General updates | JM – JW – Welcome back, please fill in your clockifys for June BW folded in the QCSubmit 2d torsiondrive vignette into the result retrieval example Re: PDB loading PEastman is updating PDBFixer to load noncanonical amino acids using the CCD as a reference. Could be cool to include that in the current project if automatable https://github.com/openmm/pdbfixer/pull/295/files JM – Cool, I’ll check this out. JW – Awesome. If it gets hairy this isn’t a “must”, but it would be great to test this out and give PEastman feedback during the implementation phase
I’m refactoring our substructure library code to work for NAs, and be more straightforward. Going from PDB → SDF using… the MDAnalysis guesser is actually kinda good. Pretty quick and seems to get stuff right. JM – Redundant with PDBFixer? JW – We may need H assignment from PDBFixer. JM – Kinda overlapping domains though. I’ll think about this.
import MDAnalysis as mda
from rdkit.Chem import rdmolops
u = mda.Universe('../../examples/toolkit_showcase/5tbm_prepared.pdb', guess_bonds=True)
rdmol = u.atoms.convert_to('RDKit', force=True)the RDKit guesser is bad, since it 1) requires total charge and 2) never finished for a 100AA protein
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