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Add the option to minimize structures with coordgen (#3319)
* backup * works; needs testing * add some better tests and do some cleanup * rescale coordgen output to recover original bond lengths * patch coordgen so that we can do a windows DLL build * patch coordgen so that we can do a windows DLL build * changes in response to review
This commit is contained in:
Greg Landrum
GitHub
13
External/CoordGen/CMakeLists.txt
vendored
13
External/CoordGen/CMakeLists.txt
vendored
@@ -89,8 +89,17 @@ if(RDK_BUILD_COORDGEN_SUPPORT)
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execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
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${CMAKE_CURRENT_SOURCE_DIR}/coordgenlibs-${RELEASE_NO}.tar.gz
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WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
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# FIX: this is a workaround until https://github.com/schrodinger/coordgenlibs/pull/76
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# is merged and a new coordgen release is done
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file(RENAME "coordgenlibs-${RELEASE_NO}" "${COORDGEN_DIR}")
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set(fileToPatch "${COORDGEN_DIR}/CoordgenFragmenter.h")
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configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY)
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file(READ "${fileToPatch}" buffer)
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string(REPLACE "class CoordgenFragmenter"
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"#include \"CoordgenConfig.hpp\"\nclass EXPORT_COORDGEN CoordgenFragmenter"
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buffer "${buffer}")
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file(WRITE "${fileToPatch}" "${buffer}")
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else()
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message("-- Found coordgenlibs source in ${COORDGEN_DIR}")
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endif()
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@@ -116,7 +125,7 @@ if(RDK_BUILD_COORDGEN_SUPPORT)
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rdkit_test(testCoordGen test.cpp
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LINK_LIBRARIES
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${RDK_COORDGEN_LIBS} Depictor
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${RDK_COORDGEN_LIBS} Depictor ChemTransforms
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FileParsers SmilesParse SubstructMatch GraphMol
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RDGeneral DataStructs RDGeneral RDGeometryLib
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${RDKit_THREAD_LIBS})
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85
External/CoordGen/CoordGen.h
vendored
85
External/CoordGen/CoordGen.h
vendored
@@ -16,6 +16,7 @@
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#include <cstdlib>
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#include "coordgen/sketcherMinimizer.h"
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#include "coordgen/CoordgenFragmenter.h"
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namespace RDKit {
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namespace CoordGen {
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@@ -32,6 +33,7 @@ struct CoordGenParams {
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SKETCHER_STANDARD_PRECISION; // controls sketch precision
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bool dbg_useConstrained = true; // debugging
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bool dbg_useFixed = false; // debugging
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bool minimizeOnly = false; // don't actually generate full coords
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};
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static CoordGenParams defaultParams;
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@@ -58,6 +60,12 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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templateFileDir += "/Data/";
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}
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}
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if (params->minimizeOnly && !mol.getNumConformers()) {
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throw ValueErrorException(
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"minimizeOnly set but molecule has no conformers");
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}
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double scaleFactor = params->coordgenScaling;
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sketcherMinimizer minimizer(params->minimizerPrecision);
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@@ -70,12 +78,21 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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}
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bool hasTemplateMatch = false;
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MatchVectType mv;
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if (params->templateMol && params->templateMol->getNumConformers() == 1) {
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if (!params->minimizeOnly && params->templateMol &&
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params->templateMol->getNumConformers() == 1) {
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if (SubstructMatch(mol, *(params->templateMol), mv)) {
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hasTemplateMatch = true;
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}
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}
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// if we're doing coordinate minimization it makes our life easier to
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// start by translating to the origin
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RDGeom::Point3D centroid{0.0, 0.0, 0.0};
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if (params->minimizeOnly) {
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auto conf = mol.getConformer();
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centroid = MolTransforms::computeCentroid(conf);
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}
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std::vector<sketcherMinimizerAtom*> ats(mol.getNumAtoms());
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for (auto atit = mol.beginAtoms(); atit != mol.endAtoms(); ++atit) {
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auto oatom = *atit;
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@@ -83,11 +100,17 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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atom->molecule = min_mol; // seems like this should be in addNewAtom()
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atom->atomicNumber = oatom->getAtomicNum();
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atom->charge = oatom->getFormalCharge();
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if (hasTemplateMatch ||
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params->coordMap.find(oatom->getIdx()) != params->coordMap.end()) {
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if (params->minimizeOnly) {
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auto coords = mol.getConformer().getAtomPos(oatom->getIdx());
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coords -= centroid;
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atom->coordinates = sketcherMinimizerPointF(coords.x * scaleFactor,
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coords.y * scaleFactor);
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atom->fixed = false;
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atom->constrained = false;
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} else if (hasTemplateMatch || params->coordMap.find(oatom->getIdx()) !=
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params->coordMap.end()) {
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atom->constrained = params->dbg_useConstrained;
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atom->fixed = params->dbg_useFixed;
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RDGeom::Point2D coords;
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if (hasTemplateMatch) {
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for (auto& pr : mv) {
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if (pr.second == static_cast<int>(oatom->getIdx())) {
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@@ -98,7 +121,6 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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break;
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}
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}
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coords = params->coordMap.find(oatom->getIdx())->second;
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} else {
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const RDGeom::Point2D& coords =
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params->coordMap.find(oatom->getIdx())->second;
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@@ -109,6 +131,14 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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ats[oatom->getIdx()] = atom;
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}
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// coordgen has its own ideas about what bond lengths should be
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// if we are doing minimizeOnly we want to do a rigid scaling after the
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// minimization in order to try and get as close to where we started as
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// possible
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double singleBondLenAccum = 0.0;
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double bondLenAccum = 0.0;
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unsigned nSingle = 0;
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std::vector<sketcherMinimizerBond*> bnds(mol.getNumBonds());
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for (auto bndit = mol.beginBonds(); bndit != mol.endBonds(); ++bndit) {
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auto obnd = *bndit;
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@@ -118,6 +148,13 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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switch (obnd->getBondType()) {
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case Bond::SINGLE:
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bnd->bondOrder = 1;
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if (params->minimizeOnly) {
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++nSingle;
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singleBondLenAccum +=
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(mol.getConformer().getAtomPos(obnd->getBeginAtomIdx()) -
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mol.getConformer().getAtomPos(obnd->getEndAtomIdx()))
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.length();
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}
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break;
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case Bond::DOUBLE:
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bnd->bondOrder = 2;
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@@ -132,6 +169,19 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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BOOST_LOG(rdWarningLog) << "unrecognized bond type";
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}
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bnds[obnd->getIdx()] = bnd;
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if (params->minimizeOnly) {
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bondLenAccum += (mol.getConformer().getAtomPos(obnd->getBeginAtomIdx()) -
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mol.getConformer().getAtomPos(obnd->getEndAtomIdx()))
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.length();
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}
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}
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double avgBondLen = 1.0;
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if (params->minimizeOnly) {
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if (nSingle) {
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avgBondLen = singleBondLenAccum / nSingle;
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} else if (mol.getNumBonds()) {
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avgBondLen = bondLenAccum / mol.getNumBonds();
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}
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}
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// setup double bond stereo
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@@ -156,19 +206,30 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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}
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minimizer.initialize(min_mol);
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minimizer.runGenerateCoordinates();
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if (!params->minimizeOnly) {
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minimizer.runGenerateCoordinates();
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} else {
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CoordgenFragmenter::splitIntoFragments(min_mol);
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minimizer.m_minimizer.minimizeMolecule(min_mol);
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}
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auto conf = new Conformer(mol.getNumAtoms());
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for (size_t i = 0; i < mol.getNumAtoms(); ++i) {
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conf->setAtomPos(
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i, RDGeom::Point3D(ats[i]->coordinates.x() / scaleFactor,
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ats[i]->coordinates.y() / scaleFactor, 0.0));
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auto coords = RDGeom::Point3D(ats[i]->coordinates.x() / scaleFactor,
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ats[i]->coordinates.y() / scaleFactor, 0.0);
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if (params->minimizeOnly) {
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// readjust the average bond length from 1 (coordgen's target)
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// to whatever we started with
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coords *= avgBondLen;
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coords += centroid;
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}
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conf->setAtomPos(i, coords);
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// std::cerr << atom->coordinates << std::endl;
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}
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conf->set3D(false);
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mol.clearConformers();
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auto res = mol.addConformer(conf, true);
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if (params->coordMap.empty() && !params->templateMol) {
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if (!params->minimizeOnly && params->coordMap.empty() &&
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!params->templateMol) {
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// center the coordinates
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RDGeom::Transform3D tf;
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auto centroid = MolTransforms::computeCentroid(*conf);
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@@ -179,4 +240,4 @@ unsigned int addCoords(T& mol, const CoordGenParams* params = nullptr) {
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return res;
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}
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} // end of namespace CoordGen
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} // end of namespace RDKit
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} // namespace RDKit
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5
External/CoordGen/Wrap/rdCoordGen.cpp
vendored
5
External/CoordGen/Wrap/rdCoordGen.cpp
vendored
@@ -71,7 +71,10 @@ struct coordgen_wrapper {
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"directory containing the templates.mae file")
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.def_readwrite("minimizerPrecision",
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&CoordGen::CoordGenParams::minimizerPrecision,
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"controls sketcher precision");
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"controls sketcher precision")
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.def_readwrite("minimizeOnly", &CoordGen::CoordGenParams::minimizeOnly,
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"uses coordgen's force field to cleanup the 2D "
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"coordinates of the active conformation");
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python::def("SetDefaultTemplateFileDir", SetDefaultTemplateFileDir);
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docString =
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"Add 2D coordinates.\n"
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189
External/CoordGen/Wrap/testCoordGen.py
vendored
189
External/CoordGen/Wrap/testCoordGen.py
vendored
@@ -22,60 +22,145 @@ def compareConfs(c1,c2,match, tol=1e-2, alignIt=False):
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return True
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class TestCase(unittest.TestCase) :
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def test_basics(self):
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mol = Chem.MolFromSmiles('CCOC')
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self.assertEqual(mol.GetNumConformers(),0)
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rdCoordGen.AddCoords(mol)
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self.assertEqual(mol.GetNumConformers(),1)
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rdCoordGen.AddCoords(mol)
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self.assertEqual(mol.GetNumConformers(),1)
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rwmol = Chem.RWMol(mol)
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rdCoordGen.AddCoords(rwmol)
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self.assertEqual(rwmol.GetNumConformers(),1)
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def test_template1(self):
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template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
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template.SetProp("_Name",'template')
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mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
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mol.SetProp("_Name","mol")
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rdCoordGen.AddCoords(template)
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rdCoordGen.AddCoords(mol)
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self.assertFalse(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
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match = mol.GetSubstructMatch(template)
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mapd = dict()
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for i,aid in enumerate(match):
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p = template.GetConformer().GetAtomPosition(i)
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mapd[aid] = Geometry.Point2D(p.x,p.y)
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ps = rdCoordGen.CoordGenParams()
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ps.SetCoordMap(mapd)
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ps.dbg_useFixed = True
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rdCoordGen.AddCoords(mol,ps)
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self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
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def test_basics(self):
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mol = Chem.MolFromSmiles('CCOC')
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self.assertEqual(mol.GetNumConformers(),0)
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rdCoordGen.AddCoords(mol)
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self.assertEqual(mol.GetNumConformers(),1)
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rdCoordGen.AddCoords(mol)
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self.assertEqual(mol.GetNumConformers(),1)
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rwmol = Chem.RWMol(mol)
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rdCoordGen.AddCoords(rwmol)
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self.assertEqual(rwmol.GetNumConformers(),1)
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def test_template1(self):
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template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
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template.SetProp("_Name",'template')
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mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
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mol.SetProp("_Name","mol")
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rdCoordGen.AddCoords(template)
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rdCoordGen.AddCoords(mol)
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self.assertFalse(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
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match = mol.GetSubstructMatch(template)
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mapd = dict()
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for i,aid in enumerate(match):
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p = template.GetConformer().GetAtomPosition(i)
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mapd[aid] = Geometry.Point2D(p.x,p.y)
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ps = rdCoordGen.CoordGenParams()
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ps.SetCoordMap(mapd)
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ps.dbg_useFixed = True
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rdCoordGen.AddCoords(mol,ps)
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self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
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def test_template2(self):
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# the easier way...
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template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
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template.SetProp("_Name",'template')
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mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
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mol.SetProp("_Name","mol")
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rdCoordGen.AddCoords(template)
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ps = rdCoordGen.CoordGenParams()
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ps.SetTemplateMol(template)
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ps.dbg_useFixed = True
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rdCoordGen.AddCoords(mol,ps)
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self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
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def test_template2(self):
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# the easier way...
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template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
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template.SetProp("_Name",'template')
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mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
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mol.SetProp("_Name","mol")
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rdCoordGen.AddCoords(template)
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ps = rdCoordGen.CoordGenParams()
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ps.SetTemplateMol(template)
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ps.dbg_useFixed = True
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rdCoordGen.AddCoords(mol,ps)
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self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
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def test_template3(self):
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# the easier way, test lifetime...
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template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
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mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
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rdCoordGen.AddCoords(template)
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template2 = Chem.Mol(template)
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ps = rdCoordGen.CoordGenParams()
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ps.SetTemplateMol(template2)
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template2 = None
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ps.dbg_useFixed = True
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rdCoordGen.AddCoords(mol,ps)
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self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
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def testMinimizeOnly(self):
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m = Chem.MolFromMolBlock('''
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Mrv2014 08052005392D
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||||
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||||
0 0 0 0 0 999 V3000
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||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 14 15 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C -1.4287 -1.4523 0 0
|
||||
M V30 2 C -2.9638 -1.5752 0 0
|
||||
M V30 3 C -3.8377 -0.3072 0 0
|
||||
M V30 4 C -3.1766 1.0837 0 0
|
||||
M V30 5 C -1.6416 1.2066 0 0
|
||||
M V30 6 C -0.7675 -0.0614 0 0
|
||||
M V30 7 C 0.7675 0.0614 0 0
|
||||
M V30 8 C 1.6416 -1.2066 0 0
|
||||
M V30 9 C 0.9804 -2.5975 0 0
|
||||
M V30 10 N 3.1766 -1.0837 0 0
|
||||
M V30 11 C 3.8377 0.3072 0 0
|
||||
M V30 12 C 2.9638 1.5752 0 0
|
||||
M V30 13 C 1.4287 1.4523 0 0
|
||||
M V30 14 F -0.5548 -2.7203 0 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 2 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 2 3 4
|
||||
M V30 4 1 4 5
|
||||
M V30 5 2 5 6
|
||||
M V30 6 1 6 7
|
||||
M V30 7 2 7 8
|
||||
M V30 8 1 8 9
|
||||
M V30 9 1 8 10
|
||||
M V30 10 2 10 11
|
||||
M V30 11 1 11 12
|
||||
M V30 12 2 12 13
|
||||
M V30 13 1 6 1
|
||||
M V30 14 1 13 7
|
||||
M V30 15 1 1 14
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
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||||
M END
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||||
''')
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||||
ref = Chem.MolFromMolBlock('''
|
||||
RDKit 2D
|
||||
|
||||
14 15 0 0 0 0 0 0 0 0999 V2000
|
||||
-1.5379 -1.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.1218 -1.5958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.9595 -0.2554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.2641 1.1663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.6778 1.2217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7941 -0.0886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.7983 0.0383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.7524 -1.2209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.1246 -2.6443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.3306 -1.0787 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.9439 0.3747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.0337 1.6656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.4617 1.4692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.6924 -2.7917 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 2 0
|
||||
2 3 1 0
|
||||
3 4 2 0
|
||||
4 5 1 0
|
||||
5 6 2 0
|
||||
6 7 1 0
|
||||
7 8 2 0
|
||||
8 9 1 0
|
||||
8 10 1 0
|
||||
10 11 2 0
|
||||
11 12 1 0
|
||||
12 13 2 0
|
||||
6 1 1 0
|
||||
13 7 1 0
|
||||
1 14 1 0
|
||||
M END''')
|
||||
ps = rdCoordGen.CoordGenParams()
|
||||
ps.minimizeOnly = True
|
||||
m2 = Chem.Mol(m)
|
||||
rdCoordGen.AddCoords(m2,ps)
|
||||
self.assertGreater(rdMolAlign.AlignMol(m, ref), 0.1)
|
||||
self.assertLess(rdMolAlign.AlignMol(m2, ref), 0.1)
|
||||
|
||||
def test_template3(self):
|
||||
# the easier way, test lifetime...
|
||||
template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
|
||||
mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
|
||||
rdCoordGen.AddCoords(template)
|
||||
template2 = Chem.Mol(template)
|
||||
ps = rdCoordGen.CoordGenParams()
|
||||
ps.SetTemplateMol(template2)
|
||||
template2 = None
|
||||
ps.dbg_useFixed = True
|
||||
rdCoordGen.AddCoords(mol,ps)
|
||||
self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
|
||||
75
External/CoordGen/test.cpp
vendored
75
External/CoordGen/test.cpp
vendored
@@ -16,6 +16,7 @@
|
||||
#include <GraphMol/Substruct/SubstructMatch.h>
|
||||
#include <GraphMol/MolAlign/AlignMolecules.h>
|
||||
#include <GraphMol/MolTransforms/MolTransforms.h>
|
||||
#include <GraphMol/ChemTransforms/ChemTransforms.h>
|
||||
|
||||
#include <RDGeneral/RDLog.h>
|
||||
|
||||
@@ -487,12 +488,86 @@ void testGithub3131() {
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
}
|
||||
|
||||
void testCoordgenMinimize() {
|
||||
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
|
||||
BOOST_LOG(rdInfoLog) << "testing coordgen minimize" << std::endl;
|
||||
{
|
||||
auto m1 =
|
||||
R"CTAB(
|
||||
Mrv2014 08052005142D
|
||||
|
||||
0 0 0 0 0 999 V3000
|
||||
M V30 BEGIN CTAB
|
||||
M V30 COUNTS 8 8 0 0 0
|
||||
M V30 BEGIN ATOM
|
||||
M V30 1 C -2.1121 -0.3399 0 0
|
||||
M V30 2 C -3.3708 0.5474 0 0
|
||||
M V30 3 C -1.9835 0.9311 0 0
|
||||
M V30 4 C -0.7248 0.0437 0 0
|
||||
M V30 5 C 0.7926 0.3064 0 0
|
||||
M V30 6 O 1.3239 1.7518 0 0
|
||||
M V30 7 O 0.612 -1.2514 0 0
|
||||
M V30 8 C 1.3429 -0.2989 0 0
|
||||
M V30 END ATOM
|
||||
M V30 BEGIN BOND
|
||||
M V30 1 1 1 2
|
||||
M V30 2 1 2 3
|
||||
M V30 3 1 3 4
|
||||
M V30 4 1 4 5
|
||||
M V30 5 2 5 6
|
||||
M V30 6 1 5 7
|
||||
M V30 7 1 7 8
|
||||
M V30 8 1 4 1
|
||||
M V30 END BOND
|
||||
M V30 END CTAB
|
||||
M END
|
||||
)CTAB"_ctab;
|
||||
TEST_ASSERT(m1);
|
||||
TEST_ASSERT(m1->getNumConformers() == 1);
|
||||
auto ref = R"CTAB(
|
||||
RDKit 2D
|
||||
|
||||
8 8 0 0 0 0 0 0 0 0999 V2000
|
||||
-1.5738 -1.1409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.7946 -0.3071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.9122 0.8790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.6914 0.0452 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.7517 0.2885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.2665 1.6721 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.6941 -0.8483 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.1500 -0.6002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0
|
||||
2 3 1 0
|
||||
3 4 1 0
|
||||
4 5 1 0
|
||||
5 6 2 0
|
||||
5 7 1 0
|
||||
7 8 1 0
|
||||
4 1 1 0
|
||||
M END
|
||||
)CTAB"_ctab;
|
||||
TEST_ASSERT(ref);
|
||||
TEST_ASSERT(ref->getNumConformers() == 1);
|
||||
|
||||
CoordGen::CoordGenParams ps;
|
||||
ps.minimizeOnly = true;
|
||||
CoordGen::addCoords(*m1, &ps);
|
||||
ROMol m2(*m1);
|
||||
double rmsd = MolAlign::alignMol(m2, *ref);
|
||||
TEST_ASSERT(rmsd < 0.1);
|
||||
}
|
||||
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
||||
}
|
||||
|
||||
int main(int argc, char* argv[]) {
|
||||
(void)argc;
|
||||
(void)argv;
|
||||
RDLog::InitLogs();
|
||||
#if 1
|
||||
test2();
|
||||
test1();
|
||||
testGithub1929();
|
||||
testGithub3131();
|
||||
#endif
|
||||
testCoordgenMinimize();
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user