Comments (9)
If we have new_to_old_atom_map
, we can do something like:
n_old_atoms = old_system.getNumParticles()
unique_old_atoms = [atom for atom in range(n_old_atoms) if atom not in new_to_old_atom_map.values()]
from perses.
Hm. OK. I think it would be useful to have convenient access to all the bits of information through TopologyProposal
, though:
new_to_old_atom_map
old_to_new_atom_map
old_atoms_to_be_deleted
old_core_atoms
new_atoms_to_be_added
new_core_atoms
etc. Maybe we can make TopologyProposal
a class that has methods/fields/properties to retrieve all of these, but they are computed as needed for convenience?
Would still maybe be useful to have the old topology in case we need to write PDB files of these transformations for debugging.
from perses.
I do generally agree that we should promote TopologyProposal
to a class, and that it should have some of those convenience attributes.
from perses.
There is a test that is failing because old_topology
is needed, I think. Not sure if critical or not.
from perses.
Ok... looking into this. I thought I had removed that dependency previously.
from perses.
Ok, these are the import problems I was talking about. I don't think the TopologyProposal
has been imported properly in the tests.
(https://travis-ci.org/choderalab/perses#L847)[this] looks like that problem.
There are also some API issues. I'm going to open a PR and promote the TopologyProposal
to a class now.
from perses.
Ah. topology_proposal
is both used as a module name (from perses.rjmc import topology_proposal
) and an object name.
Let me fix that.
from perses.
Oh! Sorry about that!
from perses.
Addressed by #27
from perses.
Related Issues (20)
- Integrate new atom mappers HOT 7
- Write initial initial and final structures in subdir
- AtomMapper fails when scaffolds have radicals HOT 1
- Creating legacy 0.10.x branch for longer term support -- main branch will become `gufe` refactor HOT 1
- Make sure we merge latest 0.10 branch before working on 0.11 refactor
- perses with mpi HOT 1
- Duplicate instances of `self._setup_complex_phase()` in relative_setup.py HOT 2
- Make `offline-freq` be the same as `checkpoint_interval` by default HOT 1
- Migrate from PDB to PDBx/mmcif HOT 1
- Protein mutation protocol for alchemiscale HOT 1
- Adapt MPi example with perses at least for protein mutation HOT 1
- Fix potential bug in counterion implementation: get_water_indices()
- Allow user to specify list of atom indices to override default behavior for selecting the REST region
- Support for use of custom force fields (e.g., one generated from openff-bespokefit) HOT 5
- Error with spectator ligands HOT 8
- Allow specification of mapping dictionary in the pipeline
- Update README? HOT 1
- Retrieving exact topology used for an endpoint in a relative transformation HOT 11
- Improved reporting and state detection when passing tautomers as `old_residue`
- IndexError with `_vacdg_history` if there is no vacuum trajectory HOT 3
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from perses.