2021-05-27 Wagner/Pulido/Wang Check in

Task updates

• Update Trello – Remove AM1 and conformer-atom-order-dependent stuff?

  • IP will keep conformer-atom-order-dependence stuff, JW will take over AM1 stuff.

• Update on progress + working session

• Substructure matching performance update – Possibly issues with some residues, but possible it’s a bug in SMARTS generation method

  • Started debugging, may be complex. We can return to this later in the meeting if there’s time.

  • The problem was that some SDFs have the guanidinium double bond between the C and the nonterminal N

• LYS_LFOH may be mislabeled re: leaving atoms

  • (This isn’t really mis-labeled, but there aren’t any entries that are have the “main chain” variant of AAs with peprotonated side chains, so we had to make a manual workaround for those)

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Update on PDB/PDBx reader

• JW – OpenMM seems to have a way to assign connectivity by atom name

  • JW – It turns out that openMM will ASSIGN bonds to PDB files that follow standard residues. We can use this to perceive the CONECT records, and with a hack to the underlying code, we can make openMM write out PDBs with conect records for all atoms. But, since we already have OpenMM as a toolkit dependency, we can just use the PDB reader directly, without needing to write a non-spec “PDB-with-all-CONECT-records” file.

• LW – A few weeks ago, I tried to use OpenMM’s PDB reader, but when I named atoms according to their element and listed all bonds explicitly as CONECT, OpenMM added ADDITIONAL bonds. This problem went away when I renamed the atoms.

• Using LW’s example PDB, with CONECT records for everything but the AHA residue stripped:

from simtk.openmm.app import PDBFile, PDBxFile
pdb = PDBFile('aha.pdb')
print([*pdb.topology.bonds()][-50:])

This shows that all the standard AA have bonds assigned (even without CONECT records), while the nonstandard AHA residue has bonds read from the CONECT records. This is good news – It means that we can load PDBs with nonstandard AAs and use networkx graph matching to assign bond orders and stuff!