moleculekit
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Acellera
MoleculeKit: Your favorite molecule manipulation kit
This returns a smallmol object with Hydrogens ` SmallMolLib(reflig_sdf, removeHs=True)[0]` This returns a smallmol object without hydrogens: ` SmallMolLib(reflig_sdf, removeHs=True, fixHs=False)[0]` fixHs is by default set to True, so hydrogens...
Current fingerprint does not take chirality into account. This needs to be updated in the following location: return AllChem.GetHashedMorganFingerprint(self._mol, radius, num_bits) to return AllChem.GetHashedMorganFingerprint(self._mol, radius, num_bits, useChirality=True)
The current pip doesn't like the package's metadata: pip install moleculekit results in [...] has inconsistent version: filename has '1.2.0', but metadata has '0' The explanation [may be](https://stackoverflow.com/questions/67074684/pip-has-problems-with-metadata) in the...
I should add a database of residues including full bond information and names
Right now it has a very limited list of residues. I should add a database of protein residues to moleculekit with full bond/type/atomnames information so that I can detect dihedrals...
 On some systems the HIS residues had HD1 and HD2 atoms which is incorrect. teLeap then tries to convert the residues to HIE and fails due to the HD1...
Whenever I run getVoxelDescriptors I got OpenBabel warning. I tried to install the older version of OpenBabel but it's deprecated, so I stick with the newest one. 
@Acellera/maciej mentioned that it would be nice to be able to flip a residue's sidechain at will to improve hydrogen networking when there are ligands involved, which proteinPrepare does not...
```python from moleculekit.smallmol.smallmol import SmallMol sm = SmallMol('CCOO') sm.generateConformers(10) for i in range(10): sm.write(f'/tmp/stefan{i}.pdb', frames=i) ``` crashes with ```pytb NameError Traceback (most recent call last) in 1 for i in...