choderalab/perses issues and pull requests

#1122 - Examples run phases in expected order

Pull Request - State: closed - Opened by ijpulidos about 2 years ago - 4 comments

#1121 - Make examples and templates run solvent phase first

Issue - State: closed - Opened by ijpulidos about 2 years ago
Labels: effort: low

#1120 - Change perses cli protein-ligand examples to use Tyk2

Issue - State: open - Opened by ijpulidos about 2 years ago

#1119 - Nans in an unstable Non-eq. cycling calculation (across a mutation)

Issue - State: open - Opened by sukritsingh about 2 years ago - 15 comments

#1117 - Enable only solvent phase to be specified

Issue - State: open - Opened by jchodera about 2 years ago - 1 comment
Labels: enhancement :sparkles:, priority: low

#1114 - Small molecule pipeline workflow is reassigning velocities by default on resume

Issue - State: closed - Opened by ijpulidos about 2 years ago - 1 comment
Labels: priority: low, effort: low

#1113 - test_relative_setup_charge_change failure

Issue - State: closed - Opened by mikemhenry about 2 years ago - 3 comments
Labels: potential bug :thinking: :bug:, priority: high

#1112 - Constrained C-H bond mapped onto unconstrained C-F bond

Issue - State: closed - Opened by jchodera about 2 years ago - 13 comments
Labels: bug :bug:, priority: high

#1109 - Avoid using `settattr()` in lambda protocols

Issue - State: closed - Opened by zhang-ivy about 2 years ago - 3 comments
Labels: potential bug :thinking: :bug:, priority: high, effort: low

#1108 - AtomMapping distance scoring functions not working with OFF tk 0.11

Issue - State: closed - Opened by richardjgowers about 2 years ago - 3 comments
Labels: priority: high

#1107 - Add analysis script variant to integrate and weight protonation/tautomer states

Issue - State: closed - Opened by jchodera about 2 years ago - 3 comments
Labels: effort: low

#1105 - Speed up RTD env generation

Pull Request - State: closed - Opened by mikemhenry about 2 years ago - 5 comments
Labels: documentation :bookmark_tabs:, priority: low

#1103 - set aromatic draw style to `OEAromaticStyle_Circle` in atom mapper

Pull Request - State: closed - Opened by mikemhenry about 2 years ago - 4 comments

#1088 - Integrate new RIPK2 dataset into perses/examples/new-cli/

Issue - State: closed - Opened by jchodera over 2 years ago - 1 comment
Labels: benchmarking

#1087 - add docker files

Pull Request - State: closed - Opened by mikemhenry over 2 years ago - 3 comments

#1086 - Fix feptasks.minimize()'s minimisation_steps argument

Issue - State: open - Opened by zhang-ivy over 2 years ago - 1 comment

#1082 - Change aromaticity drawing style

Issue - State: closed - Opened by ijpulidos over 2 years ago - 2 comments
Labels: priority: low

#1081 - Refine the tests for RESTTopologyFactory

Issue - State: open - Opened by ijpulidos over 2 years ago
Labels: priority: low

#1066 - [WIP] Protocol : Nonequilibrium Cycling

Pull Request - State: open - Opened by dotsdl over 2 years ago - 22 comments

#1065 - Add small molecule repex consistency tests

Pull Request - State: closed - Opened by zhang-ivy over 2 years ago - 36 comments
Labels: tests

#1061 - Add host-guest charge changing repex consistency test

Issue - State: closed - Opened by zhang-ivy over 2 years ago - 6 comments
Labels: tests

#1058 - Speed up protein mutation charge changing repex consistency test

Issue - State: closed - Opened by zhang-ivy over 2 years ago - 30 comments
Labels: tests

#1016 - Document how to set log level in new CLI

Issue - State: closed - Opened by mikemhenry over 2 years ago

#1000 - Determine why number of equilibrium iterations is almost always 1

Issue - State: closed - Opened by jchodera over 2 years ago - 3 comments
Labels: enhancement :sparkles:, potential bug :thinking: :bug:, priority: high, effort: medium

#962 - Use AminoAcidAtomMapper and AminoAcidAtomMapping for protein mutation atom mappings

Pull Request - State: closed - Opened by zhang-ivy over 2 years ago - 4 comments

#960 - Feat/robust retry logic

Pull Request - State: closed - Opened by mikemhenry over 2 years ago - 3 comments

#959 - Add some A->B and B->A consistency tests to our GPU CI

Issue - State: closed - Opened by mikemhenry over 2 years ago - 2 comments
Labels: tests, priority: high

#957 - [WIP] Use openeye MCS functionality to generate protein mutation atom mappings

Pull Request - State: closed - Opened by zhang-ivy over 2 years ago - 2 comments

#873 - Add scaled water rest implementation (second attempt)

Pull Request - State: closed - Opened by zhang-ivy about 3 years ago - 3 comments

#870 - Possable stocastic issue with AtomMapping during test_run_point_mutation_propose test

Issue - State: closed - Opened by mikemhenry about 3 years ago - 2 comments
Labels: potential bug :thinking: :bug:, priority: medium

#869 - Version CUDA Support Better With Dockerfiles

Pull Request - State: closed - Opened by mikemhenry about 3 years ago - 5 comments

#861 - Add scaled water implementation

Pull Request - State: closed - Opened by zhang-ivy about 3 years ago - 5 comments

#819 - Create RestCapablePMEHybridTopologyFactory (OLD)

Pull Request - State: closed - Opened by zhang-ivy over 3 years ago - 1 comment

#808 - Allow global setting of random number seed + better RepartitionedHybridTopologyFactory test

Pull Request - State: open - Opened by mikemhenry over 3 years ago - 3 comments
Labels: enhancement :sparkles:, tests, priority: low

#785 - [WIP] reaction field

Pull Request - State: closed - Opened by dominicrufa over 3 years ago - 14 comments
Labels: priority: high

#777 - Adapt protein mutation setup pipeline to handle glycosylated RBD:ACE2

Pull Request - State: closed - Opened by zhang-ivy over 3 years ago - 4 comments
Labels: do not merge

#679 - CustomNonbondedForce discrepancies between CPU and OpenCL for OpenMM 7.4.1

Issue - State: closed - Opened by jchodera over 4 years ago - 2 comments
Labels: blocked, potential bug :thinking: :bug:

#663 - Remove hard-coding of the `CUDA` platform in `rjmc.geometry.py`

Issue - State: closed - Opened by hannahbrucemacdonald over 4 years ago - 2 comments
Labels: optimization, priority: low

#601 - [WIP] Experiments

Pull Request - State: closed - Opened by dominicrufa almost 5 years ago - 5 comments
Labels: do not merge

GitHub / choderalab/perses issues and pull requests