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normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter (#8107)

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* normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter

* Update Code/GraphMol/Depictor/catch_tests.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* fix catch test

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
This commit is contained in:
Paolo Tosco
2024-12-18 13:40:57 +01:00
committed by GitHub
parent e589f173fd
commit 74fc77f959
2 changed files with 69 additions and 1 deletions
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5
Code/GraphMol/Depictor/RDDepictor.cpp
View File

@@ -1295,14 +1295,17 @@ double normalizeDepiction(RDKit::ROMol &mol, int confId, int canonicalize,
} }
} }
std::unique_ptr<RDGeom::Transform3D> canonTrans; std::unique_ptr<RDGeom::Transform3D> canonTrans;
auto ctd = MolTransforms::computeCentroid(conf);
if (canonicalize) { if (canonicalize) {
auto ctd = MolTransforms::computeCentroid(conf);
canonTrans.reset(MolTransforms::computeCanonicalTransform(conf, &ctd)); canonTrans.reset(MolTransforms::computeCanonicalTransform(conf, &ctd));
if (canonicalize < 0) { if (canonicalize < 0) {
RDGeom::Transform3D rotate90; RDGeom::Transform3D rotate90;
rotate90.SetRotation(0., 1., RDGeom::Point3D(0., 0., 1.)); rotate90.SetRotation(0., 1., RDGeom::Point3D(0., 0., 1.));
*canonTrans *= rotate90; *canonTrans *= rotate90;
} }
} else {
canonTrans.reset(new RDGeom::Transform3D());
canonTrans->SetTranslation(-ctd);
} }
bool isScaleFactorSane = (scaleFactor > SCALE_FACTOR_THRESHOLD); bool isScaleFactorSane = (scaleFactor > SCALE_FACTOR_THRESHOLD);
if (isScaleFactorSane && fabs(scaleFactor - 1.0) > SCALE_FACTOR_THRESHOLD) { if (isScaleFactorSane && fabs(scaleFactor - 1.0) > SCALE_FACTOR_THRESHOLD) {

65
Code/GraphMol/Depictor/catch_tests.cpp
View File

@@ -2272,3 +2272,68 @@ M END
*methotrexateAnalog, *methotrexate, -1, refPatt.get(), p); *methotrexateAnalog, *methotrexate, -1, refPatt.get(), p);
CHECK(match == expected); CHECK(match == expected);
} }
TEST_CASE("Normalize should always center in centroid, irrespective of canonicalize parameter") {
auto m = R"CTAB(
RDKit 2D
25 27 0 0 0 0 0 0 0 0999 V2000
18.2425 6.6594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.8948 6.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.3808 7.4101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.8817 7.3567 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
14.4692 5.9146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.7134 5.0766 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
13.0271 6.3270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.4395 7.7692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.7114 9.0806 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.7156 5.5989 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
10.4294 6.3705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.4545 7.8703 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.1179 5.6424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8316 6.4141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8568 7.9139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5705 8.6855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2591 7.9574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2339 6.4576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5202 5.6860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9728 8.7291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.0928 4.1426 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
17.2187 8.6543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.5602 10.0020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
18.7151 8.5507 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
17.6905 4.7294 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 1 6
5 7 1 0
7 8 1 0
8 9 2 0
7 10 1 6
10 11 1 0
11 12 2 0
11 13 1 0
13 14 1 0
14 15 2 0
15 16 1 0
16 17 2 0
17 18 1 0
18 19 2 0
17 20 1 0
13 21 1 6
3 22 1 1
22 23 2 0
22 24 1 0
2 25 1 0
6 2 1 0
8 4 1 0
19 14 1 0
M END)CTAB"_ctab;
REQUIRE(m);
RDDepict::normalizeDepiction(*m, -1, 0);
auto ctd = MolTransforms::computeCentroid(m->getConformer());
CHECK_THAT(ctd.x, Catch::Matchers::WithinAbs(0.0, 1.0e-4));
CHECK_THAT(ctd.y, Catch::Matchers::WithinAbs(0.0, 1.0e-4));
}