mda equivalent of Rdkit's addHs

[corey-taylor2]

G'day all,

Looking to extract a ligand and surrounding residues from a Universe but then to cap valences in a manner similar to Rdkit's addHs module to feed into some qchem workflows. Directly saving the selection as a pdb shows there are indeed unsatisfied valences.

I've Googled and searched and can't find a way to do this, so either it's so blindingly obvious that this topic will prove a useful reminder to others.... Or it's not as straightforward as I'd like it to be. Anyone have some code laying around to achieve my dreams? Cheers all.

[hmacdope]

You can use the RDKit converter to go directly to RDKit and then add the Hs there!

from rdkit import Chem
import MDAnalysis as mda
u = mda.Universe("protein.pdb")
atoms = u.select_atoms("name CA")
rdkit_mol = atoms.convert_to("RDKIT")
# do whatever you like in RDKit.

[corey-taylor2]

Sounds reasonable, thanks. I assume the conversion retains 3D coords I can convert into .xyz?

[hmacdope]

Yep should work!

[orbeckst]

@corey-taylor2 if this works for you, can you mark @hmacdope 's answer as this will help other readers, too (and I am sure it will make @hmacdope happy)? If it doesn't work, let us know why, that's also valuable feedback!

[corey-taylor2]

Yup, done!