Preserve residue IDs, insertion codes, and bond orders in OpenMM topology conversions #1316
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added 2 commits
September 11, 2023 17:35
swails
reviewed
Sep 12, 2023
| order = n | ||
| top.addBond( | ||
| atoms[bond.atom1.idx], atoms[bond.atom2.idx], type=type, order=order | ||
| ) |
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I've also recently added a qualitative_type that is basically a translation of the RDKit bond types. Not sure if that would be useful here or not.
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Hmm... maybe. Would it make sense to add
qualitative_type = None
if b.type is not None:
name = repr(b.type).upper()
if hasattr(QualitativeBondType, name):
qualitative_type = getattr(QualitativeBondType, name)to parmed.openmm.load_topology(), and do something like
type = None
if bond.qualitative_type is not None:
name = bond.qualitative_type.name.lower().capitalize()
if hasattr(app, name):
t = getattr(app, name)
if t in bond_orders_by_openmm_type: # ensure t is a recognized type
type = t
else: # try determining the type from the bond order
for t, o in bond_orders_by_openmm_type.items():
if math.isclose(bond.order, o):
type = tin Structure.topology.getter()?
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I'm tempted to say let's hold off on that until and unless it proves useful, and let's just get this change merged.
|
The build failures are fixed in #1315, so once that is merged this can be rebased and should run to completion. The failures are a result of downstream updates in dependencies (scipy, AmberTools, and OpenMM). |
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This PR modifies
parmed.openmm.load_topology()andStructure.topology.getter()in order to preserve additional topology information.Changes to
parmed.openmm.load_topology():idis the string representation of an integer, set the corresponding ParmEd residuenumberto that integer.insertion_code<- OpenMM residueinsertionCodetypedata, use it to set the corresponding ParmEd bondorder. Otherwise, use the OpenMM bondorder(converted to a float).Changes to
Structure.topology.getter():id<- string representation of ParmEd residuenumberinsertionCode<- ParmEd residueinsertion_codeorderto determine OpenMM bondtypeandorder.