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Fixes #7509 (#7513)

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* add a test

* scale pseudo 3d offset

* update inchi test

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
This commit is contained in:
Ricardo Rodriguez
2024-06-13 23:39:48 -04:00
committed by GitHub
parent ea6fbeec30
commit d6171aaade
3 changed files with 55 additions and 8 deletions
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13
Code/GraphMol/Chirality.cpp
View File

@@ -477,8 +477,16 @@ std::optional<Atom::ChiralType> atomChiralTypeFromBondDirPseudo3D(
auto centerLoc = conf->getAtomPos(atom->getIdx());
centerLoc.z = 0.0;
auto refPt = conf->getAtomPos(bondAtom->getIdx());
// Github #7305: in some odd cases, we get conformers with
// weird scalings. In these, we need to scale the 3d offset
// or it might be irrelevant or dominate over the coordinates.
auto refLength = (centerLoc - refPt).length();
refPt.z =
bondDir == Bond::BondDir::BEGINWEDGE ? pseudo3DOffset : -pseudo3DOffset;
if (refLength) {
refPt.z *= refLength;
}
//----------------------------------------------------------
//
@@ -512,9 +520,14 @@ std::optional<Atom::ChiralType> atomChiralTypeFromBondDirPseudo3D(
if (nbrBond->getBeginAtomIdx() == atom->getIdx() &&
(nbrBond->getBondDir() == Bond::BondDir::BEGINWEDGE ||
nbrBond->getBondDir() == Bond::BondDir::BEGINDASH)) {
// scale the 3d offset based on the reference bond here too
tmpPt.z = nbrBond->getBondDir() == Bond::BondDir::BEGINWEDGE
? pseudo3DOffset
: -pseudo3DOffset;
if (refLength) {
tmpPt.z *= refLength;
}
} else {
tmpPt.z = 0;
}

36
Code/GraphMol/catch_chirality.cpp
View File

@@ -5840,4 +5840,40 @@ M END
CHECK(mol->getBondWithIdx(13)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW);
}
}
TEST_CASE(
"GitHub #7509: atomChiralTypeFromBondDirPseudo3D fails for poorly scaled molecular coordinates") {
auto m = R"CTAB(
RDKit 2D
5 4 0 0 0 0 0 0 0 0999 V2000
-2.0785 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7794 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5196 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8187 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5196 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 1
3 5 1 0
M END
)CTAB"_ctab;
REQUIRE(m);
auto at = m->getAtomWithIdx(2);
REQUIRE(at->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW);
auto &pos = m->getConformer().getPositions();
std::for_each(pos.begin(), pos.end(),
[](RDGeom::Point3D &pos) { pos *= 6.0; });
// Reset chirality and the original bond direction
// (it was stripper after parsing m for the first time)
at->setChiralTag(Atom::ChiralType::CHI_UNSPECIFIED);
m->getBondBetweenAtoms(2, 3)->setBondDir(Bond::BondDir::BEGINWEDGE);
MolOps::assignChiralTypesFromBondDirs(*m);
CHECK(at->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW);
}

14
rdkit/Chem/UnitTestInchi.py
View File

@@ -37,14 +37,12 @@ import re
import unittest
from rdkit import RDConfig, RDLogger
from rdkit.Chem import (INCHI_AVAILABLE, ForwardSDMolSupplier, MolFromMolBlock,
MolFromSmiles, MolToMolBlock, MolToSmiles, SanitizeMol,
rdDepictor)
from rdkit.Chem import (INCHI_AVAILABLE, ForwardSDMolSupplier, MolFromMolBlock, MolFromSmiles,
MolToMolBlock, MolToSmiles, SanitizeMol, rdDepictor)
if INCHI_AVAILABLE:
from rdkit.Chem import (InchiReadWriteError, InchiToInchiKey,
MolBlockToInchi, MolFromInchi, MolToInchi,
MolToInchiKey)
from rdkit.Chem import (InchiReadWriteError, InchiToInchiKey, MolBlockToInchi, MolFromInchi,
MolToInchi, MolToInchiKey)
COLOR_RED = '\033[31m'
COLOR_GREEN = '\033[32m'
@@ -167,9 +165,9 @@ class TestCase(unittest.TestCase):
fmt = "\n{0}InChI write Summary: {1} identical, {2} suffix variance, {3} reasonable{4}"
print(fmt.format(COLOR_GREEN, same, diff, reasonable, COLOR_RESET))
self.assertEqual(same, 1160)
self.assertEqual(same, 1162)
self.assertEqual(diff, 0)
self.assertEqual(reasonable, 21)
self.assertEqual(reasonable, 19)
def test1InchiReadPubChem(self):
for f in self.dataset.values():