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Only apply transformation to reference centre when overlaying molecule onto molecule. (#8463)

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This commit is contained in:
David Cosgrove
2025-04-25 09:57:32 +01:00
committed by GitHub
parent 15e0f784b7
commit fee128300c
2 changed files with 48 additions and 7 deletions
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21
External/pubchem_shape/PubChemShape.cpp vendored
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@@ -400,12 +400,10 @@ std::pair<double, double> AlignMolecule(const ShapeInput &refShape, ROMol &fit,
fit.getNumAtoms(), matrix.data());
for (unsigned i = 0; i < fit.getNumAtoms(); ++i) {
// both conformers have been translated to the origin, translate the fit
// conformer back to the steric center of the reference.
RDGeom::Point3D &pos = fit_conformer.getAtomPos(i);
pos.x = transformed[i * 3] - refShape.shift[0];
pos.y = transformed[(i * 3) + 1] - refShape.shift[1];
pos.z = transformed[(i * 3) + 2] - refShape.shift[2];
pos.x = transformed[i * 3];
pos.y = transformed[(i * 3) + 1];
pos.z = transformed[(i * 3) + 2];
}
fit.setProp("shape_align_shape_tanimoto", nbr_st);
fit.setProp("shape_align_color_tanimoto", nbr_ct);
@@ -424,6 +422,15 @@ std::pair<double, double> AlignMolecule(const ROMol &ref, ROMol &fit,
DEBUG_MSG("Reference details:");
auto refShape = PrepareConformer(ref, refConfId, useColors);
return AlignMolecule(refShape, fit, matrix, fitConfId, useColors, opt_param,
max_preiters, max_postiters);
auto scores = AlignMolecule(refShape, fit, matrix, fitConfId, useColors,
opt_param, max_preiters, max_postiters);
// translate the fit conformer back to the steric center of the reference.
Conformer &fit_conformer = fit.getConformer(fitConfId);
for (unsigned i = 0; i < fit.getNumAtoms(); ++i) {
RDGeom::Point3D &pos = fit_conformer.getAtomPos(i);
pos.x -= refShape.shift[0];
pos.y -= refShape.shift[1];
pos.z -= refShape.shift[2];
}
return scores;
}

34
External/pubchem_shape/test.cpp vendored
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@@ -321,3 +321,37 @@ TEST_CASE("d2CutOff set") {
auto shape2 = PrepareConformer(*m1, -1, true);
CHECK(shape1.sov == shape2.sov);
}
TEST_CASE("Overlay onto shape bug (Github8462)") {
auto m1 =
"c1ccc(-c2ccccc2)cc1 |(-3.26053,-0.0841607,-0.741909;-2.93383,0.123873,0.593407;-1.60713,0.377277,0.917966;-0.644758,0.654885,-0.0378428;0.743308,0.219134,0.168663;1.82376,1.0395,-0.0112769;3.01462,0.695405,0.613858;3.18783,-0.589771,1.09649;2.15761,-1.50458,1.01949;0.988307,-1.1313,0.385783;-1.1048,0.797771,-1.34022;-2.39754,0.435801,-1.69921)|"_smiles;
REQUIRE(m1);
ROMol m2(*m1);
for (auto a : m2.atoms()) {
auto &pos = m2.getConformer().getAtomPos(a->getIdx());
pos.x += 3.0;
pos.y += 2.0;
}
ROMol m3(m2);
std::vector<float> matrix(12, 0.0);
auto [st, ct] = AlignMolecule(*m1, m2, matrix);
CHECK_THAT(st, Catch::Matchers::WithinAbs(1.0, 0.005));
CHECK_THAT(ct, Catch::Matchers::WithinAbs(1.0, 0.005));
for (unsigned int i = 0; i < m1->getNumAtoms(); ++i) {
auto pos1 = m1->getConformer().getAtomPos(i);
auto pos2 = m2.getConformer().getAtomPos(i);
CHECK_THAT((pos1 - pos2).length(), Catch::Matchers::WithinAbs(0.0, 0.005));
}
auto s1 = PrepareConformer(*m1, -1, true);
auto [st1, ct1] = AlignMolecule(s1, m3, matrix);
CHECK_THAT(st1, Catch::Matchers::WithinAbs(1.0, 0.005));
CHECK_THAT(ct1, Catch::Matchers::WithinAbs(1.0, 0.005));
for (unsigned int i = 0; i < m3.getNumAtoms(); ++i) {
RDGeom::Point3D pos1(s1.coord[3 * i], s1.coord[3 * i + 1],
s1.coord[3 * i + 2]);
auto pos2 = m3.getConformer().getAtomPos(i);
CHECK_THAT((pos1 - pos2).length(), Catch::Matchers::WithinAbs(0.0, 0.005));
}
}