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https://github.com/rdkit/rdkit.git
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91008ff11d
* Address compile warnings & trivial improvements * revert unwanted initializers; use RDUNUSED_PARAM for unused params * revert fix in testRDFcustom; marked with 'TO DO' comment
317 lines
11 KiB
C++
317 lines
11 KiB
C++
// $Id$
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//
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// Copyright (C) 2004-2012 Greg Landrum and Rational Discovery LLC
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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 <RDGeneral/Invariant.h>
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#include <GraphMol/GraphMol.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include "MolDescriptors.h"
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#include "Crippen.h"
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#include <iostream>
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#include <sstream>
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#include <RDGeneral/StreamOps.h>
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#include <boost/lexical_cast.hpp>
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#include <boost/dynamic_bitset.hpp>
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#include <boost/tokenizer.hpp>
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typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/flyweight.hpp>
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#include <boost/flyweight/key_value.hpp>
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#include <boost/flyweight/no_tracking.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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namespace RDKit {
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namespace Descriptors {
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extern const std::string defaultParamData;
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void getCrippenAtomContribs(const ROMol &mol, std::vector<double> &logpContribs,
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std::vector<double> &mrContribs, bool force,
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std::vector<unsigned int> *atomTypes,
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std::vector<std::string> *atomTypeLabels) {
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PRECONDITION(logpContribs.size() == mol.getNumAtoms() &&
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mrContribs.size() == mol.getNumAtoms(),
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"bad result vector size");
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PRECONDITION((!atomTypes || atomTypes->size() == mol.getNumAtoms()),
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"bad atomTypes vector");
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PRECONDITION((!atomTypeLabels || atomTypeLabels->size() == mol.getNumAtoms()),
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"bad atomTypeLabels vector");
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if (!force && mol.hasProp(common_properties::_crippenLogPContribs)) {
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std::vector<double> tmpVect1, tmpVect2;
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mol.getProp(common_properties::_crippenLogPContribs, tmpVect1);
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mol.getProp(common_properties::_crippenMRContribs, tmpVect2);
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if (tmpVect1.size() == mol.getNumAtoms() &&
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tmpVect2.size() == mol.getNumAtoms()) {
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logpContribs = tmpVect1;
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mrContribs = tmpVect2;
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return;
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}
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}
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boost::dynamic_bitset<> atomNeeded(mol.getNumAtoms());
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atomNeeded.set();
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const CrippenParamCollection *params = CrippenParamCollection::getParams();
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for (const auto ¶m : *params) {
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std::vector<MatchVectType> matches;
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SubstructMatch(mol, *(param.dp_pattern.get()), matches, false, true);
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for (std::vector<MatchVectType>::const_iterator matchIt = matches.begin();
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matchIt != matches.end(); ++matchIt) {
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int idx = (*matchIt)[0].second;
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if (atomNeeded[idx]) {
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atomNeeded[idx] = 0;
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logpContribs[idx] = param.logp;
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mrContribs[idx] = param.mr;
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if (atomTypes) (*atomTypes)[idx] = param.idx;
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if (atomTypeLabels) (*atomTypeLabels)[idx] = param.label;
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}
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}
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// no need to keep matching stuff if we already found all the atoms:
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if (atomNeeded.none()) break;
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}
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mol.setProp(common_properties::_crippenLogPContribs, logpContribs, true);
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mol.setProp(common_properties::_crippenMRContribs, mrContribs, true);
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}
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void calcCrippenDescriptors(const ROMol &mol, double &logp, double &mr,
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bool includeHs, bool force) {
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if (!force && mol.hasProp(common_properties::_crippenLogP)) {
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mol.getProp(common_properties::_crippenLogP, logp);
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mol.getProp(common_properties::_crippenMR, mr);
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return;
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}
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// this isn't as bad as it looks, we aren't actually going
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// to harm the molecule in any way!
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ROMol *workMol = const_cast<ROMol *>(&mol);
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if (includeHs) {
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workMol = MolOps::addHs(mol, false, false);
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}
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std::vector<double> logpContribs(workMol->getNumAtoms());
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std::vector<double> mrContribs(workMol->getNumAtoms());
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getCrippenAtomContribs(*workMol, logpContribs, mrContribs, force);
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logp = 0.0;
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for (std::vector<double>::const_iterator iter = logpContribs.begin();
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iter != logpContribs.end(); ++iter) {
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logp += *iter;
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}
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mr = 0.0;
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for (std::vector<double>::const_iterator iter = mrContribs.begin();
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iter != mrContribs.end(); ++iter) {
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mr += *iter;
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}
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if (includeHs) {
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delete workMol;
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}
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mol.setProp(common_properties::_crippenLogP, logp, true);
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mol.setProp(common_properties::_crippenMR, mr, true);
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};
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double calcClogP(const ROMol &mol) {
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double clogp,mr;
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calcCrippenDescriptors(mol, clogp, mr);
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return clogp;
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}
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double calcMR(const ROMol &mol) {
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double clogp,mr;
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calcCrippenDescriptors(mol, clogp, mr);
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return mr;
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}
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typedef boost::flyweight<
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boost::flyweights::key_value<std::string, CrippenParamCollection>,
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boost::flyweights::no_tracking> param_flyweight;
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const CrippenParamCollection *CrippenParamCollection::getParams(
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const std::string ¶mData) {
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const CrippenParamCollection *res = &(param_flyweight(paramData).get());
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return res;
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}
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CrippenParamCollection::CrippenParamCollection(const std::string ¶mData) {
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std::string params;
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boost::char_separator<char> tabSep("\t", "", boost::keep_empty_tokens);
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if (paramData == "")
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params = defaultParamData;
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else
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params = paramData;
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std::istringstream inStream(params);
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std::string inLine = RDKit::getLine(inStream);
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unsigned int idx = 0;
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while (!inStream.eof()) {
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if (inLine[0] != '#') {
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CrippenParams paramObj;
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paramObj.idx = idx++;
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tokenizer tokens(inLine, tabSep);
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tokenizer::iterator token = tokens.begin();
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paramObj.label = *token;
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++token;
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paramObj.smarts = *token;
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++token;
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if (*token != "") {
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paramObj.logp = boost::lexical_cast<double>(*token);
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} else {
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paramObj.logp = 0.0;
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}
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++token;
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if (*token != "") {
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try {
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paramObj.mr = boost::lexical_cast<double>(*token);
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} catch (boost::bad_lexical_cast &) {
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paramObj.mr = 0.0;
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}
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} else {
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paramObj.mr = 0.0;
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}
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paramObj.dp_pattern =
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boost::shared_ptr<const ROMol>(SmartsToMol(paramObj.smarts));
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d_params.push_back(paramObj);
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}
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inLine = RDKit::getLine(inStream);
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}
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}
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CrippenParams::~CrippenParams() { dp_pattern.reset(); }
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const std::string defaultParamData =
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"#ID SMARTS logP MR Notes/Questions\n"
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"C1 [CH4] 0.1441 2.503 \n"
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"C1 [CH3]C 0.1441 2.503 \n"
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"C1 [CH2](C)C 0.1441 2.503 \n"
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"C2 [CH](C)(C)C 0 2.433 \n"
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"C2 [C](C)(C)(C)C 0 2.433 \n"
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"C3 [CH3][N,O,P,S,F,Cl,Br,I] -0.2035 2.753 \n"
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"C3 [CH2X4]([N,O,P,S,F,Cl,Br,I])[A;!#1] -0.2035 2.753 \n"
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"C4 [CH1X4]([N,O,P,S,F,Cl,Br,I])([A;!#1])[A;!#1] -0.2051 2.731 \n"
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"C4 [CH0X4]([N,O,P,S,F,Cl,Br,I])([A;!#1])([A;!#1])[A;!#1] -0.2051 "
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"2.731 \n"
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"C5 [C]=[!C;A;!#1] -0.2783 5.007 \n"
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"C6 [CH2]=C 0.1551 3.513 \n"
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"C6 [CH1](=C)[A;!#1] 0.1551 3.513 \n"
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"C6 [CH0](=C)([A;!#1])[A;!#1] 0.1551 3.513 \n"
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"C6 [C](=C)=C 0.1551 3.513 \n"
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"C7 [CX2]#[A;!#1] 0.0017 3.888 \n"
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"C8 [CH3]c 0.08452 2.464 \n"
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"C9 [CH3]a -0.1444 2.412 \n"
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"C10 [CH2X4]a -0.0516 2.488 \n"
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"C11 [CHX4]a 0.1193 2.582 \n"
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"C12 [CH0X4]a -0.0967 2.576 \n"
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"C13 [cH0]-[A;!C;!N;!O;!S;!F;!Cl;!Br;!I;!#1] -0.5443 4.041 \n"
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"C14 [c][#9] 0 3.257 \n"
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"C15 [c][#17] 0.245 3.564 \n"
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"C16 [c][#35] 0.198 3.18 \n"
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"C17 [c][#53] 0 3.104 \n"
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"C18 [cH] 0.1581 3.35 \n"
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"C19 [c](:a)(:a):a 0.2955 4.346 \n"
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"C20 [c](:a)(:a)-a 0.2713 3.904 \n"
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"C21 [c](:a)(:a)-C 0.136 3.509 \n"
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"C22 [c](:a)(:a)-N 0.4619 4.067 \n"
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"C23 [c](:a)(:a)-O 0.5437 3.853 \n"
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"C24 [c](:a)(:a)-S 0.1893 2.673 \n"
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"C25 [c](:a)(:a)=[C,N,O] -0.8186 3.135 \n"
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"C26 [C](=C)(a)[A;!#1] 0.264 4.305 \n"
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"C26 [C](=C)(c)a 0.264 4.305 \n"
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"C26 [CH1](=C)a 0.264 4.305 \n"
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"C26 [C]=c 0.264 4.305 \n"
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"C27 [CX4][A;!C;!N;!O;!P;!S;!F;!Cl;!Br;!I;!#1] 0.2148 "
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"2.693 "
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"\n"
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"CS [#6] 0.08129 3.243 \n"
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"H1 [#1][#6,#1] 0.123 1.057 \n"
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"H2 [#1]O[CX4,c] -0.2677 1.395 \n"
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"H2 [#1]O[!#6;!#7;!#8;!#16] -0.2677 1.395 \n"
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"H2 [#1][!#6;!#7;!#8] -0.2677 1.395 \n"
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"H3 [#1][#7] 0.2142 0.9627 \n"
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"H3 [#1]O[#7] 0.2142 0.9627 \n"
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"H4 [#1]OC=[#6,#7,O,S] 0.298 1.805 \n"
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"H4 [#1]O[O,S] 0.298 1.805 \n"
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"HS [#1] 0.1125 1.112 \n"
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"N1 [NH2+0][A;!#1] -1.019 2.262 \n"
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"N2 [NH+0]([A;!#1])[A;!#1] -0.7096 2.173 \n"
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"N3 [NH2+0]a -1.027 2.827 \n"
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"N4 [NH1+0]([!#1;A,a])a -0.5188 3 \n"
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"N5 [NH+0]=[!#1;A,a] 0.08387 1.757 \n"
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"N6 [N+0](=[!#1;A,a])[!#1;A,a] 0.1836 2.428 \n"
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"N7 [N+0]([A;!#1])([A;!#1])[A;!#1] -0.3187 1.839 \n"
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"N8 [N+0](a)([!#1;A,a])[A;!#1] -0.4458 2.819 \n"
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"N8 [N+0](a)(a)a -0.4458 2.819 \n"
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"N9 [N+0]#[A;!#1] 0.01508 1.725 \n"
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"N10 [NH3,NH2,NH;+,+2,+3] -1.95 \n"
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"N11 [n+0] -0.3239 2.202 \n"
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"N12 [n;+,+2,+3] -1.119 \n"
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"N13 [NH0;+,+2,+3]([A;!#1])([A;!#1])([A;!#1])[A;!#1] -0.3396 "
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"0.2604 "
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"\n"
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"N13 [NH0;+,+2,+3](=[A;!#1])([A;!#1])[!#1;A,a] -0.3396 "
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"0.2604 "
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"\n"
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"N13 [NH0;+,+2,+3](=[#6])=[#7] -0.3396 0.2604 \n"
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"N14 [N;+,+2,+3]#[A;!#1] 0.2887 3.359 \n"
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"N14 [N;-,-2,-3] 0.2887 3.359 \n"
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"N14 [N;+,+2,+3](=[N;-,-2,-3])=N 0.2887 3.359 \n"
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"NS [#7] -0.4806 2.134 \n"
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"O1 [o] 0.1552 1.08 \n"
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"O2 [OH,OH2] -0.2893 0.8238 \n"
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"O3 [O]([A;!#1])[A;!#1] -0.0684 1.085 \n"
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"O4 [O](a)[!#1;A,a] -0.4195 1.182 \n"
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"O5 [O]=[#7,#8] 0.0335 3.367 \n"
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"O5 [OX1;-,-2,-3][#7] 0.0335 3.367 \n"
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"O6 [OX1;-,-2,-2][#16] -0.3339 0.7774 \n"
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"O6 [O;-0]=[#16;-0] -0.3339 0.7774 \n"
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"O12 [O-]C(=O) -1.326 \"order flip here "
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"intentional\"\n"
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"O7 [OX1;-,-2,-3][!#1;!N;!S] -1.189 0 \n"
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"O8 [O]=c 0.1788 3.135 \n"
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"O9 [O]=[CH]C -0.1526 0 \n"
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"O9 [O]=C(C)([A;!#1]) -0.1526 0 \n"
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"O9 [O]=[CH][N,O] -0.1526 0 \n"
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"O9 [O]=[CH2] -0.1526 0 \n"
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"O9 [O]=[CX2]=O -0.1526 0 \n"
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"O10 [O]=[CH]c 0.1129 0.2215 \n"
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"O10 [O]=C([C,c])[a;!#1] 0.1129 0.2215 \n"
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"O10 [O]=C(c)[A;!#1] 0.1129 0.2215 \n"
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"O11 [O]=C([!#1;!#6])[!#1;!#6] 0.4833 0.389 \n"
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"OS [#8] -0.1188 0.6865 \n"
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"F [#9-0] 0.4202 1.108 \n"
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"Cl [#17-0] 0.6895 5.853 \n"
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"Br [#35-0] 0.8456 8.927 \n"
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"I [#53-0] 0.8857 14.02 \n"
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"Hal [#9,#17,#35,#53;-] -2.996 \n"
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"Hal [#53;+,+2,+3] -2.996 \n"
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"Hal [+;#3,#11,#19,#37,#55] -2.996 \"Footnote h indicates "
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"these should be here?\"\n"
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"P [#15] 0.8612 6.92 \n"
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"S2 [S;-,-2,-3,-4,+1,+2,+3,+5,+6] -0.0024 7.365 \"Order flip "
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"here is intentional\"\n"
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"S2 [S-0]=[N,O,P,S] -0.0024 7.365 \"Expanded definition of "
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"(pseudo-)ionic S\"\n"
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"S1 [S;A] 0.6482 7.591 \"Order flip here is intentional\"\n"
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"S3 [s;a] 0.6237 6.691 \n"
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"Me1 [#3,#11,#19,#37,#55] -0.3808 5.754 \n"
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"Me1 [#4,#12,#20,#38,#56] -0.3808 5.754 \n"
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"Me1 [#5,#13,#31,#49,#81] -0.3808 5.754 \n"
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"Me1 [#14,#32,#50,#82] -0.3808 5.754 \n"
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"Me1 [#33,#51,#83] -0.3808 5.754 \n"
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"Me1 [#34,#52,#84] -0.3808 5.754 \n"
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"Me2 [#21,#22,#23,#24,#25,#26,#27,#28,#29,#30] -0.0025 "
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" "
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"\n"
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"Me2 [#39,#40,#41,#42,#43,#44,#45,#46,#47,#48] -0.0025 "
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" "
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"\n"
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"Me2 [#72,#73,#74,#75,#76,#77,#78,#79,#80] -0.0025 \n";
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} // end of namespace Descriptors
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}
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