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//
// Copyright (C) 2017 Greg Landrum
//
// @@ 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/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <cstdlib>
#include "coordgenlibs/sketcherMinimizer.h"
namespace RDKit {
namespace CoordGen {
struct CoordGenParams {
RDGeom::INT_POINT2D_MAP
coordMap; // coordinates for fixing particular atoms of a template
const ROMol* templateMol = nullptr; // a molecule to use as a template
double coordgenScaling = 50.0; // at the time this was written, coordgen
// returned coordinates with a single bond
// length of 50.
std::string templateFileDir = "";
float minimizerPrecision =
SKETCHER_STANDARD_PRECISION; // controls sketch precision
bool dbg_useConstrained = true; // debugging
bool dbg_useFixed = false; // debugging
};
static CoordGenParams defaultParams;
//! Generates a 2D conformer for a molecule and replaces the existing conformers
/*!
This call uses the CoordGen library from Schroedinger
\param mol the molecule we are working with
\param params a pointer to a parameter object
*/
template <typename T>
unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
if (!params) params = &defaultParams;
// FIX: the default value of this should be handled once in a threadsafe way
std::string templateFileDir;
if (params->templateFileDir != "") {
templateFileDir = params->templateFileDir;
} else {
auto rdbase = std::getenv("RDBASE");
if (rdbase != nullptr) {
templateFileDir += rdbase;
templateFileDir += "/Data/";
}
}
double scaleFactor = params->coordgenScaling;
sketcherMinimizer minimizer(params->minimizerPrecision);
auto min_mol = new sketcherMinimizerMolecule();
// FIX: only do this check once.
// std::cerr << " TEMPLATES: " << templateFileDir << std::endl;
if (templateFileDir != "") {
minimizer.setTemplateFileDir(templateFileDir);
}
bool hasTemplateMatch = false;
MatchVectType mv;
if (params->templateMol && params->templateMol->getNumConformers() == 1) {
if (SubstructMatch(mol, *(params->templateMol), mv)) {
hasTemplateMatch = true;
}
}
std::vector<sketcherMinimizerAtom*> ats(mol.getNumAtoms());
for (auto atit = mol.beginAtoms(); atit != mol.endAtoms(); ++atit) {
auto oatom = *atit;
auto atom = min_mol->addNewAtom();
atom->molecule = min_mol; // seems like this should be in addNewAtom()
atom->atomicNumber = oatom->getAtomicNum();
atom->charge = oatom->getFormalCharge();
if (hasTemplateMatch ||
params->coordMap.find(oatom->getIdx()) != params->coordMap.end()) {
atom->constrained = params->dbg_useConstrained;
atom->fixed = params->dbg_useFixed;
RDGeom::Point2D coords;
if (hasTemplateMatch) {
for (auto& pr : mv) {
if (pr.second == static_cast<int>(oatom->getIdx())) {
const RDGeom::Point3D& coords =
params->templateMol->getConformer().getAtomPos(pr.first);
atom->templateCoordinates = sketcherMinimizerPointF(
coords.x * scaleFactor, coords.y * scaleFactor);
break;
}
}
coords = params->coordMap.find(oatom->getIdx())->second;
} else {
const RDGeom::Point2D& coords =
params->coordMap.find(oatom->getIdx())->second;
atom->templateCoordinates = sketcherMinimizerPointF(
coords.x * scaleFactor, coords.y * scaleFactor);
}
}
ats[oatom->getIdx()] = atom;
}
std::vector<sketcherMinimizerBond*> bnds(mol.getNumBonds());
for (auto bndit = mol.beginBonds(); bndit != mol.endBonds(); ++bndit) {
auto obnd = *bndit;
auto bnd = min_mol->addNewBond(ats[obnd->getBeginAtomIdx()],
ats[obnd->getEndAtomIdx()]);
// FIX: This is no doubt wrong
switch (obnd->getBondType()) {
case Bond::SINGLE:
bnd->bondOrder = 1;
break;
case Bond::DOUBLE:
bnd->bondOrder = 2;
break;
case Bond::TRIPLE:
bnd->bondOrder = 3;
break;
case Bond::AROMATIC:
bnd->bondOrder = 1;
break;
default:
BOOST_LOG(rdWarningLog) << "unrecognized bond type";
}
bnds[obnd->getIdx()] = bnd;
}
// setup double bond stereo
min_mol->assignBondsAndNeighbors(ats, bnds);
for (auto bndit = mol.beginBonds(); bndit != mol.endBonds(); ++bndit) {
auto obnd = *bndit;
if (obnd->getBondType() != Bond::DOUBLE ||
obnd->getStereo() <= Bond::STEREOANY ||
obnd->getStereo() > Bond::STEREOTRANS)
continue;
sketcherMinimizerBondStereoInfo sinfo;
sinfo.atom1 = ats[obnd->getStereoAtoms()[0]];
sinfo.atom2 = ats[obnd->getStereoAtoms()[1]];
sinfo.stereo = (obnd->getStereo() == Bond::STEREOZ ||
obnd->getStereo() == Bond::STEREOCIS)
? sketcherMinimizerBondStereoInfo::cis
: sketcherMinimizerBondStereoInfo::trans;
auto bnd = bnds[obnd->getIdx()];
bnd->setStereoChemistry(sinfo);
bnd->setAbsoluteStereoFromStereoInfo();
}
minimizer.initialize(min_mol);
minimizer.runGenerateCoordinates();
auto conf = new Conformer(mol.getNumAtoms());
for (size_t i = 0; i < mol.getNumAtoms(); ++i) {
conf->setAtomPos(
i, RDGeom::Point3D(ats[i]->coordinates.x() / scaleFactor,
ats[i]->coordinates.y() / scaleFactor, 0.0));
// std::cerr << atom->coordinates << std::endl;
}
conf->set3D(false);
mol.clearConformers();
return (mol.addConformer(conf, true));
}
} // end of namespace CoordGen
} // end of namespace RDKit
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