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Issues list

OpenEye dependencies are a barrier to using perses
#1248 opened Nov 21, 2024 by danielguion
1
IndexError with _vacdg_history if there is no vacuum trajectory
#1247 opened Apr 13, 2024 by slochower
3
Improved reporting and state detection when passing tautomers as old_residue
#1246 opened Apr 5, 2024 by sukritsingh
Update README? documentation 📑 Documentation enhancements
#1244 opened Dec 7, 2023 by zhang-ivy
1
Allow specification of mapping dictionary in the pipeline enhancement ✨
#1241 opened Nov 6, 2023 by ijpulidos 0.11.0: New top-level API
Allow user to specify list of atom indices to override default behavior for selecting the REST region
#1226 opened Aug 9, 2023 by zhang-ivy
@ijpulidos
Fix potential bug in counterion implementation: get_water_indices()
#1225 opened Aug 9, 2023 by zhang-ivy
@ijpulidos
Protein mutation protocol for alchemiscale effort: medium future priority: medium priority medium
#1222 opened Aug 1, 2023 by ijpulidos 0.11.0: New top-level API
@ijpulidos
1
Migrate from PDB to PDBx/mmcif enhancement ✨
#1221 opened Jul 31, 2023 by ijpulidos 0.11.0: New top-level API
1
Duplicate instances of self._setup_complex_phase() in relative_setup.py priority: low low priority
#1219 opened Jul 28, 2023 by zhang-ivy
1
@ijpulidos
2
perses with mpi
#1216 opened Jul 25, 2023 by mikemhenry 0.11.0: New top-level API
1
Make sure we merge latest 0.10 branch before working on 0.11 refactor
#1213 opened Jul 19, 2023 by ijpulidos 0.11.0: New top-level API
Creating legacy 0.10.x branch for longer term support -- main branch will become gufe refactor
#1211 opened Jul 11, 2023 by ijpulidos 0.11.0: New top-level API
@ijpulidos
1
AtomMapper fails when scaffolds have radicals potential bug 🤔 🐛
#1209 opened Jul 5, 2023 by ijpulidos 0.11.0: New top-level API
1
Write initial initial and final structures in subdir enhancement ✨
#1205 opened Jun 13, 2023 by ijpulidos 0.11.0: New top-level API
@ijpulidos
Integrate new atom mappers enhancement ✨
#1204 opened Jun 13, 2023 by ijpulidos 0.11.0: New top-level API
7
REST max temperature from CLI bug 🐛
#1195 opened May 18, 2023 by ijpulidos 0.11.0: New top-level API
1
2
[HybridTopologyFactory] Copying virtual sites from old/new systems to hybrid system leads to exception
#1193 opened May 5, 2023 by IAlibay 0.11.0: New top-level API
2
Support for cofactor-bound proteins?
#1191 opened Apr 28, 2023 by sukritsingh
1
Move non-alchemical REST system code to openmmtools
#1187 opened Apr 21, 2023 by zhang-ivy 0.11.0: New top-level API
Run complete protein-ligand benchmark set with openff-2.1.0rc1 to test benchmark scripts
#1184 opened Apr 18, 2023 by jchodera
Update benchmarks scripts to run entire protein-ligand benchmarks set benchmarking effort: medium
#1183 opened Apr 18, 2023 by jchodera
@ijpulidos
1
Integrate OpenFF / OpenFE protein loaders so that entire system has Molecule representations
#1182 opened Apr 18, 2023 by jchodera
2
Update examples to openff-2.1.0rc1
#1181 opened Apr 18, 2023 by jchodera
Migrate solute-only trajectory writing from NetCDF to XTC effort: medium enhancement ✨
#1180 opened Apr 12, 2023 by jchodera 0.11.0: New top-level API
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