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Shape overlay initial start aligned to principal axes (#8999)
* Add MolTransforms library. * Transform to inertial frame of reference before overlay. * Vital fix of typo in comment. * Tidy up debugging cruft. * Comment in CMakeLists.txt. * Fix python wrappers. * Extra tidy. * Response to review. * Tidy includes. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
This commit is contained in:
David Cosgrove
GitHub
@@ -85,7 +85,7 @@ class RDKIT_RDGEOMETRYLIB_EXPORT Transform3D
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*
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* The order is important here, on two transforms t1 and t2
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* t3 = t1*t2
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* The resulting transform t3 has the folliwng effect
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* The resulting transform t3 has the following effect
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* t3(point) = t1(t2(point))
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*/
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RDKIT_RDGEOMETRYLIB_EXPORT RDGeom::Transform3D operator*(
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3
External/pubchem_shape/CMakeLists.txt
vendored
3
External/pubchem_shape/CMakeLists.txt
vendored
@@ -37,6 +37,7 @@ if(needDownload)
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endif()
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# simple patch for a typo in the pubchem_align library
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# This should no longer be necessary, as it has been fixed upstream. Maybe take it out?
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file(READ ${PUBCHEMSHAPE_DIR}/shape_neighbor.cpp FILE_CONTENTS)
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string(REPLACE "memcpy( qom, old_quattrans, 7 * sizeof( float ) );" "memcpy( qom, old_quattrans, 7 * sizeof( double ) );" FILE_CONTENTS "${FILE_CONTENTS}")
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file(WRITE ${PUBCHEMSHAPE_DIR}/shape_neighbor.cpp "${FILE_CONTENTS}")
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@@ -48,7 +49,7 @@ if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32))
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endif()
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rdkit_library(PubChemShape PubChemShape.cpp SHARED
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LINK_LIBRARIES pubchem_align3d SmilesParse SubstructMatch)
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LINK_LIBRARIES pubchem_align3d SmilesParse SubstructMatch MolTransforms)
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target_compile_definitions(PubChemShape PRIVATE RDKIT_PUBCHEMSHAPE_BUILD)
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rdkit_headers(PubChemShape.hpp DEST GraphMol)
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186
External/pubchem_shape/PubChemShape.cpp
vendored
186
External/pubchem_shape/PubChemShape.cpp
vendored
@@ -3,7 +3,10 @@
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#include <stdexcept>
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#include <GraphMol/RWMol.h>
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#include <Geometry/Transform3D.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <RDGeneral/BoostStartInclude.h>
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@@ -371,14 +374,17 @@ void extractFeatureCoords(
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}
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}
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void extractCustomFeatureCoords(const unsigned int nSelectedAtoms,
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const ShapeInputOptions &shapeOpts,
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const RDGeom::Point3D &ave,
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unsigned int &numFeatures, ShapeInput &res,
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std::vector<double> &rad_vector) {
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void extractCustomFeatureCoords(
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const unsigned int nSelectedAtoms, const ShapeInputOptions &shapeOpts,
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const RDGeom::Point3D &ave, unsigned int &numFeatures, ShapeInput &res,
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std::vector<double> &rad_vector,
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const std::unique_ptr<RDGeom::Transform3D> &trans) {
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for (const auto &feature : shapeOpts.customFeatures) {
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unsigned int feature_type = std::get<0>(feature);
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RDGeom::Point3D floc = std::get<1>(feature);
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if (trans) {
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trans->TransformPoint(floc);
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}
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double radius = std::get<2>(feature);
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floc -= ave;
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DEBUG_MSG("custom feature type " << feature_type << " (" << floc << ")");
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@@ -394,7 +400,8 @@ void extractCustomFeatureCoords(const unsigned int nSelectedAtoms,
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}
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} // namespace
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// The conformer is left where it is, the shape is translated to the origin.
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// The conformer is left where it is, the shape is translated to the origin
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// and aligned to the principal axes.
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ShapeInput PrepareConformer(const ROMol &mol, int confId,
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const ShapeInputOptions &shapeOpts) {
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Align3D::setUseCutOff(true);
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@@ -420,24 +427,61 @@ ShapeInput PrepareConformer(const ROMol &mol, int confId,
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std::vector<double> rad_vector(nAlignmentAtoms);
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res.atom_type_vector.resize(nAlignmentAtoms, 0);
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Conformer confCp(conformer);
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std::unique_ptr<RDGeom::Transform3D> trans;
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RDGeom::Point3D initialCentroid;
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if (shapeOpts.normalize) {
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// This ignores hydrogens by default, which is what is needed here.
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trans.reset(MolTransforms::computeCanonicalTransform(confCp));
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MolTransforms::transformConformer(confCp, *trans);
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// Save the rotation part of the transformation. The coords will be centred
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// below and left that way so we don't need to keep the translation.
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for (unsigned int i = 0, k = 0; i < 3; ++i) {
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for (unsigned int j = 0; j < 3; ++j, ++k) {
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res.inertialRot[k] = trans->getValUnchecked(i, j);
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}
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}
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// Work back from the canonical transformation to get the initial
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// centroid by the inverse rotation of the current translation
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// but not taking its negative so it can be used directly as the shift.
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initialCentroid = RDGeom::Point3D{trans->getValUnchecked(0, 3),
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trans->getValUnchecked(1, 3),
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trans->getValUnchecked(2, 3)};
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RDGeom::Transform3D invTrans;
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invTrans.setValUnchecked(0, 0, trans->getValUnchecked(0, 0));
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invTrans.setValUnchecked(0, 1, trans->getValUnchecked(1, 0));
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invTrans.setValUnchecked(0, 2, trans->getValUnchecked(2, 0));
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invTrans.setValUnchecked(1, 0, trans->getValUnchecked(0, 1));
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invTrans.setValUnchecked(1, 1, trans->getValUnchecked(1, 1));
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invTrans.setValUnchecked(1, 2, trans->getValUnchecked(2, 1));
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invTrans.setValUnchecked(2, 0, trans->getValUnchecked(0, 2));
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invTrans.setValUnchecked(2, 1, trans->getValUnchecked(1, 2));
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invTrans.setValUnchecked(2, 2, trans->getValUnchecked(2, 2));
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invTrans.TransformPoint(initialCentroid);
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}
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RWMol molCp(mol);
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molCp.removeConformer(0);
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molCp.addConformer(new Conformer(confCp), true);
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RDGeom::Point3D ave;
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unsigned int nSelectedAtoms = 0;
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extractAtomRadii(conformer, nAtoms, shapeOpts, ave, nSelectedAtoms,
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rad_vector);
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// Calculates the average coord as by-product
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extractAtomRadii(confCp, nAtoms, shapeOpts, ave, nSelectedAtoms, rad_vector);
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// translate steric center to origin
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DEBUG_MSG("steric center: (" << ave << ")");
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res.shift = {-ave.x, -ave.y, -ave.z};
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res.coord.resize(nAlignmentAtoms * 3);
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extractAtomCoords(conformer, nAtoms, shapeOpts, ave, res.coord);
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extractAtomCoords(confCp, nAtoms, shapeOpts, ave, res.coord);
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unsigned int numFeatures = 0;
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if (shapeOpts.customFeatures.empty()) {
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extractFeatureCoords(conformer, nAtoms, nSelectedAtoms, feature_idx_type,
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extractFeatureCoords(confCp, nAtoms, nSelectedAtoms, feature_idx_type,
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shapeOpts, ave, numFeatures, res, rad_vector);
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} else if (shapeOpts.useColors) {
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extractCustomFeatureCoords(nSelectedAtoms, shapeOpts, ave, numFeatures, res,
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rad_vector);
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rad_vector, trans);
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}
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// Now cut the final vectors down to the actual number of atoms and
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@@ -467,6 +511,9 @@ ShapeInput PrepareConformer(const ROMol &mol, int confId,
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res.coord.data(), res.alpha_vector, res.colorAtomType2IndexVectorMap);
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DEBUG_MSG("sof: " << res.sof);
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}
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// Finally set the shift to the negative of the original average coords.
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res.shift = {initialCentroid.x, initialCentroid.y, initialCentroid.z};
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return res;
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}
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@@ -499,7 +546,6 @@ std::pair<double, double> AlignShape(const ShapeInput &refShape,
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fitShape.volumeAtomIndexVector, fitMapCp, fitShape.sov, fitShape.sof,
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!jointColorAtomTypeSet.empty(), max_preiters, max_postiters, opt_param,
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matrix.data(), nbr_st, nbr_ct);
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DEBUG_MSG("Done!");
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DEBUG_MSG("nbr_st: " << nbr_st);
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DEBUG_MSG("nbr_ct: " << nbr_ct);
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@@ -512,36 +558,73 @@ std::pair<double, double> AlignShape(const ShapeInput &refShape,
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}
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void TransformConformer(const std::vector<double> &finalTrans,
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const std::vector<float> &matrix, ShapeInput &fitShape,
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Conformer &fitConf) {
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// we reuse/modify the coord member of fitShape in order to avoid memory
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// allocations
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const unsigned int nAtoms = fitConf.getOwningMol().getNumAtoms();
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if (nAtoms > fitShape.volumeAtomIndexVector.size()) {
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// Hs are missing... make sure we have space for them
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fitShape.coord.resize(3 * nAtoms);
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}
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// initialize the fitShape coords with the starting atomic positions from
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// the conformer shifted to the center of "mass" coordinates.
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for (unsigned int i = 0; i < nAtoms; ++i) {
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const auto &pos = fitConf.getAtomPos(i);
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fitShape.coord[i * 3] = pos.x + fitShape.shift[0];
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fitShape.coord[i * 3 + 1] = pos.y + fitShape.shift[1];
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fitShape.coord[i * 3 + 2] = pos.z + fitShape.shift[2];
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}
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const std::vector<double> &finalRot,
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const std::vector<float> &matrix,
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const ShapeInput &fitShape, Conformer &fitConf) {
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// Move fitConf to fitShape's initial centroid and principal axes
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RDGeom::Transform3D transform0;
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transform0.SetTranslation(
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RDGeom::Point3D{fitShape.shift[0], fitShape.shift[1], fitShape.shift[2]});
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std::vector<float> transformed(nAtoms * 3);
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Align3D::VApplyRotTransMatrix(transformed.data(), fitShape.coord.data(),
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nAtoms, matrix.data());
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RDGeom::Transform3D transform1;
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transform1.setValUnchecked(0, 0, fitShape.inertialRot[0]);
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transform1.setValUnchecked(0, 1, fitShape.inertialRot[1]);
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transform1.setValUnchecked(0, 2, fitShape.inertialRot[2]);
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transform1.setValUnchecked(1, 0, fitShape.inertialRot[3]);
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transform1.setValUnchecked(1, 1, fitShape.inertialRot[4]);
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transform1.setValUnchecked(1, 2, fitShape.inertialRot[5]);
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transform1.setValUnchecked(2, 0, fitShape.inertialRot[6]);
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transform1.setValUnchecked(2, 1, fitShape.inertialRot[7]);
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transform1.setValUnchecked(2, 2, fitShape.inertialRot[8]);
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transform1.setValUnchecked(2, 3, 0.0);
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transform1.setValUnchecked(3, 0, 0.0);
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transform1.setValUnchecked(3, 1, 0.0);
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transform1.setValUnchecked(3, 2, 0.0);
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transform1.setValUnchecked(3, 3, 1.0);
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// now set the coordinates in the conformer; undo the shift of the reference
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// shape to center of "mass" coordinates
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for (unsigned i = 0; i < nAtoms; ++i) {
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RDGeom::Point3D &pos = fitConf.getAtomPos(i);
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pos.x = transformed[i * 3] - finalTrans[0];
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pos.y = transformed[(i * 3) + 1] - finalTrans[1];
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pos.z = transformed[(i * 3) + 2] - finalTrans[2];
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}
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// Apply the overlay matrix.
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// The matrix comes in as a linear form of a 3x3 rotation matrix and a
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// 3x1 translation. Convert that into a RDGeom::Trans3D
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RDGeom::Transform3D transform2;
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transform2.setValUnchecked(0, 0, matrix[0]);
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transform2.setValUnchecked(0, 1, matrix[1]);
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transform2.setValUnchecked(0, 2, matrix[2]);
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transform2.setValUnchecked(0, 3, matrix[9]);
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transform2.setValUnchecked(1, 0, matrix[3]);
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transform2.setValUnchecked(1, 1, matrix[4]);
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transform2.setValUnchecked(1, 2, matrix[5]);
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transform2.setValUnchecked(1, 3, matrix[10]);
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transform2.setValUnchecked(2, 0, matrix[6]);
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transform2.setValUnchecked(2, 1, matrix[7]);
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transform2.setValUnchecked(2, 2, matrix[8]);
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transform2.setValUnchecked(2, 3, matrix[11]);
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transform2.setValUnchecked(3, 0, 0.0);
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transform2.setValUnchecked(3, 1, 0.0);
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transform2.setValUnchecked(3, 2, 0.0);
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transform2.setValUnchecked(3, 3, 1.0);
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// Now apply the final rotation and final translation, which
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// is to put it into the reference shape's frame of reference.
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RDGeom::Transform3D transform3;
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transform3.setValUnchecked(0, 0, finalRot[0]);
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transform3.setValUnchecked(0, 1, finalRot[1]);
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transform3.setValUnchecked(0, 2, finalRot[2]);
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transform3.setValUnchecked(0, 3, finalTrans[0]);
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transform3.setValUnchecked(1, 0, finalRot[3]);
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transform3.setValUnchecked(1, 1, finalRot[4]);
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transform3.setValUnchecked(1, 2, finalRot[5]);
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transform3.setValUnchecked(1, 3, finalTrans[1]);
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transform3.setValUnchecked(2, 0, finalRot[6]);
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transform3.setValUnchecked(2, 1, finalRot[7]);
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transform3.setValUnchecked(2, 2, finalRot[8]);
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transform3.setValUnchecked(2, 3, finalTrans[2]);
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transform3.setValUnchecked(3, 0, 0.0);
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transform3.setValUnchecked(3, 1, 0.0);
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transform3.setValUnchecked(3, 2, 0.0);
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transform3.setValUnchecked(3, 3, 1.0);
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auto finalTransform = transform3 * transform2 * transform1 * transform0;
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MolTransforms::transformConformer(fitConf, finalTransform);
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}
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std::pair<double, double> AlignMolecule(
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@@ -555,14 +638,23 @@ std::pair<double, double> AlignMolecule(
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auto fitShape = PrepareConformer(fit, fitConfId, shapeOpts);
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auto tanis = AlignShape(refShape, fitShape, matrix, opt_param, max_preiters,
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max_postiters);
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// transform fit coords
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Conformer &fit_conformer = fit.getConformer(fitConfId);
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std::vector<double> finalTrans{0.0, 0.0, 0.0};
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std::vector<double> finalRot{1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0};
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if (applyRefShift) {
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finalTrans = refShape.shift;
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finalTrans = std::vector<double>{-refShape.shift[0], -refShape.shift[1],
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-refShape.shift[2]};
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// set the final rotation to the inverse of the original inertialRot
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// of the reference.
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finalRot =
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std::vector<double>{refShape.inertialRot[0], refShape.inertialRot[3],
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refShape.inertialRot[6], refShape.inertialRot[1],
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refShape.inertialRot[4], refShape.inertialRot[7],
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refShape.inertialRot[2], refShape.inertialRot[5],
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refShape.inertialRot[8]};
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}
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TransformConformer(finalTrans, matrix, fitShape, fit_conformer);
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TransformConformer(finalTrans, finalRot, matrix, fitShape, fit_conformer);
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fit.setProp("shape_align_shape_tanimoto", tanis.first);
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fit.setProp("shape_align_color_tanimoto", tanis.second);
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@@ -582,11 +674,11 @@ std::pair<double, double> AlignMolecule(
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std::pair<double, double> AlignMolecule(
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const ROMol &ref, ROMol &fit, std::vector<float> &matrix,
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const ShapeInputOptions &refShapeOpts,
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const ShapeInputOptions &probeShapeOpts, int refConfId, int fitConfId,
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const ShapeInputOptions &fitShapeOpts, int refConfId, int fitConfId,
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double opt_param, unsigned int max_preiters, unsigned int max_postiters) {
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Align3D::setUseCutOff(true);
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if (refShapeOpts.useColors != probeShapeOpts.useColors) {
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if (refShapeOpts.useColors != fitShapeOpts.useColors) {
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BOOST_LOG(rdWarningLog)
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<< "useColor values inconsistent between the reference and fit molecules. Colors will not be used in the alignment."
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<< std::endl;
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@@ -596,7 +688,7 @@ std::pair<double, double> AlignMolecule(
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auto refShape = PrepareConformer(ref, refConfId, refShapeOpts);
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bool applyRefShift = true;
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auto scores =
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AlignMolecule(refShape, fit, matrix, probeShapeOpts, fitConfId, opt_param,
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AlignMolecule(refShape, fit, matrix, fitShapeOpts, fitConfId, opt_param,
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max_preiters, max_postiters, applyRefShift);
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return scores;
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}
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20
External/pubchem_shape/PubChemShape.hpp
vendored
20
External/pubchem_shape/PubChemShape.hpp
vendored
@@ -1,6 +1,8 @@
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#ifndef RDKIT_PUBCHEMSHAPE_GUARD
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#define RDKIT_PUBCHEMSHAPE_GUARD
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#include "Geometry/Transform3D.h"
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#include <GraphMol/ROMol.h>
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#include <map>
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#include <vector>
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@@ -54,6 +56,7 @@ struct RDKIT_PUBCHEMSHAPE_EXPORT ShapeInput {
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ar & shift;
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ar & sov;
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ar & sof;
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ar & inertialRot;
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}
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#endif
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@@ -64,6 +67,10 @@ struct RDKIT_PUBCHEMSHAPE_EXPORT ShapeInput {
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std::map<unsigned int, std::vector<unsigned int>>
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colorAtomType2IndexVectorMap;
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std::vector<double> shift;
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// If the conformer the shape was created from was rotated into the
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// inertial reference frame at the start, this is the rotation that
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// did that, assuming it was already centred on the origin.
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std::vector<double> inertialRot{1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0};
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double sov{0.0};
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double sof{0.0};
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};
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@@ -98,7 +105,8 @@ struct RDKIT_PUBCHEMSHAPE_EXPORT ShapeInputOptions {
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\param confId (optional) the conformer to use
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\param shapeOpts (optional) Change the default behaviour.
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\return a ShapeInput object, translated to the origin
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\return a ShapeInput object, translated to the origin and aligned along its
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principal axes.
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*/
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RDKIT_PUBCHEMSHAPE_EXPORT ShapeInput
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PrepareConformer(const RDKit::ROMol &mol, int confId = -1,
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@@ -123,18 +131,20 @@ RDKIT_PUBCHEMSHAPE_EXPORT std::pair<double, double> AlignShape(
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unsigned int max_preiters = 10u, unsigned int max_postiters = 30u);
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//! Assuming that fitShape has been overlaid onto a reference shape to give
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//! the ! transformation matrix, apply the same transformation to the given
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//! the transformation matrix, apply the same transformation to the given
|
||||
//! conformer.
|
||||
/*!
|
||||
\param finalTrans the final translation to apply to the fitConf coords.
|
||||
\param finalRot the final rotation to apply to the fitConf coords.
|
||||
\param matrix the transformation matrix produced from alignment
|
||||
\param fitShape the shape that was aligned. The coord vector of this is
|
||||
modified
|
||||
\param fitConf the conformation to be transformed
|
||||
*/
|
||||
RDKIT_PUBCHEMSHAPE_EXPORT void TransformConformer(
|
||||
const std::vector<double> &finalTrans, const std::vector<float> &matrix,
|
||||
ShapeInput &fitShape, RDKit::Conformer &fitConf);
|
||||
const std::vector<double> &finalTrans, const std::vector<double> &finalRot,
|
||||
const std::vector<float> &matrix, const ShapeInput &fitShape,
|
||||
RDKit::Conformer &fitConf);
|
||||
|
||||
//! Align a molecule to a reference shape
|
||||
/*!
|
||||
@@ -202,7 +212,7 @@ RDKIT_PUBCHEMSHAPE_EXPORT std::pair<double, double> AlignMolecule(
|
||||
RDKIT_PUBCHEMSHAPE_EXPORT std::pair<double, double> AlignMolecule(
|
||||
const RDKit::ROMol &ref, RDKit::ROMol &fit, std::vector<float> &matrix,
|
||||
const ShapeInputOptions &refShapeOpts,
|
||||
const ShapeInputOptions &probeShapeOpts, int refConfId = -1,
|
||||
const ShapeInputOptions &fitShapeOpts, int refConfId = -1,
|
||||
int fitConfId = -1, double opt_param = 1.0, unsigned int max_preiters = 10u,
|
||||
unsigned int max_postiters = 30u);
|
||||
|
||||
|
||||
21
External/pubchem_shape/Wrap/cshapealign.cpp
vendored
21
External/pubchem_shape/Wrap/cshapealign.cpp
vendored
@@ -96,6 +96,7 @@ python::tuple scoreShape(const ShapeInput &shape1, ShapeInput &shape2,
|
||||
return python::make_tuple(nbr_st, nbr_ct);
|
||||
}
|
||||
void transformConformer(const python::list &pyFinalTrans,
|
||||
const python::list &pyFinalRot,
|
||||
const python::list &pyMatrix, ShapeInput probeShape,
|
||||
RDKit::Conformer &probeConf) {
|
||||
std::vector<float> matrix;
|
||||
@@ -112,7 +113,14 @@ void transformConformer(const python::list &pyFinalTrans,
|
||||
"The final translation vector must have 3 values. It had " +
|
||||
std::to_string(finalTrans.size()) + ".");
|
||||
}
|
||||
TransformConformer(finalTrans, matrix, probeShape, probeConf);
|
||||
std::vector<double> finalRot;
|
||||
pythonObjectToVect<double>(pyFinalRot, finalRot);
|
||||
if (finalRot.size() != 9) {
|
||||
throw_value_error("The final rotation vector must have 9 values. It had " +
|
||||
std::to_string(finalRot.size()) + ".");
|
||||
}
|
||||
|
||||
TransformConformer(finalTrans, finalRot, matrix, probeShape, probeConf);
|
||||
}
|
||||
ShapeInput *prepConf(const RDKit::ROMol &mol, int confId,
|
||||
const python::object &py_opts) {
|
||||
@@ -175,6 +183,14 @@ python::list get_shapeShift(const ShapeInput &shp) {
|
||||
return py_list;
|
||||
}
|
||||
|
||||
python::list get_inertialRot(const ShapeInput &shp) {
|
||||
python::list py_list;
|
||||
for (const auto &val : shp.inertialRot) {
|
||||
py_list.append(val);
|
||||
}
|
||||
return py_list;
|
||||
}
|
||||
|
||||
void set_customFeatures(ShapeInputOptions &shp, const python::object &s) {
|
||||
shp.customFeatures.clear();
|
||||
auto len = python::len(s);
|
||||
@@ -428,6 +444,9 @@ Returns
|
||||
&ShapeInput::volumeAtomIndexVector)
|
||||
.add_property("shift", &helpers::get_shapeShift, &helpers::set_shapeShift,
|
||||
"Translation of centre of shape coordinates to origin.")
|
||||
.add_property(
|
||||
"inertialRot", &helpers::get_inertialRot,
|
||||
"Rotation applied to put the shape into its principal axes frame of reference.")
|
||||
.def_readwrite("sov", &ShapeInput::sov)
|
||||
.def_readwrite("sof", &ShapeInput::sof);
|
||||
|
||||
|
||||
20
External/pubchem_shape/Wrap/test_rdshapealign.py
vendored
20
External/pubchem_shape/Wrap/test_rdshapealign.py
vendored
@@ -18,7 +18,7 @@ class TestCase(unittest.TestCase):
|
||||
tpl = rdShapeAlign.AlignMol(self.ref, self.probe, opt_param=0.5, max_preiters=3,
|
||||
max_postiters=16)
|
||||
self.assertAlmostEqual(tpl[0], 0.773, places=3)
|
||||
self.assertAlmostEqual(tpl[1], 0.303, places=3)
|
||||
self.assertAlmostEqual(tpl[1], 0.305, places=3)
|
||||
|
||||
def test2_NoColor(self):
|
||||
tpl = rdShapeAlign.AlignMol(self.ref, self.probe, useColors=False, opt_param=0.5,
|
||||
@@ -31,7 +31,7 @@ class TestCase(unittest.TestCase):
|
||||
self.assertTrue(type(shp) == rdShapeAlign.ShapeInput)
|
||||
tpl = rdShapeAlign.AlignMol(shp, self.probe, opt_param=0.5, max_preiters=3, max_postiters=16)
|
||||
self.assertAlmostEqual(tpl[0], 0.773, places=3)
|
||||
self.assertAlmostEqual(tpl[1], 0.303, places=3)
|
||||
self.assertAlmostEqual(tpl[1], 0.305, places=3)
|
||||
|
||||
def test4_ShapeInputOptions(self):
|
||||
opts = rdShapeAlign.ShapeInputOptions()
|
||||
@@ -58,13 +58,17 @@ class TestCase(unittest.TestCase):
|
||||
probeShp = rdShapeAlign.PrepareConformer(self.probe, -1)
|
||||
tpl = rdShapeAlign.AlignShapes(refShp, probeShp)
|
||||
probeCp = Chem.Mol(self.probe)
|
||||
rdShapeAlign.TransformConformer(refShp.shift, tpl[2], probeShp, probeCp.GetConformer(-1))
|
||||
rdShapeAlign.TransformConformer(refShp.shift, refShp.inertialRot, tpl[2], probeShp, probeCp.GetConformer(-1))
|
||||
self.assertEqual(len(refShp.inertialRot), 9)
|
||||
self.assertAlmostEqual(refShp.inertialRot[0], -0.926125, places=6)
|
||||
self.assertAlmostEqual(refShp.inertialRot[8], -0.852890, places=6)
|
||||
|
||||
# Just show it did something. The full test is in the C++ layer.
|
||||
self.assertNotEqual(self.probe.GetConformer().GetAtomPosition(0),
|
||||
probeCp.GetConformer().GetAtomPosition(0))
|
||||
matrix = tpl[2][:10]
|
||||
with self.assertRaises(ValueError):
|
||||
rdShapeAlign.TransformConformer(refShp.shift, matrix, probeShp, probeCp.GetConformer(-1))
|
||||
rdShapeAlign.TransformConformer(refShp.shift, refShp.inertialRot, matrix, probeShp, probeCp.GetConformer(-1))
|
||||
|
||||
def test6_notColorAtoms(self):
|
||||
m1 = Chem.MolFromSmiles("Nc1ccccc1 |(0.392086,-2.22477,0.190651;"
|
||||
@@ -91,8 +95,8 @@ class TestCase(unittest.TestCase):
|
||||
0), 1.0), (1, Point3D(1.7571, -0.120174, 0.1), 1.0))
|
||||
shp2 = rdShapeAlign.PrepareConformer(m2, -1, opts2)
|
||||
tpl = rdShapeAlign.AlignShapes(shp, shp2, opt_param=0.5)
|
||||
self.assertAlmostEqual(tpl[0], 0.997, places=3)
|
||||
self.assertAlmostEqual(tpl[1], 0.978, places=3)
|
||||
self.assertAlmostEqual(tpl[0], 1.000, places=3)
|
||||
self.assertAlmostEqual(tpl[1], 0.997, places=3)
|
||||
tf = tpl[2]
|
||||
self.assertGreater(0.0, tf[0])
|
||||
self.assertLess(0.0, tf[3 * 3])
|
||||
@@ -114,8 +118,8 @@ class TestCase(unittest.TestCase):
|
||||
opts2.customFeatures = ((2, Point3D(-1.75978, 0.148897,
|
||||
0), 1.0), (1, Point3D(1.7571, -0.120174, 0.1), 1.0))
|
||||
tpl = rdShapeAlign.AlignMol(m1, m2, opts, opts2, opt_param=0.5)
|
||||
self.assertAlmostEqual(tpl[0], 0.997, places=3)
|
||||
self.assertAlmostEqual(tpl[1], 0.978, places=3)
|
||||
self.assertAlmostEqual(tpl[0], 1.000, places=3)
|
||||
self.assertAlmostEqual(tpl[1], 0.997, places=3)
|
||||
|
||||
def test9_FixedScore(self):
|
||||
# Just to make sure it's there and returns a value.
|
||||
|
||||
90
External/pubchem_shape/test.cpp
vendored
90
External/pubchem_shape/test.cpp
vendored
@@ -1,16 +1,19 @@
|
||||
#include <catch2/catch_test_macros.hpp>
|
||||
#include <catch2/matchers/catch_matchers_floating_point.hpp>
|
||||
|
||||
#include <iostream>
|
||||
#include <sstream>
|
||||
#include <stdexcept>
|
||||
|
||||
#include <GraphMol/FileParsers/MolSupplier.h>
|
||||
#include <GraphMol/FileParsers/MolWriters.h>
|
||||
#include <GraphMol/FileParsers/FileParsers.h>
|
||||
#include <GraphMol/MolAlign/AlignMolecules.h>
|
||||
#include <GraphMol/MolTransforms/MolTransforms.h>
|
||||
#include <GraphMol/RWMol.h>
|
||||
|
||||
#include "PubChemShape.hpp"
|
||||
#include "GraphMol/SmilesParse/SmilesWrite.h"
|
||||
|
||||
using namespace RDKit;
|
||||
|
||||
@@ -83,11 +86,16 @@ TEST_CASE("basic alignment") {
|
||||
test_opt_param, test_max_preiters, test_max_postiters);
|
||||
CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(nbr_st2, 0.005));
|
||||
CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(nbr_ct2, 0.005));
|
||||
|
||||
for (auto i = 0u; i < probe->getNumAtoms(); ++i) {
|
||||
CHECK_THAT(cp.getConformer().getAtomPos(i).x,
|
||||
Catch::Matchers::WithinAbs(cp2.getConformer().getAtomPos(i).x,
|
||||
0.005));
|
||||
CHECK_THAT(
|
||||
cp.getConformer().getAtomPos(i).x,
|
||||
Catch::Matchers::WithinAbs(cp2.getConformer().getAtomPos(i).x, 0.05));
|
||||
CHECK_THAT(
|
||||
cp.getConformer().getAtomPos(i).y,
|
||||
Catch::Matchers::WithinAbs(cp2.getConformer().getAtomPos(i).y, 0.05));
|
||||
CHECK_THAT(
|
||||
cp.getConformer().getAtomPos(i).z,
|
||||
Catch::Matchers::WithinAbs(cp2.getConformer().getAtomPos(i).z, 0.05));
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -126,14 +134,15 @@ TEST_CASE("handling molecules with Hs") {
|
||||
REQUIRE(ref);
|
||||
auto probe = suppl[1];
|
||||
REQUIRE(probe);
|
||||
ShapeInputOptions mol1Opts, mol2Opts;
|
||||
SECTION("basics") {
|
||||
RWMol cp(*probe);
|
||||
std::vector<float> matrix(12, 0.0);
|
||||
auto [nbr_st, nbr_ct] =
|
||||
AlignMolecule(*ref, cp, matrix, -1, -1, test_use_colors, test_opt_param,
|
||||
test_max_preiters, test_max_postiters);
|
||||
CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.837, 0.005));
|
||||
CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.694, 0.005));
|
||||
CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.840, 0.005));
|
||||
CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.753, 0.005));
|
||||
for (auto i = 0u; i < cp.getNumAtoms(); ++i) {
|
||||
// the failure mode here was that Hs had HUGE coordinates
|
||||
auto pos = cp.getConformer().getAtomPos(i);
|
||||
@@ -253,17 +262,19 @@ $$$$
|
||||
auto [nbr_st, nbr_ct] =
|
||||
AlignMolecule(*ref, cp, matrix, refConfId, prbConfId, useColors,
|
||||
opt_param, preiters, postiters);
|
||||
CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.501, 0.005));
|
||||
CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.107, 0.005));
|
||||
|
||||
CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.483, 0.005));
|
||||
CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.046, 0.005));
|
||||
RWMol cp2(cp);
|
||||
auto [nbr_st2, nbr_ct2] =
|
||||
AlignMolecule(*ref, cp2, matrix, refConfId, prbConfId, useColors,
|
||||
opt_param, preiters, postiters);
|
||||
CHECK_THAT(nbr_st2, Catch::Matchers::WithinAbs(nbr_st2, 0.005));
|
||||
CHECK_THAT(nbr_ct2, Catch::Matchers::WithinAbs(nbr_ct2, 0.005));
|
||||
|
||||
CHECK_THAT(nbr_st2, Catch::Matchers::WithinAbs(nbr_st, 0.005));
|
||||
CHECK_THAT(nbr_ct2, Catch::Matchers::WithinAbs(nbr_ct, 0.005));
|
||||
|
||||
auto rmsd = MolAlign::CalcRMS(cp, cp2);
|
||||
CHECK_THAT(rmsd, Catch::Matchers::WithinAbs(0.017, 0.005));
|
||||
CHECK_THAT(rmsd, Catch::Matchers::WithinAbs(0.007, 0.005));
|
||||
}
|
||||
}
|
||||
|
||||
@@ -437,36 +448,14 @@ TEST_CASE("Shape-Shape alignment") {
|
||||
|
||||
std::vector<float> matrix(12, 0.0);
|
||||
auto [mol_st, mol_ct] = AlignMolecule(*ref, *probe, matrix, -1, -1);
|
||||
|
||||
auto [shape_st, shape_ct] = AlignShape(refShape, probeShape, matrix);
|
||||
|
||||
// Check that the same results are achieved when overlaying the probe
|
||||
// molecule onto the reference and the probe shape onto the reference shape
|
||||
|
||||
// molecule onto the reference molecule and the probe shape onto the reference
|
||||
// shape. The shapes are transformed to their centroid and principal axes, so
|
||||
// the final coords will not match. Just check the tanimotos.
|
||||
CHECK_THAT(shape_st, Catch::Matchers::WithinAbs(mol_st, 0.001));
|
||||
CHECK_THAT(shape_ct, Catch::Matchers::WithinAbs(mol_ct, 0.001));
|
||||
for (unsigned int i = 0; i < probe->getNumAtoms(); i++) {
|
||||
const auto &pos = probe->getConformer().getAtomPos(i);
|
||||
CHECK_THAT(pos.x, Catch::Matchers::WithinAbs(
|
||||
probeShape.coord[3 * i] - refShape.shift[0], 0.001));
|
||||
CHECK_THAT(pos.y,
|
||||
Catch::Matchers::WithinAbs(
|
||||
probeShape.coord[3 * i + 1] - refShape.shift[1], 0.001));
|
||||
CHECK_THAT(pos.z,
|
||||
Catch::Matchers::WithinAbs(
|
||||
probeShape.coord[3 * i + 2] - refShape.shift[2], 0.001));
|
||||
}
|
||||
|
||||
// Also check the TransformConformer function
|
||||
TransformConformer(refShape.shift, matrix, probeShape,
|
||||
probeCP.getConformer(-1));
|
||||
for (unsigned int i = 0; i < probe->getNumAtoms(); i++) {
|
||||
const auto &pos = probe->getConformer().getAtomPos(i);
|
||||
const auto &poscp = probeCP.getConformer().getAtomPos(i);
|
||||
CHECK_THAT(pos.x, Catch::Matchers::WithinAbs(poscp.x, 0.001));
|
||||
CHECK_THAT(pos.y, Catch::Matchers::WithinAbs(poscp.y, 0.001));
|
||||
CHECK_THAT(pos.z, Catch::Matchers::WithinAbs(poscp.z, 0.001));
|
||||
}
|
||||
}
|
||||
|
||||
TEST_CASE("Atoms excluded from Color features") {
|
||||
@@ -559,13 +548,13 @@ TEST_CASE("custom feature points") {
|
||||
double opt_param = 0.5;
|
||||
std::vector<float> matrix(12, 0.0);
|
||||
auto [st, ct] = AlignShape(shape2, shape3, matrix, opt_param);
|
||||
CHECK_THAT(st, Catch::Matchers::WithinAbs(0.997, 0.001));
|
||||
CHECK_THAT(ct, Catch::Matchers::WithinAbs(0.978, 0.001));
|
||||
CHECK_THAT(st, Catch::Matchers::WithinAbs(1.000, 0.001));
|
||||
CHECK_THAT(ct, Catch::Matchers::WithinAbs(0.997, 0.001));
|
||||
CHECK(shape3.coord[0] > 0); // x coord of first atom
|
||||
CHECK(shape3.coord[3 * 3] < 0); // x coord of fourth atom
|
||||
|
||||
auto conf = m2.getConformer(-1);
|
||||
TransformConformer(shape2.shift, matrix, shape3, conf);
|
||||
TransformConformer(shape2.shift, shape2.inertialRot, matrix, shape3, conf);
|
||||
CHECK(conf.getAtomPos(0).x > 0);
|
||||
CHECK(conf.getAtomPos(3).x < 0);
|
||||
}
|
||||
@@ -585,8 +574,8 @@ TEST_CASE("custom feature points") {
|
||||
std::vector<float> matrix(12, 0.0);
|
||||
auto [st, ct] =
|
||||
AlignMolecule(*m1, m2, matrix, opts2, opts3, -2, -2, opt_param);
|
||||
CHECK_THAT(st, Catch::Matchers::WithinAbs(0.997, 0.001));
|
||||
CHECK_THAT(ct, Catch::Matchers::WithinAbs(0.978, 0.001));
|
||||
CHECK_THAT(st, Catch::Matchers::WithinAbs(1.000, 0.001));
|
||||
CHECK_THAT(ct, Catch::Matchers::WithinAbs(0.997, 0.001));
|
||||
auto conf = m2.getConformer(-1);
|
||||
CHECK(conf.getAtomPos(0).x > 0);
|
||||
CHECK(conf.getAtomPos(3).x < 0);
|
||||
@@ -656,4 +645,21 @@ TEST_CASE("Score No Overlay") {
|
||||
CHECK_THAT(singleShape, Catch::Matchers::WithinAbs(0.3376, 0.0005));
|
||||
CHECK_THAT(singleColor, Catch::Matchers::WithinAbs(0.2674, 0.0005));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
TEST_CASE("Iressa onto Tagrisso") {
|
||||
// Conformations from PubChem produced by Omega. Iressa rotated and translated
|
||||
// by a random amount. PubChem puts them both in their inertial frame which
|
||||
// makes things too easy.
|
||||
auto tagrisso =
|
||||
"C=CC(=O)Nc1cc(Nc2nccc(-c3cn(C)c4ccccc34)n2)c(OC)cc1N(C)CCN(C)C |(-0.9161,3.8415,-2.9811;0.1848,3.1933,-2.588;0.1064,1.7789,-2.12;-0.9619,1.1797,-2.0847;1.3654,1.2872,-1.7553;1.6841,0.0144,-1.273;0.6638,-0.9235,-1.1146;0.9578,-2.1997,-0.6343;-0.0813,-3.1358,-0.4783;-1.4556,-2.9979,-0.1847;-2.1716,-4.1359,-0.1085;-3.4803,-3.9673,0.173;-4.0689,-2.7353,0.3728;-3.2269,-1.647,0.2676;-3.7311,-0.317,0.4568;-5.0275,0.0291,0.153;-5.1887,1.3569,0.4454;-6.4231,2.0889,0.2595;-4.0141,1.8811,0.9361;-3.7121,3.1796,1.3615;-2.4139,3.4249,1.8179;-1.4588,2.4106,1.8467;-1.7752,1.1164,1.4181;-3.0776,0.8453,0.9537;-1.9103,-1.7423,-0.011;2.2723,-2.5382,-0.3127;2.58,-3.7798,0.1575;2.539,-3.9651,1.571;3.2927,-1.6003,-0.4713;2.9986,-0.324,-0.9514;4.0475,0.61,-1.1047;4.7738,0.6956,-2.3546;4.4021,1.497,-0.0162;5.4401,0.8254,0.8736;5.8294,1.7155,1.9601;4.8213,1.7057,3.0218;7.1361,1.3324,2.4981)|"_smiles;
|
||||
REQUIRE(tagrisso);
|
||||
auto iressa =
|
||||
"COc1cc2ncnc(Nc3ccc(F)c(Cl)c3)c2cc1OCCCN1CCOCC1 |(11.4672,-0.467948,5.63989;12.0133,0.532631,6.49693;11.2039,1.5801,6.81985;11.2014,2.71958,6.00975;10.3926,3.81652,6.29699;10.4038,4.90395,5.50623;9.58889,5.91871,5.85946;8.76443,5.96486,6.91838;8.77814,4.86059,7.68868;7.92337,4.86224,8.81914;7.44878,5.8925,9.64622;8.22182,7.03851,9.85619;7.75051,8.06265,10.6777;6.50441,7.94546,11.2936;6.06567,8.93802,12.0809;5.72932,6.80403,11.0875;4.19056,6.65372,11.8447;6.20047,5.78015,10.2656;9.57161,3.74547,7.43436;9.56851,2.60328,8.25407;10.3868,1.52933,7.93769;10.3797,0.419365,8.74203;11.3064,0.402096,9.81907;10.7104,-0.399165,10.9685;9.40938,0.22121,11.4678;9.64205,1.59049,11.9223;8.38006,2.22985,12.3199;8.64991,3.65266,12.8011;9.56883,3.64192,13.8942;10.8103,3.05101,13.5078;10.5931,1.61394,13.0425)|"_smiles;
|
||||
REQUIRE(iressa);
|
||||
std::vector<float> matrix(12, 0.0);
|
||||
auto sims =
|
||||
AlignMolecule(*tagrisso, *iressa, matrix, -1, -1, true, 0.5, 10, 30);
|
||||
CHECK_THAT(sims.first, Catch::Matchers::WithinAbs(0.582, 0.005));
|
||||
CHECK_THAT(sims.second, Catch::Matchers::WithinAbs(0.092, 0.005));
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user