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Properties are not extracted from SDF files #489
Description
Describe the bug
I am trying to ingest an SDF file with RDKit JS and am running into an issue where the properties tagged on an SDF file are missing
To Reproduce
Consider the following code:
const molString = `
ww csweb09162414372D 0 0.00000 0.00000
9 9 0 0 0 0 0 0 0 0999 V2000
137.0000 319.8763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
108.1690 305.9919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
101.0483 274.7943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
121.0000 249.7757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
153.0000 249.7757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
172.9517 274.7943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
165.8310 305.9919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
242.0000 338.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
280.0000 298.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
1 7 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
M END
> <some_property>
0
> <PUBCHEM_COMPONENT_COUNT>
1
$$$$
`
const mol = window.RDKit.get_mol("\n" + molSDF + "$$$$\n");
const keys: string[] = mol.get_prop_list();
const metadata = {};
for (var key in keys) {
console.log("mol." + key + " = " + mol.get_prop(key));
metadata[key] = mol.get_prop(key);
}
console.log(metadata);
Expected behavior
I would expect to see the properties "some_property" and "PUBCHEM_COMPONENT_COUNT", but instead these are missing.
Screenshots
Output of metadata in the example:
Version
This issue was noticed in RDKit version: 2024.03.5
Additional context
This is maybe medium priority for me, my current workaround is just to manually extract the properties outside of RDKit. It would be nice to update get_mol but it would also be even more useful to export functionality from Chem.SDMolSupplier as defined here: https://www.rdkit.org/docs/GettingStartedInPython.html#reading-sets-of-molecules
Activity
ptosco commentedon Sep 17, 2024
This is not a bug.
get_molwill only parse the molblock up to theM ENDtag, as it mimics the functionality of the Python functionChem.MolFromMolBlockrather than fromChem.SDMolSupplier.nishanthmerwin commentedon Sep 17, 2024
@ptosco is there an alternative in rdkitjs that would allow me to get the properties?
ptosco commentedon Sep 17, 2024
No, at the moment there isn’t one.