Comments (4)
I assume here we need it to be both the topology & coordinates?
How about AlchemicalSystem
? (unless we don't want to have the full system environment here? although long term we will need to support proteins to allow for side chain mutations)
How about:
AtomMapping
-> easily to obtain core, appearing, and disappearing atoms- Two interchange objects for each state?
- Since the API isn't very mature, short term: either two OpenMM
System
objects or two ParmedStructure
objects? (maybe we should just jump the gun early here and go directly with the interchange API rather than waste time implementing a temporary solution?)
- Since the API isn't very mature, short term: either two OpenMM
from openfe.
What does this add beyond AtomMapping
, since AtomMapping
now includes the 2x Molecule
? Does this still need to be an additional object?
from openfe.
I think this isn't required since the Mapping got beefed up a little. I think AtomMapping
is enough for edge descriptions.
from openfe.
Moving to done as a "not going to do" -- we no longer see this as necessary.
from openfe.
Related Issues (20)
- Frequent "Should have \sum_n W_nk = 1" errors in analysis HOT 4
- Add a warning/note in the setup that protein inputs may need to be equilibrated before running RBFE? HOT 1
- Get macos-12+, including osx-arm64 (i.e. macos-latest) runners working in CI HOT 1
- [docs] Showcase notebook failing to render HOT 2
- Unpin rdkit on mypy HOT 3
- Run through tutorial using 1.0 release HOT 3
- mark gaff tests as xfail HOT 1
- [docs] find new home for `OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb` example
- Using customized force field for small molecules HOT 8
- raise a warning if a user supplies an unsupported key in a settings yaml
- CalledProcessError: 9 HOT 2
- Fix OpenFE tests to match main on Lomap
- Validate OpenFE working on latest of our key tools
- Add rever instructions to release instructions in the wiki
- Add install instructions for the conda lock files
- Issue with PyMBAR4
- Using OPC water models for RBFE calculations HOT 1
- Using other versions of small ligand ff (GAFF) instead of the default one HOT 1
- [CLI] inspect command for json output files
- Review zenodo authors
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