smallmol containing Hs

[z-linlinlin]

Use SmallMol to transform a molecule with 30 heavy atoms, in version 0.1.12, it retrurns: SmallMol with 30 atoms and 1 conformers
But when I updated the moleculekit version to 0.4.7 , it becomes : SmallMol with 52 atoms and 1 conformers

[z-linlinlin]

And I tried SmallMol(mol, fixHs=False, removeHs=True), it didn't work

[stefdoerr]

Hi, did you use force_reading by any chance?
Can you provide me with the molecule to test?

If it's a mol2 file you can also try directly with rdkit to see if it does the same:

from rdkit import Chem
mol = Chem.MolFromMol2File("mylig.mol2", removeHs=False)
mol.GetNumAtoms()

[z-linlinlin]

Here is a simple example:

import moleculekit.smallmol.smallmol as mk
import moleculekit.tools.voxeldescriptors as mk_voxel
from rdkit import Chem
from rdkit.Chem import AllChem
smiles = "CN"
mol = Chem.MolFromSmiles(smiles)
mol_H = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol_H)
mol_conformer = Chem.RemoveHs(mol_H)
smallmol = mk.SmallMol(mol_conformer, fixHs=False)
coords_mol = smallmol.get("coords")[:, :, 0]
channel_mol = mk_voxel.getChannels(smallmol)[0]
print(coords_mol.shape, channel_mol.shape)

I hope the channel_mol to be of shape (2, 8) as before, but I got (7, 8).

[stefdoerr]

Oh nice! You found a bug in copying of molecule. I'm fixing it now and will report once it's release in a new moleculekit version (in an hour or so hopefully).
Thanks a lot!

[stefdoerr]

Ok version 0.5.5 of moleculekit is out which should fix this. Give it a try and tell me if it worked for you

[z-linlinlin]

Ok version 0.5.5 of moleculekit is out which should fix this. Give it a try and tell me if it worked for you

It works well !
Thanks