mirror of
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a59997b7e4
* move _embedPoints over to use EmbedArgs structure * move _embedWithExpTorsions over * a few pointer cleanups * step by step * more * wrap the ETKDG paramaters into a struct * fix a typo * additional cleanup * more * simplify the embedargs struct * pass embedParams instead of having them in embedargs * a bit more cleanup * response to code review
307 lines
10 KiB
C++
307 lines
10 KiB
C++
//
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// Copyright (C) 2017 Sereina Riniker
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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 "TorsionPreferences.h"
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#include <GraphMol/RDKitBase.h>
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#include <Geometry/Utils.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <RDGeneral/utils.h>
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#include <RDGeneral/RDLog.h>
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#include <RDGeneral/Exceptions.h>
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#include <boost/dynamic_bitset.hpp>
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#include <algorithm>
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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/tokenizer.hpp>
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typedef boost::tokenizer<boost::char_separator<char>> tokenizer;
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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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namespace ForceFields {
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namespace CrystalFF {
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using namespace RDKit;
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/* SMARTS patterns for experimental torsion angle preferences
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* Version 1 taken from J. Med. Chem. 56, 1026-2028 (2013)
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* Version 2 taken from J. Chem. Inf. Model. 56, 1 (2016)
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*
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* torsion-angle potential form:
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* V = V1*(1 + s1*cos(1x)) + V2*(1 + s2*cos(2x)) + V3*(1 + s3*cos(1x))
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* + V4*(1 + s4*cos(1x)) + V5*(1 + s5*cos(1x)) + V6*(1 + s6*cos(1x))
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*
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* format: [SMARTS, s1, V1, s2, V2, s3, V3, s4, V4, s5, V5, s6, V6]
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*/
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#include "torsionPreferences_v1.in"
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#include "torsionPreferences_v2.in"
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//! A structure used to the experimental torsion patterns
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struct ExpTorsionAngle {
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std::string smarts;
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std::vector<double> V;
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std::vector<int> signs;
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boost::shared_ptr<const ROMol> dp_pattern;
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unsigned int idx[4];
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};
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// class to store the experimental torsion angles
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class ExpTorsionAngleCollection {
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public:
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typedef std::vector<ExpTorsionAngle> ParamsVect;
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static const ExpTorsionAngleCollection *getParams(
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unsigned int version, const std::string ¶mData = "");
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ParamsVect::const_iterator begin() const { return d_params.begin(); };
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ParamsVect::const_iterator end() const { return d_params.end(); };
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ExpTorsionAngleCollection(const std::string ¶mData);
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private:
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ParamsVect d_params; //!< the parameters
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};
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typedef boost::flyweight<
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boost::flyweights::key_value<std::string, ExpTorsionAngleCollection>,
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boost::flyweights::no_tracking>
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param_flyweight;
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const ExpTorsionAngleCollection *ExpTorsionAngleCollection::getParams(
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unsigned int version, const std::string ¶mData) {
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std::string params;
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if (paramData == "") {
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switch (version) {
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case 1:
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params = torsionPreferencesV1;
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break;
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case 2:
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params = torsionPreferencesV2;
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break;
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default:
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throw ValueErrorException("ETversion must be 1 or 2.");
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}
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} else {
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params = paramData;
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}
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const ExpTorsionAngleCollection *res = &(param_flyweight(params).get());
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return res;
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}
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ExpTorsionAngleCollection::ExpTorsionAngleCollection(
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const std::string ¶mData) {
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boost::char_separator<char> tabSep(" ", "", boost::drop_empty_tokens);
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std::istringstream inStream(paramData);
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std::string inLine = RDKit::getLine(inStream);
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while (!inStream.eof()) {
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if (inLine[0] != '#') {
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ExpTorsionAngle angle;
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tokenizer tokens(inLine, tabSep);
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tokenizer::iterator token = tokens.begin();
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angle.smarts = *token;
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++token;
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for (unsigned int i = 0; i < 12; i += 2) {
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angle.signs.push_back(boost::lexical_cast<int>(*token));
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++token;
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angle.V.push_back(boost::lexical_cast<double>(*token));
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++token;
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}
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angle.dp_pattern =
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boost::shared_ptr<const ROMol>(SmartsToMol(angle.smarts));
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// get the atom indices for atom 1, 2, 3, 4 in the pattern
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for (unsigned int i = 0; i < (angle.dp_pattern.get())->getNumAtoms();
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++i) {
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Atom const *atom = (angle.dp_pattern.get())->getAtomWithIdx(i);
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int num;
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if (atom->getPropIfPresent("molAtomMapNumber", num)) {
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if (num > 0 && num < 5) {
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angle.idx[num - 1] = i;
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}
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}
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}
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d_params.push_back(angle);
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}
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inLine = RDKit::getLine(inStream);
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} // while loop
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// std::cerr << "Exp. torsion angles = " << d_params.size() << " "
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// << d_params[d_params.size()-1].smarts << std::endl;
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}
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void getExperimentalTorsions(const RDKit::ROMol &mol, CrystalFFDetails &details,
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bool useExpTorsions, bool useBasicKnowledge,
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unsigned int version, bool verbose) {
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unsigned int nb = mol.getNumBonds();
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unsigned int na = mol.getNumAtoms();
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if (!na) {
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throw ValueErrorException("molecule has no atoms");
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}
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// check that vectors are empty
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details.expTorsionAtoms.clear();
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details.expTorsionAngles.clear();
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details.improperAtoms.clear();
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unsigned int aid1, aid2, aid3, aid4;
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unsigned int bid2;
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boost::dynamic_bitset<> doneBonds(nb);
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if (useExpTorsions) {
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// we set the torsion angles with experimental data
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const ExpTorsionAngleCollection *params =
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ExpTorsionAngleCollection::getParams(version);
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// loop over patterns
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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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// loop over matches
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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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// get bond indices
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aid1 = (*matchIt)[param.idx[0]].second;
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aid2 = (*matchIt)[param.idx[1]].second;
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aid3 = (*matchIt)[param.idx[2]].second;
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aid4 = (*matchIt)[param.idx[3]].second;
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// FIX: check if bond is NULL
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bid2 = mol.getBondBetweenAtoms(aid2, aid3)->getIdx();
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if (!doneBonds[bid2]) {
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doneBonds[bid2] = 1;
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std::vector<int> atoms(4);
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atoms[0] = aid1;
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atoms[1] = aid2;
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atoms[2] = aid3;
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atoms[3] = aid4;
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details.expTorsionAtoms.push_back(atoms);
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details.expTorsionAngles.push_back(
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std::make_pair(param.signs, param.V));
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if (verbose) {
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std::cout << param.smarts << ": " << aid1 << " " << aid2 << " "
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<< aid3 << " " << aid4 << ", (";
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for (unsigned int i = 0; i < param.V.size() - 1; ++i) {
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std::cout << param.V[i] << ", ";
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}
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std::cout << param.V[param.V.size() - 1] << ") " << std::endl;
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}
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} // if not donePaths
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} // end loop over matches
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} // end loop over patterns
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}
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// apply basic knowledge such as flat aromatic rings, other sp2-centers,
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// straight triple bonds, etc.
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if (useBasicKnowledge) {
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boost::dynamic_bitset<> doneAtoms(na);
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ROMol::ADJ_ITER nbrIdx;
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ROMol::ADJ_ITER endNbrs;
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// inversion terms (improper torsions / out-of-plane bends / inversion)
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// loop over atoms
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for (aid2 = 0; aid2 < na; ++aid2) {
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if (!(doneAtoms[aid2])) {
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std::vector<int> atoms(4, -1);
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atoms[1] = aid2;
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const Atom *atom2 = mol.getAtomWithIdx(atoms[1]);
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int at2AtomicNum = atom2->getAtomicNum();
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// if atom is a N,O or C and SP2-hybridized
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if (((at2AtomicNum == 6) || (at2AtomicNum == 7) ||
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(at2AtomicNum == 8)) &&
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(atom2->getHybridization() == Atom::SP2)) {
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// get neighbors
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boost::tie(nbrIdx, endNbrs) = mol.getAtomNeighbors(atom2);
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// check if enough neighbours
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if (mol.getAtomDegree(atom2) != 3) {
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continue;
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}
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unsigned int i = 0;
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unsigned int isBoundToSP2O = 0; // false
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for (; nbrIdx != endNbrs; ++nbrIdx) {
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const Atom *atomX = mol[*nbrIdx];
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atoms[i] = atomX->getIdx();
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// if the central atom is sp2 carbon and is bound to sp2 oxygen, set
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// a flag
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if (!isBoundToSP2O) {
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isBoundToSP2O =
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((at2AtomicNum == 6) && (atomX->getAtomicNum() == 8) &&
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(atomX->getHybridization() == Atom::SP2));
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}
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if (!i) {
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++i;
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}
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++i;
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}
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atoms.push_back(at2AtomicNum);
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atoms.push_back(isBoundToSP2O);
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details.improperAtoms.push_back(atoms);
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/*if (verbose) {
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std::cout << "out-of-plane bend: " << atoms[0] << " " << atoms[1] <<
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" "
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<< atoms[2] << " " << atoms[3] << std::endl;
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}*/
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}
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} // if atom is a N,O or C and SP2-hybridized
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}
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// torsions for flat rings
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const RingInfo *rinfo =
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mol.getRingInfo(); // FIX: make sure we have ring info
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CHECK_INVARIANT(rinfo, "");
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const VECT_INT_VECT &atomRings = rinfo->atomRings();
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for (const auto &atomRing : atomRings) {
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unsigned int rSize = atomRing.size();
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// we don't need to deal with 3 membered rings
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// and we do not treat rings greater than 6
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if (rSize < 4 || rSize > 6) {
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continue;
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}
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// loop over ring atoms
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for (unsigned int i = 0; i < rSize; ++i) {
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// proper torsions
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aid1 = atomRing[i];
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aid2 = atomRing[(i + 1) % rSize];
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aid3 = atomRing[(i + 2) % rSize];
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aid4 = atomRing[(i + 3) % rSize];
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bid2 = mol.getBondBetweenAtoms(aid2, aid3)->getIdx();
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// if all 4 atoms are SP2, add torsion
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if (!(doneBonds[bid2]) &&
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(mol.getAtomWithIdx(aid1)->getHybridization() == Atom::SP2) &&
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(mol.getAtomWithIdx(aid2)->getHybridization() == Atom::SP2) &&
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(mol.getAtomWithIdx(aid3)->getHybridization() == Atom::SP2) &&
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(mol.getAtomWithIdx(aid4)->getHybridization() == Atom::SP2)) {
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doneBonds[bid2] = 1;
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std::vector<int> atoms(4);
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atoms[0] = aid1;
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atoms[1] = aid2;
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atoms[2] = aid3;
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atoms[3] = aid4;
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details.expTorsionAtoms.push_back(atoms);
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std::vector<int> signs(6, 1);
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signs[1] = -1; // MMFF sign for m = 2
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std::vector<double> fconsts(6, 0.0);
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fconsts[1] = 100.0; // 7.0 is MMFF force constants for aromatic rings
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details.expTorsionAngles.push_back(std::make_pair(signs, fconsts));
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/*if (verbose) {
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std::cout << "SP2 ring: " << aid1 << " " << aid2 << " " << aid3 << "
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" << aid4 << std::endl;
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}*/
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}
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} // loop over atoms in ring
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} // loop over rings
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} // if useBasicKnowledge
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} // end function
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} // namespace CrystalFF
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} // namespace ForceFields
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