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Added JSON parameters to MinimalLib get_(cx)?sm(ile|art)s() functions (#7194)

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* - renamed getParamsFromJSON() to updateSmilesWriteParamsFromJSON() and moved it from the anonymous namespace to the RDKit namespace such that it is publicly available
- implemented updateCXSmilesFieldsAndRestoreBondDirOptionFromJSON()
- added CFFI and JS tests
- get_smiles(), get_smarts(), get_cxsmiles() and get_cxsmarts() are now available in MinimalLib in both CFFI and JS layers and they can be passed JSON parameters
- CFFI get_qmol() now returns NULL if it fails to generate a RWMol rather than returning the "Error!" const char[] string, for consistency with what get_mol() and get_rxn() do. This was documented in release notes

* suggestions

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
This commit is contained in:
Paolo Tosco
2024-04-18 06:28:36 +02:00
committed by GitHub
parent a087cfd894
commit 2bb8952d7b
10 changed files with 529 additions and 106 deletions
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96
Code/MinimalLib/tests/tests.js
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@@ -2807,6 +2807,101 @@ function test_assign_cip_labels() {
}
}
function test_smiles_smarts_params() {
{
const amoxicillinPubChem = 'CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](C3=CC=C(C=C3)O)N)C(=O)O)C';
const mol = RDKitModule.get_mol(amoxicillinPubChem);
{
const canonicalSmiles = mol.get_smiles();
assert(canonicalSmiles === 'CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccc(O)cc3)C(=O)N2[C@H]1C(=O)O');
}
['{}', ''].forEach((emptyJson) => {
const canonicalSmiles = mol.get_smiles(emptyJson);
assert(canonicalSmiles === 'CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccc(O)cc3)C(=O)N2[C@H]1C(=O)O');
});
const nonCanonicalSmiles = mol.get_smiles(JSON.stringify({canonical: false}));
assert(nonCanonicalSmiles === 'CC1(C)[C@H](C(=O)O)N2[C@H](S1)[C@H](NC(=O)[C@@H](c1ccc(O)cc1)N)C2=O');
const canonicalSmilesNoStereo = mol.get_smiles(JSON.stringify({doIsomericSmiles: false}));
assert(canonicalSmilesNoStereo === 'CC1(C)SC2C(NC(=O)C(N)c3ccc(O)cc3)C(=O)N2C1C(=O)O');
const nonCanonicalSmilesNoStereo = mol.get_smiles(JSON.stringify({doIsomericSmiles: false, canonical: false}));
assert(nonCanonicalSmilesNoStereo === 'CC1(C)C(C(=O)O)N2C(S1)C(NC(=O)C(c1ccc(O)cc1)N)C2=O');
mol.delete();
}
{
const bicyclo221heptane = `
RDKit 2D
9 10 0 0 1 0 0 0 0 0999 V2000
-2.8237 -1.3088 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.5723 -0.3996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5723 1.1473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1011 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3701 1.1474 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3701 -0.3995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6217 -1.3087 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.1009 -0.8775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8083 0.3739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1
2 3 1 0
4 3 1 0
4 5 1 0
6 5 1 0
6 7 1 1
6 8 1 0
8 9 1 1
8 2 1 0
4 9 1 1
M END
`;
const mol = RDKitModule.get_mol(bicyclo221heptane, JSON.stringify({useMolBlockWedging: true}));
{
const canonicalCXSmiles = mol.get_cxsmiles();
const [_, canonicalSmiles, wedging] = canonicalCXSmiles.match(/^(\S+) \|\([^\)]+\),([^\|]+)\|$/);
assert(canonicalSmiles === 'N[C@@H]1C[C@@H]2C[C@H]1[C@@H](O)C2');
assert(wedging === 'wD:3.9,wU:1.0,5.4,6.7');
}
['{}', ''].forEach((emptyJson) => {
const canonicalCXSmiles = mol.get_cxsmiles(emptyJson);
const [_, canonicalSmiles, wedging] = canonicalCXSmiles.match(/^(\S+) \|\([^\)]+\),([^\|]+)\|$/);
assert(canonicalSmiles === 'N[C@@H]1C[C@@H]2C[C@H]1[C@@H](O)C2');
assert(wedging === 'wD:3.9,wU:1.0,5.4,6.7');
});
{
const canonicalCXSmiles = mol.get_cxsmiles(JSON.stringify({restoreBondDirOption: 'RestoreBondDirOptionTrue'}));
const [_, canonicalSmiles, wedging] = canonicalCXSmiles.match(/^(\S+) \|\([^\)]+\),([^\|]+)\|$/);
assert(canonicalSmiles === 'N[C@@H]1C[C@@H]2C[C@H]1[C@@H](O)C2');
assert(wedging === 'wU:1.0,3.3,5.4,6.7');
}
{
const nonCanonicalCXSmilesNoStereo = mol.get_cxsmiles(JSON.stringify({doIsomericSmiles: false, canonical: false, CX_ALL_BUT_COORDS: true}));
assert(nonCanonicalCXSmilesNoStereo === 'OC1CC2CC(N)C1C2');
const nonCanonicalCXSmilesNoStereoAtomProp = `${nonCanonicalCXSmilesNoStereo} |atomProp:1.atomProp.1&#46;234|`;
const molWithAtomProp = RDKitModule.get_mol(nonCanonicalCXSmilesNoStereoAtomProp);
assert(molWithAtomProp);
const cxSmilesWithAtomProp = molWithAtomProp.get_cxsmiles(JSON.stringify({CX_ALL_BUT_COORDS: true}));
assert(cxSmilesWithAtomProp === 'NC1CC2CC(O)C1C2 |atomProp:5.atomProp.1&#46;234|');
molWithAtomProp.delete();
}
mol.delete();
}
{
const chiralQuery = RDKitModule.get_qmol('N-[C@H](-C(-O)=O)-C(-C)-C');
assert(chiralQuery.get_smarts() === 'N-[C@&H1](-C(-O)=O)-C(-C)-C');
['', '{}'].forEach((emptyJson) => {
assert(chiralQuery.get_smarts(emptyJson) === 'N-[C@&H1](-C(-O)=O)-C(-C)-C');
});
assert(chiralQuery.get_smarts(JSON.stringify({doIsomericSmiles: false})) === 'N-[C&H1](-C(-O)=O)-C(-C)-C');
}
{
const chiralQuery = RDKitModule.get_qmol('N-[C@H](-C(-O)=O)-C(-C)-C |atomProp:1.atomProp.1&#46;234|');
assert(chiralQuery.get_cxsmarts() === 'N-[C@&H1](-C(-O)=O)-C(-C)-C |atomProp:1.atomProp.1&#46;234|');
['', '{}'].forEach((emptyJson) => {
assert(chiralQuery.get_cxsmarts(emptyJson) === 'N-[C@&H1](-C(-O)=O)-C(-C)-C |atomProp:1.atomProp.1&#46;234|');
});
assert(chiralQuery.get_cxsmarts(JSON.stringify({doIsomericSmiles: false})) === 'N-[C&H1](-C(-O)=O)-C(-C)-C |atomProp:1.atomProp.1&#46;234|');
}
}
initRDKitModule().then(function(instance) {
var done = {};
const waitAllTestsFinished = () => {
@@ -2881,6 +2976,7 @@ initRDKitModule().then(function(instance) {
test_get_sss_json();
test_relabel_mapped_dummies();
test_assign_cip_labels();
test_smiles_smarts_params();
waitAllTestsFinished().then(() =>
console.log("Tests finished successfully")
);