Comments (8)
Going to hold off on this for now. I'm looking at the openmoltools travis but I'm not really sure what happened there (where did those environment variables with the encrypted key come from? they aren't defined in the part below. Why not define them like the binstar token?). I'd play around myself, but I don't want to do anything that breaks the license terms.
from perses.
I can add those! Unfortunately they don't work in pull requests from forks, only branches of the main repo. Do we still want to do that?
from perses.
Ok. Maybe it would be better/easier to skip the tests if they involve openeye. Either way is fine with me.
from perses.
Are the OpenEye tools required for most of the interesting functionality? Or just some of it? We can definitely skip the tests in the same way openmoltools does if we think testing would still be useful.
from perses.
They're required for some of the earlier stuff that we wrote (in particular, multitopology stuff). They aren't required for any of the RJMC stuff, except possibly the proposal mechanism.
from perses.
I'm working on this now! Will open a PR.
from perses.
Update: I haven't added the OpenEye tools yet, but I can do that tomorrow.
from perses.
This is added now.
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.