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rdkit/Code/GraphMol/Descriptors/Crippen.cpp

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// $Id$
//
// Copyright (C) 2004-2012 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/Invariant.h>
#include <GraphMol/GraphMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include "MolDescriptors.h"
#include "Crippen.h"
#include <iostream>
#include <sstream>
#include <RDGeneral/StreamOps.h>
#include <boost/lexical_cast.hpp>
#include <boost/dynamic_bitset.hpp>
#include <boost/tokenizer.hpp>
typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
#include <boost/flyweight.hpp>
#include <boost/flyweight/key_value.hpp>
#include <boost/flyweight/no_tracking.hpp>
namespace RDKit{
namespace Descriptors {
extern const std::string defaultParamData;
void getCrippenAtomContribs(const ROMol &mol,
std::vector< double > &logpContribs,
std::vector< double > &mrContribs,
bool force,
std::vector<unsigned int> *atomTypes,
std::vector<std::string> *atomTypeLabels
){
PRECONDITION(logpContribs.size()==mol.getNumAtoms() &&
mrContribs.size()==mol.getNumAtoms(),
"bad result vector size");
PRECONDITION((!atomTypes || atomTypes->size()==mol.getNumAtoms()),
"bad atomTypes vector");
PRECONDITION((!atomTypeLabels || atomTypeLabels->size()==mol.getNumAtoms()),
"bad atomTypeLabels vector");
if(!force && mol.hasProp("_crippenLogPContribs")){
std::vector<double> tmpVect1,tmpVect2;
mol.getProp("_crippenLogPContribs",tmpVect1);
mol.getProp("_crippenMRContribs",tmpVect2);
if(tmpVect1.size()==mol.getNumAtoms() &&
tmpVect2.size()==mol.getNumAtoms() ){
logpContribs=tmpVect1;
mrContribs=tmpVect2;
return;
}
}
boost::dynamic_bitset<> atomNeeded(mol.getNumAtoms());
atomNeeded.set();
const CrippenParamCollection *params=CrippenParamCollection::getParams();
for(CrippenParamCollection::ParamsVect::const_iterator it=params->begin();
it!=params->end(); ++it){
std::vector<MatchVectType> matches;
SubstructMatch(mol,*(it->dp_pattern.get()),matches,
false,true);
for(std::vector<MatchVectType>::const_iterator matchIt=matches.begin();
matchIt!=matches.end();++matchIt){
int idx=(*matchIt)[0].second;
if(atomNeeded[idx]){
atomNeeded[idx]=0;
logpContribs[idx] = it->logp;
mrContribs[idx] = it->mr;
if(atomTypes) (*atomTypes)[idx]=it->idx;
if(atomTypeLabels) (*atomTypeLabels)[idx]=it->label;
}
}
// no need to keep matching stuff if we already found all the atoms:
if(atomNeeded.none()) break;
}
mol.setProp("_crippenLogPContribs",logpContribs,true);
mol.setProp("_crippenMRContribs",mrContribs,true);
}
void calcCrippenDescriptors(const ROMol &mol,double &logp,double &mr,bool includeHs,
bool force){
if(!force && mol.hasProp("_crippenLogP")){
mol.getProp("_crippenLogP",logp);
mol.getProp("_crippenMR",mr);
return;
}
// this isn't as bad as it looks, we aren't actually going
// to harm the molecule in any way!
ROMol *workMol=const_cast<ROMol *>(&mol);
if(includeHs){
workMol = MolOps::addHs(mol,false,false);
}
std::vector<double> logpContribs(workMol->getNumAtoms());
std::vector<double> mrContribs(workMol->getNumAtoms());
getCrippenAtomContribs(*workMol,logpContribs,mrContribs,force);
logp=0.0;
for(std::vector<double>::const_iterator iter=logpContribs.begin();
iter!=logpContribs.end();++iter){
logp+= *iter;
}
mr=0.0;
for(std::vector<double>::const_iterator iter=mrContribs.begin();
iter!=mrContribs.end();++iter){
mr+= *iter;
}
if(includeHs){
delete workMol;
}
mol.setProp("_crippenLogP",logp,true);
mol.setProp("_crippenMR",mr,true);
};
typedef boost::flyweight<boost::flyweights::key_value<std::string,CrippenParamCollection>,
boost::flyweights::no_tracking > param_flyweight;
const CrippenParamCollection *CrippenParamCollection::getParams(const std::string &paramData){
const CrippenParamCollection *res = &(param_flyweight(paramData).get());
return res;
}
CrippenParamCollection::CrippenParamCollection(const std::string &paramData){
std::string params;
boost::char_separator<char> tabSep("\t","",boost::keep_empty_tokens);
if(paramData=="") params=defaultParamData;
else params=paramData;
std::istringstream inStream(params);
std::string inLine=RDKit::getLine(inStream);
unsigned int idx=0;
while(!inStream.eof()){
if(inLine[0] != '#'){
CrippenParams paramObj;
paramObj.idx=idx++;
tokenizer tokens(inLine,tabSep);
tokenizer::iterator token=tokens.begin();
paramObj.label=*token;
++token;
paramObj.smarts=*token;
++token;
if(*token!=""){
paramObj.logp=boost::lexical_cast<double>(*token);
} else {
paramObj.logp=0.0;
}
++token;
if(*token!=""){
try{
paramObj.mr=boost::lexical_cast<double>(*token);
} catch (boost::bad_lexical_cast){
paramObj.mr=0.0;
}
} else {
paramObj.mr=0.0;
}
paramObj.dp_pattern=boost::shared_ptr<const ROMol>(SmartsToMol(paramObj.smarts));
d_params.push_back(paramObj);
}
inLine = RDKit::getLine(inStream);
}
}
CrippenParams::~CrippenParams() {
dp_pattern.reset();
}
const std::string defaultParamData=
"#ID SMARTS logP MR Notes/Questions\n"
"C1 [CH4] 0.1441 2.503 \n"
"C1 [CH3]C 0.1441 2.503 \n"
"C1 [CH2](C)C 0.1441 2.503 \n"
"C2 [CH](C)(C)C 0 2.433 \n"
"C2 [C](C)(C)(C)C 0 2.433 \n"
"C3 [CH3][N,O,P,S,F,Cl,Br,I] -0.2035 2.753 \n"
"C3 [CH2X4]([N,O,P,S,F,Cl,Br,I])[A;!#1] -0.2035 2.753 \n"
"C4 [CH1X4]([N,O,P,S,F,Cl,Br,I])([A;!#1])[A;!#1] -0.2051 2.731 \n"
"C4 [CH0X4]([N,O,P,S,F,Cl,Br,I])([A;!#1])([A;!#1])[A;!#1] -0.2051 2.731 \n"
"C5 [C]=[!C;A;!#1] -0.2783 5.007 \n"
"C6 [CH2]=C 0.1551 3.513 \n"
"C6 [CH1](=C)[A;!#1] 0.1551 3.513 \n"
"C6 [CH0](=C)([A;!#1])[A;!#1] 0.1551 3.513 \n"
"C6 [C](=C)=C 0.1551 3.513 \n"
"C7 [CX2]#[A;!#1] 0.0017 3.888 \n"
"C8 [CH3]c 0.08452 2.464 \n"
"C9 [CH3]a -0.1444 2.412 \n"
"C10 [CH2X4]a -0.0516 2.488 \n"
"C11 [CHX4]a 0.1193 2.582 \n"
"C12 [CH0X4]a -0.0967 2.576 \n"
"C13 [cH0]-[A;!C;!N;!O;!S;!F;!Cl;!Br;!I;!#1] -0.5443 4.041 \n"
"C14 [c][#9] 0 3.257 \n"
"C15 [c][#17] 0.245 3.564 \n"
"C16 [c][#35] 0.198 3.18 \n"
"C17 [c][#53] 0 3.104 \n"
"C18 [cH] 0.1581 3.35 \n"
"C19 [c](:a)(:a):a 0.2955 4.346 \n"
"C20 [c](:a)(:a)-a 0.2713 3.904 \n"
"C21 [c](:a)(:a)-C 0.136 3.509 \n"
"C22 [c](:a)(:a)-N 0.4619 4.067 \n"
"C23 [c](:a)(:a)-O 0.5437 3.853 \n"
"C24 [c](:a)(:a)-S 0.1893 2.673 \n"
"C25 [c](:a)(:a)=[C,N,O] -0.8186 3.135 \n"
"C26 [C](=C)(a)[A;!#1] 0.264 4.305 \n"
"C26 [C](=C)(c)a 0.264 4.305 \n"
"C26 [CH1](=C)a 0.264 4.305 \n"
"C26 [C]=c 0.264 4.305 \n"
"C27 [CX4][A;!C;!N;!O;!P;!S;!F;!Cl;!Br;!I;!#1] 0.2148 2.693 \n"
"CS [#6] 0.08129 3.243 \n"
"H1 [#1][#6,#1] 0.123 1.057 \n"
"H2 [#1]O[CX4,c] -0.2677 1.395 \n"
"H2 [#1]O[!C;!N;!O;!S] -0.2677 1.395 \n"
"H2 [#1][!C;!N;!O] -0.2677 1.395 \n"
"H3 [#1][#7] 0.2142 0.9627 \n"
"H3 [#1]O[#7] 0.2142 0.9627 \n"
"H4 [#1]OC=[#6,#7,O,S] 0.298 1.805 \n"
"H4 [#1]O[O,S] 0.298 1.805 \n"
"HS [#1] 0.1125 1.112 \n"
"N1 [NH2+0][A;!#1] -1.019 2.262 \n"
"N2 [NH+0]([A;!#1])[A;!#1] -0.7096 2.173 \n"
"N3 [NH2+0]a -1.027 2.827 \n"
"N4 [NH1+0]([!#1;A,a])a -0.5188 3 \n"
"N5 [NH+0]=[!#1;A,a] 0.08387 1.757 \n"
"N6 [N+0](=[!#1;A,a])[!#1;A,a] 0.1836 2.428 \n"
"N7 [N+0]([A;!#1])([A;!#1])[A;!#1] -0.3187 1.839 \n"
"N8 [N+0](a)([!#1;A,a])[A;!#1] -0.4458 2.819 \n"
"N8 [N+0](a)(a)a -0.4458 2.819 \n"
"N9 [N+0]#[A;!#1] 0.01508 1.725 \n"
"N10 [NH3,NH2,NH;+,+2,+3] -1.95 \n"
"N11 [n+0] -0.3239 2.202 \n"
"N12 [n;+,+2,+3] -1.119 \n"
"N13 [NH0;+,+2,+3]([A;!#1])([A;!#1])([A;!#1])[A;!#1] -0.3396 0.2604 \n"
"N13 [NH0;+,+2,+3](=[A;!#1])([A;!#1])[!#1;A,a] -0.3396 0.2604 \n"
"N13 [NH0;+,+2,+3](=[#6])=[#7] -0.3396 0.2604 \n"
"N14 [N;+,+2,+3]#[A;!#1] 0.2887 3.359 \n"
"N14 [N;-,-2,-3] 0.2887 3.359 \n"
"N14 [N;+,+2,+3](=[N;-,-2,-3])=N 0.2887 3.359 \n"
"NS [#7] -0.4806 2.134 \n"
"O1 [o] 0.1552 1.08 \n"
"O2 [OH,OH2] -0.2893 0.8238 \n"
"O3 [O]([A;!#1])[A;!#1] -0.0684 1.085 \n"
"O4 [O](a)[!#1;A,a] -0.4195 1.182 \n"
"O5 [O]=[#7,#8] 0.0335 3.367 \n"
"O5 [OX1;-,-2,-3][#7] 0.0335 3.367 \n"
"O6 [OX1;-,-2,-2][#16] -0.3339 0.7774 \n"
"O6 [O;-0]=[#16;-0] -0.3339 0.7774 \n"
"O12 [O-]C(=O) -1.326 \"order flip here intentional\"\n"
"O7 [OX1;-,-2,-3][!#1;!N;!S] -1.189 0 \n"
"O8 [O]=c 0.1788 3.135 \n"
"O9 [O]=[CH]C -0.1526 0 \n"
"O9 [O]=C(C)([A;!#1]) -0.1526 0 \n"
"O9 [O]=[CH][N,O] -0.1526 0 \n"
"O9 [O]=[CH2] -0.1526 0 \n"
"O9 [O]=[CX2]=O -0.1526 0 \n"
"O10 [O]=[CH]c 0.1129 0.2215 \n"
"O10 [O]=C([C,c])[a;!#1] 0.1129 0.2215 \n"
"O10 [O]=C(c)[A;!#1] 0.1129 0.2215 \n"
"O11 [O]=C([!#1;!#6])[!#1;!#6] 0.4833 0.389 \n"
"OS [#8] -0.1188 0.6865 \n"
"F [#9-0] 0.4202 1.108 \n"
"Cl [#17-0] 0.6895 5.853 \n"
"Br [#35-0] 0.8456 8.927 \n"
"I [#53-0] 0.8857 14.02 \n"
"Hal [#9,#17,#35,#53;-] -2.996 \n"
"Hal [#53;+,+2,+3] -2.996 \n"
"Hal [+;#3,#11,#19,#37,#55] -2.996 \"Footnote h indicates these should be here?\"\n"
"P [#15] 0.8612 6.92 \n"
"S2 [S;-,-2,-3,-4,+1,+2,+3,+5,+6] -0.0024 7.365 \"Order flip here is intentional\"\n"
"S2 [S-0]=[N,O,P,S] -0.0024 7.365 \"Expanded definition of (pseudo-)ionic S\"\n"
"S1 [S;A] 0.6482 7.591 \"Order flip here is intentional\"\n"
"S3 [s;a] 0.6237 6.691 \n"
"Me1 [#3,#11,#19,#37,#55] -0.3808 5.754 \n"
"Me1 [#4,#12,#20,#38,#56] -0.3808 5.754 \n"
"Me1 [#5,#13,#31,#49,#81] -0.3808 5.754 \n"
"Me1 [#14,#32,#50,#82] -0.3808 5.754 \n"
"Me1 [#33,#51,#83] -0.3808 5.754 \n"
"Me1 [#34,#52,#84] -0.3808 5.754 \n"
"Me2 [#21,#22,#23,#24,#25,#26,#27,#28,#29,#30] -0.0025 \n"
"Me2 [#39,#40,#41,#42,#43,#44,#45,#46,#47,#48] -0.0025 \n"
"Me2 [#72,#73,#74,#75,#76,#77,#78,#79,#80] -0.0025 \n";
} // end of namespace Descriptors
}
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