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add clearPropertyCache() (#8533)

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This commit is contained in:
Greg Landrum
2025-05-18 08:14:05 +02:00
committed by GitHub
parent 440171cb1d
commit 9d4afd0e08
8 changed files with 59 additions and 11 deletions
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5
Code/GraphMol/Atom.cpp
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@@ -742,6 +742,11 @@ bool Atom::needsUpdatePropertyCache() const {
(this->df_noImplicit || this->d_implicitValence >= 0));
}
void Atom::clearPropertyCache() {
d_explicitValence = -1;
d_implicitValence = -1;
}
// returns the number of swaps required to convert the ordering
// of the probe list to match the order of our incoming bonds:
//

1
Code/GraphMol/Atom.h
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@@ -345,6 +345,7 @@ class RDKIT_GRAPHMOL_EXPORT Atom : public RDProps {
void updatePropertyCache(bool strict = true);
bool needsUpdatePropertyCache() const;
void clearPropertyCache();
//! calculates and returns our explicit valence
/*!

6
Code/GraphMol/ROMol.cpp
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@@ -604,6 +604,12 @@ bool ROMol::needsUpdatePropertyCache() const {
return false;
}
void ROMol::clearPropertyCache() {
for (auto atom : atoms()) {
atom->clearPropertyCache();
}
}
const Conformer &ROMol::getConformer(int id) const {
// make sure we have more than one conformation
if (d_confs.size() == 0) {

1
Code/GraphMol/ROMol.h
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@@ -765,6 +765,7 @@ class RDKIT_GRAPHMOL_EXPORT ROMol : public RDProps {
void updatePropertyCache(bool strict = true);
bool needsUpdatePropertyCache() const;
void clearPropertyCache();
//! @}

4
Code/GraphMol/Wrap/Atom.cpp
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@@ -458,6 +458,10 @@ struct atom_wrapper {
"Returns true or false depending on whether implicit and explicit "
"valence of the molecule have already been calculated.\n\n")
.def("ClearPropertyCache", &Atom::clearPropertyCache,
(python::arg("self")),
"Clears implicit and explicit valence information.\n\n")
.def("GetMonomerInfo", AtomGetMonomerInfo,
python::return_internal_reference<
1, python::with_custodian_and_ward_postcall<0, 1>>(),

5
Code/GraphMol/Wrap/Mol.cpp
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@@ -767,6 +767,11 @@ struct mol_wrapper {
"explicit "
"valence of the molecule have already been calculated.\n\n")
.def(
"ClearPropertyCache", &ROMol::clearPropertyCache,
(python::arg("self")),
"Clears implicit and explicit valence information from all atoms.\n\n")
.def("GetStereoGroups", &ROMol::getStereoGroups,
"Returns a list of StereoGroups defining the relative "
"stereochemistry "

34
Code/GraphMol/Wrap/rough_test.py
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@@ -1797,20 +1797,22 @@ M END
child_bonds = bonds[1:]
self.assertEqual(len(list(bond.GetStereoAtoms())), 2)
bond.SetStereo(Chem.BondStereo.STEREOTRANS)
for isomer in self.recursive_enumerate_stereo_bonds(mol, done_bonds + [Chem.BondStereo.STEREOTRANS],
for isomer in self.recursive_enumerate_stereo_bonds(mol,
done_bonds + [Chem.BondStereo.STEREOTRANS],
child_bonds):
yield isomer
self.assertEqual(len(list(bond.GetStereoAtoms())), 2)
bond.SetStereo(Chem.BondStereo.STEREOCIS)
for isomer in self.recursive_enumerate_stereo_bonds(mol, done_bonds + [Chem.BondStereo.STEREOCIS],
for isomer in self.recursive_enumerate_stereo_bonds(mol,
done_bonds + [Chem.BondStereo.STEREOCIS],
child_bonds):
yield isomer
def testBondSetStereoDifficultCase(self):
origVal = Chem.GetUseLegacyStereoPerception()
Chem.SetUseLegacyStereoPerception(False)
unspec_smiles = "CCC=CC(CO)=C(C)CC"
mol = Chem.MolFromSmiles(unspec_smiles)
Chem.FindPotentialStereoBonds(mol)
@@ -1839,7 +1841,6 @@ M END
self.assertEqual(len(isomers), 4)
Chem.SetUseLegacyStereoPerception(origVal)
def getNumUnspecifiedBondStereo(self, smi):
mol = Chem.MolFromSmiles(smi)
Chem.FindPotentialStereoBonds(mol)
@@ -1847,7 +1848,7 @@ M END
count = 0
for bond in mol.GetBonds():
if bond.GetStereo() != Chem.BondStereo.STEREONONE:
print(bond.GetIdx(),bond.GetStereo())
print(bond.GetIdx(), bond.GetStereo())
if bond.GetStereo() == Chem.BondStereo.STEREOANY:
count += 1
@@ -5370,15 +5371,15 @@ width='200px' height='200px' >
self.assertEqual(atom0.GetChiralTag(), Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)
def testAssignStereochemistryFrom3D(self):
def _stereoTester(mol, expectedTag, expectedStereo):
Chem.AssignStereochemistryFrom3D(mol)
self.assertEqual(mol.GetNumAtoms(), 9)
self.assertEqual(mol.GetNumAtoms(), 9)
self.assertEqual(mol.GetAtomWithIdx(1).GetChiralTag(), expectedTag)
self.assertEqual(mol.GetBondWithIdx(3).GetStereo(), expectedStereo)
origVal = Chem.GetUseLegacyStereoPerception()
for useLegacy in (True,False):
for useLegacy in (True, False):
Chem.SetUseLegacyStereoPerception(useLegacy)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'test_data', 'stereochem.sdf')
@@ -8117,8 +8118,9 @@ M END
'ferrocene.mol')
femol = Chem.MolFromMolFile(fefile)
newfemol = Chem.rdmolops.HapticBondsToDative(femol)
self.assertEqual(Chem.MolToSmiles(newfemol),
'[cH]12->[Fe+2]3456789(<-[cH]1[cH]->3[cH-]->4[cH]->52)<-[cH]1[cH]->6[cH]->7[cH-]->8[cH]->91')
self.assertEqual(
Chem.MolToSmiles(newfemol),
'[cH]12->[Fe+2]3456789(<-[cH]1[cH]->3[cH-]->4[cH]->52)<-[cH]1[cH]->6[cH]->7[cH-]->8[cH]->91')
def test_DativeBondsToHaptic(self):
fefile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolStandardize', 'test_data',
@@ -8382,7 +8384,17 @@ M END
m.GetAtomWithIdx(1).SetChiralTag(Chem.CHI_UNSPECIFIED)
Chem.CleanupStereoGroups(m)
self.assertEqual(len(m.GetStereoGroups()), 0)
def testClearPropertyCache(self):
m = Chem.MolFromSmiles("CC")
self.assertFalse(m.NeedsUpdatePropertyCache())
for atom in m.GetAtoms():
self.assertFalse(atom.NeedsUpdatePropertyCache())
m.ClearPropertyCache()
self.assertTrue(m.NeedsUpdatePropertyCache())
for atom in m.GetAtoms():
self.assertTrue(atom.NeedsUpdatePropertyCache())
if __name__ == '__main__':
if "RDTESTCASE" in os.environ:

14
Code/GraphMol/catch_graphmol.cpp
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@@ -4823,3 +4823,17 @@ TEST_CASE("stereogroups operator<<") {
CHECK(oss.str() == "AND rId: 0 wId: 0 bonds: { 7 }");
}
}
TEST_CASE("clearPropertyCache") {
auto m = "CC"_smiles;
REQUIRE(m);
CHECK(!m->needsUpdatePropertyCache());
for (const auto atom : m->atoms()) {
CHECK(!atom->needsUpdatePropertyCache());
}
m->clearPropertyCache();
CHECK(m->needsUpdatePropertyCache());
for (const auto atom : m->atoms()) {
CHECK(atom->needsUpdatePropertyCache());
}
}