(bnd->getIsAromatic()){
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nArom[bnd->getBeginAtomIdx()]+=1;
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nArom[bnd->getEndAtomIdx()]+=1;
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} else {
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switch(bnd->getBondType()){
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case Bond::SINGLE:
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nSing[bnd->getBeginAtomIdx()]+=1;
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nSing[bnd->getEndAtomIdx()]+=1;
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break;
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case Bond::DOUBLE:
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nDoub[bnd->getBeginAtomIdx()]+=1;
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nDoub[bnd->getEndAtomIdx()]+=1;
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break;
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case Bond::TRIPLE:
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nTrip[bnd->getBeginAtomIdx()]+=1;
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nTrip[bnd->getEndAtomIdx()]+=1;
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break;
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default:
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break;
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}
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}
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}
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for(unsigned int i=0;i<nAtoms;++i){
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const Atom *atom=mol.getAtomWithIdx(i);
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int atNum=atom->getAtomicNum();
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if(atNum!=7 && atNum!=8) continue;
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nHs[i] += atom->getTotalNumHs();
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int chg=atom->getFormalCharge();
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bool in3Ring = mol.getRingInfo()->isAtomInRingOfSize(i,3);
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nNbrs[i]+=atom->getDegree();
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double tmp=-1;
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if(atNum==7){
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switch(nNbrs[i]){
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case 1:
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if(nHs[i]==0 && chg==0 && nTrip[i]==1) tmp=23.79;
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else if(nHs[i]==1 && chg==0 && nDoub[i]==1) tmp=23.85;
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else if(nHs[i]==2 && chg==0 && nSing[i]==1) tmp=26.02;
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else if(nHs[i]==2 && chg==1 && nDoub[i]==1) tmp=25.59;
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else if(nHs[i]==3 && chg==1 && nSing[i]==1) tmp=27.64;
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break;
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case 2:
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if(nHs[i]==0 && chg==0 && nSing[i]==1 && nDoub[i]==1) tmp=12.36;
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else if(nHs[i]==0 && chg==0 && nTrip[i]==1 && nDoub[i]==1) tmp=13.60;
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else if(nHs[i]==1 && chg==0 && nSing[i]==2 && in3Ring) tmp=21.94;
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else if(nHs[i]==1 && chg==0 && nSing[i]==2 && !in3Ring) tmp=12.03;
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else if(nHs[i]==0 && chg==1 && nTrip[i]==1 && nSing[i]==1) tmp=4.36;
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else if(nHs[i]==1 && chg==1 && nDoub[i]==1 && nSing[i]==1) tmp=13.97;
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else if(nHs[i]==2 && chg==1 && nSing[i]==2) tmp=16.61;
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else if(nHs[i]==0 && chg==0 && nArom[i]==2) tmp=12.89;
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else if(nHs[i]==1 && chg==0 && nArom[i]==2) tmp=15.79;
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else if(nHs[i]==1 && chg==1 && nArom[i]==2) tmp=14.14;
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break;
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case 3:
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if(nHs[i]==0 && chg==0 && nSing[i]==3 && in3Ring ) tmp=3.01;
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else if(nHs[i]==0 && chg==0 && nSing[i]==3 && !in3Ring ) tmp=3.24;
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else if(nHs[i]==0 && chg==0 && nSing[i]==1 && nDoub[i]==2 ) tmp=11.68;
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else if(nHs[i]==0 && chg==1 && nSing[i]==2 && nDoub[i]==1 ) tmp=3.01;
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else if(nHs[i]==1 && chg==1 && nSing[i]==3 ) tmp=4.44;
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else if(nHs[i]==0 && chg==0 && nArom[i]==3 ) tmp=4.41;
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else if(nHs[i]==0 && chg==0 && nSing[i]==1 && nArom[i]==2 ) tmp=4.93;
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else if(nHs[i]==0 && chg==0 && nDoub[i]==1 && nArom[i]==2 ) tmp=8.39;
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else if(nHs[i]==0 && chg==1 && nArom[i]==3 ) tmp=4.10;
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else if(nHs[i]==0 && chg==1 && nSing[i]==1 && nArom[i]==2 ) tmp=3.88;
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break;
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case 4:
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if(nHs[i]==0 && nSing[i]==4 && chg==1) tmp=0.0;
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break;
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}
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if(tmp < 0.0){
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tmp = 30.5 - nNbrs[i] * 8.2 + nHs[i] * 1.5;
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if(tmp<0) tmp=0.0;
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}
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} else if(atNum==8){
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switch(nNbrs[i]){
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case 1:
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if(nHs[i]==0 && chg==0 && nDoub[i]==1) tmp=17.07;
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else if(nHs[i]==1 && chg==0 && nSing[i]==1 ) tmp=20.23;
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else if(nHs[i]==0 && chg==-1 && nSing[i]==1 ) tmp=23.06;
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break;
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case 2:
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if(nHs[i]==0 && chg==0 && nSing[i]==2 && in3Ring) tmp=12.53;
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else if(nHs[i]==0 && chg==0 && nSing[i]==2 && !in3Ring) tmp=9.23;
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else if(nHs[i]==0 && chg==0 && nArom[i]==2) tmp=13.14;
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break;
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}
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if(tmp<0.0){
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tmp=28.5-nNbrs[i]*8.6+nHs[i]*1.5;
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if(tmp<0) tmp=0.0;
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}
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}
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Vi[i]=tmp;
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res+=tmp;
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}
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mol.setProp(common_properties::_tpsaAtomContribs,Vi,true);
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mol.setProp(common_properties::_tpsa,res,true);
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return res;
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}
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double calcTPSA(const ROMol &mol,bool force){
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if(!force && mol.hasProp(common_properties::_tpsa)){
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double res;
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mol.getProp(common_properties::_tpsa,res);
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return res;
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}
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std::vector<double> contribs;
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contribs.resize(mol.getNumAtoms());
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double res;
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res=getTPSAAtomContribs(mol,contribs,force);
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return res;
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}
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namespace {
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void assignContribsToBins(const std::vector<double> &contribs,
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const std::vector<double> &binProp,
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std::vector<double> &bins,
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std::vector<double> &res){
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PRECONDITION(contribs.size()==binProp.size(),"mismatched array sizes");
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PRECONDITION(res.size()>=bins.size()+1,"mismatched array sizes");
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for(unsigned int i=0;i<contribs.size();++i){
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double cVal = contribs[i];
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double bVal = binProp[i];
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unsigned int idx=std::upper_bound(bins.begin(),bins.end(),bVal)-bins.begin();
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res[idx]+=cVal;
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}
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}
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}
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std::vector<double> calcSlogP_VSA(const ROMol &mol,std::vector<double> *bins,
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bool force){
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// FIX: use force value to include caching
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std::vector<double> lbins;
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if(!bins){
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double blist[11]={-0.4,-0.2,0,0.1,0.15,0.2,0.25,0.3,0.4,0.5,0.6};
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lbins.resize(11);
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std::copy(blist,blist+11,lbins.begin());
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} else {
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lbins.resize(bins->size());
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std::copy(bins->begin(),bins->end(),lbins.begin());
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}
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std::vector<double> res(lbins.size()+1,0);
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std::vector<double> vsaContribs(mol.getNumAtoms());
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double tmp;
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getLabuteAtomContribs(mol,vsaContribs,tmp,true,force);
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std::vector<double> logpContribs(mol.getNumAtoms());
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std::vector<double> mrContribs(mol.getNumAtoms());
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getCrippenAtomContribs(mol,logpContribs,mrContribs,force);
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assignContribsToBins(vsaContribs,logpContribs,lbins,res);
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return res;
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}
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std::vector<double> calcSMR_VSA(const ROMol &mol,std::vector<double> *bins,
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bool force){
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std::vector<double> lbins;
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if(!bins){
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double blist[9]={1.29, 1.82, 2.24, 2.45, 2.75, 3.05, 3.63,3.8,4.0};
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lbins.resize(9);
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std::copy(blist,blist+9,lbins.begin());
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} else {
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lbins.resize(bins->size());
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std::copy(bins->begin(),bins->end(),lbins.begin());
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}
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std::vector<double> res(lbins.size()+1,0);
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std::vector<double> vsaContribs(mol.getNumAtoms());
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double tmp;
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getLabuteAtomContribs(mol,vsaContribs,tmp,true,force);
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std::vector<double> logpContribs(mol.getNumAtoms());
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std::vector<double> mrContribs(mol.getNumAtoms());
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getCrippenAtomContribs(mol,logpContribs,mrContribs,force);
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assignContribsToBins(vsaContribs,mrContribs,lbins,res);
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return res;
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}
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std::vector<double> calcPEOE_VSA(const ROMol &mol,std::vector<double> *bins,
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bool force){
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std::vector<double> lbins;
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if(!bins){
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double blist[13]={-.3,-.25,-.20,-.15,-.10,-.05,0,.05,.10,.15,.20,.25,.30};
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lbins.resize(13);
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std::copy(blist,blist+13,lbins.begin());
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} else {
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lbins.resize(bins->size());
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std::copy(bins->begin(),bins->end(),lbins.begin());
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}
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std::vector<double> res(lbins.size()+1,0);
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std::vector<double> vsaContribs(mol.getNumAtoms());
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double tmp;
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getLabuteAtomContribs(mol,vsaContribs,tmp,true,force);
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std::vector<double> chgs(mol.getNumAtoms(),0.0);
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computeGasteigerCharges(mol,chgs);
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assignContribsToBins(vsaContribs,chgs,lbins,res);
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return res;
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}
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} // end of namespace Descriptors
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} // end of namespace RDKit
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