choderalab/perses issues and pull requests

#1224 - Adapt MPi example with perses at least for protein mutation

Issue - State: open - Opened by ijpulidos 11 months ago

#1223 - Clean examples -- CLI protein-ligand example for Tyk2

Pull Request - State: closed - Opened by ijpulidos 11 months ago - 1 comment

#1222 - Protein mutation protocol for alchemiscale

Issue - State: open - Opened by ijpulidos 11 months ago - 1 comment
Labels: future, priority: medium, effort: medium

#1221 - Migrate from PDB to PDBx/mmcif

Issue - State: open - Opened by ijpulidos 11 months ago
Labels: enhancement :sparkles:

#1220 - Make `offline-freq` be the same as `checkpoint_interval` by default

Issue - State: open - Opened by jthorton 11 months ago

#1219 - Duplicate instances of `self._setup_complex_phase()` in relative_setup.py

Issue - State: open - Opened by zhang-ivy 11 months ago - 2 comments
Labels: priority: low

#1218 - CI minor fixes. Allow codecov to fail.

Pull Request - State: closed - Opened by mikemhenry 11 months ago

#1217 - CI miscellaneous fixes

Pull Request - State: closed - Opened by ijpulidos 11 months ago - 1 comment

#1216 - perses with mpi

Issue - State: open - Opened by mikemhenry 11 months ago

#1215 - [Draft] Self-consistently parameterize protein-ligand with espaloma-0.3.0

Pull Request - State: open - Opened by kntkb 11 months ago - 1 comment

#1214 - Remove example testing

Pull Request - State: closed - Opened by mikemhenry 11 months ago - 1 comment

#1213 - Make sure we merge latest 0.10 branch before working on 0.11 refactor

Issue - State: open - Opened by ijpulidos 11 months ago

#1212 - run CI on new 0.10.x branch

Pull Request - State: closed - Opened by mikemhenry 12 months ago - 4 comments

#1211 - Creating legacy 0.10.x branch for longer term support -- main branch will become `gufe` refactor

Issue - State: open - Opened by ijpulidos 12 months ago - 1 comment

#1210 - Store initial and final topologies for all phases -- small molecule pipeline

Pull Request - State: closed - Opened by ijpulidos 12 months ago - 3 comments

#1209 - AtomMapper fails when scaffolds have radicals

Issue - State: open - Opened by ijpulidos 12 months ago - 1 comment
Labels: potential bug :thinking: :bug:

#1208 - release notes for 0.10.2

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 3 comments

#1207 - Using default online analysis interval in GPU repex tests

Pull Request - State: closed - Opened by ijpulidos about 1 year ago - 1 comment

#1206 - enable merge queue

Pull Request - State: closed - Opened by mikemhenry about 1 year ago

#1205 - Write initial initial and final structures in subdir

Issue - State: open - Opened by ijpulidos about 1 year ago
Labels: enhancement :sparkles:

#1204 - Integrate new atom mappers

Issue - State: open - Opened by ijpulidos about 1 year ago - 7 comments
Labels: enhancement :sparkles:

#1203 - Fixes for new openmmtools 0.23.0

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 5 comments

#1202 - Allow specifying solvent model in input YAML file

Pull Request - State: closed - Opened by ijpulidos about 1 year ago - 3 comments

#1201 - drop 3.8, add 3.11

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 1 comment

#1200 - Improve docker building

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 5 comments

#1198 - Document how to control the log level in the CLI

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 2 comments

#1197 - REST scaling for preotein-ligand systems with the CLI

Pull Request - State: open - Opened by ijpulidos about 1 year ago - 2 comments

#1196 - Backport openfe fixes for context deletion

Issue - State: open - Opened by ijpulidos about 1 year ago

#1195 - REST max temperature from CLI

Issue - State: open - Opened by ijpulidos about 1 year ago - 2 comments
Labels: bug :bug:

#1194 - [HybridTopologyFactory] `CustomNonbondedForce` cutoff doesn't match `NonBondedForce`

Issue - State: open - Opened by IAlibay about 1 year ago - 3 comments
Labels: potential bug :thinking: :bug:, priority: high

#1193 - [HybridTopologyFactory] Copying virtual sites from old/new systems to hybrid system leads to exception

Issue - State: open - Opened by IAlibay about 1 year ago - 2 comments

#1192 - [CLI] no entry point for non-tip3p solvation model

Issue - State: closed - Opened by IAlibay about 1 year ago - 2 comments

#1191 - Support for cofactor-bound proteins?

Issue - State: open - Opened by sukritsingh about 1 year ago - 1 comment

#1189 - Update comments in `RESTCapableHybridTopologyFactory`

Pull Request - State: closed - Opened by zhang-ivy about 1 year ago - 1 comment

#1188 - Fix RESTTopologyFactory test

Pull Request - State: closed - Opened by zhang-ivy about 1 year ago - 1 comment

#1187 - Move non-alchemical REST system code to openmmtools

Issue - State: open - Opened by zhang-ivy about 1 year ago

#1186 - Skip failing openmm 8 tests

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 4 comments

#1185 - change default to none

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 4 comments

#1184 - Run complete protein-ligand benchmark set with openff-2.1.0rc1 to test benchmark scripts

Issue - State: open - Opened by jchodera about 1 year ago

#1183 - Update benchmarks scripts to run entire protein-ligand benchmarks set

Issue - State: open - Opened by jchodera about 1 year ago - 1 comment
Labels: benchmarking, effort: medium

#1182 - Integrate OpenFF / OpenFE protein loaders so that entire system has Molecule representations

Issue - State: open - Opened by jchodera about 1 year ago

#1181 - Update examples to openff-2.1.0rc1

Issue - State: open - Opened by jchodera about 1 year ago

#1180 - Migrate solute-only trajectory writing from NetCDF to XTC

Issue - State: open - Opened by jchodera about 1 year ago
Labels: enhancement :sparkles:, effort: medium

#1179 - Make solute-only trajectory writing optional

Issue - State: closed - Opened by jchodera about 1 year ago - 3 comments
Labels: enhancement :sparkles:, priority: high, effort: low

#1178 - add caching

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 2 comments

#1177 - Evaluating unit test coverage; filling in coverage where needed

Pull Request - State: closed - Opened by dotsdl about 1 year ago - 11 comments

#1176 - print perses version on startup

Pull Request - State: closed - Opened by mikemhenry about 1 year ago - 1 comment

#1175 - Make sure logging messages stream to stdout

Issue - State: closed - Opened by ijpulidos about 1 year ago - 2 comments

#1174 - use python executable from env

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 3 comments

#1173 - Support pymbar 4

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 6 comments

#1172 - `out-solvent.nc` is larger than `out-complex.nc`

Issue - State: closed - Opened by JenkeScheen over 1 year ago - 2 comments

#1171 - need a data model that contains essential information of a calculation

Issue - State: open - Opened by JenkeScheen over 1 year ago - 7 comments

#1170 - [DNM] test new openmmtools version

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 5 comments

#1169 - use `False` for reassign velocities in `ProteinMutationExecutor` docstring example.

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 4 comments

#1168 - Update docstring example for PointMutationExecutor

Issue - State: closed - Opened by zhang-ivy over 1 year ago - 1 comment

#1167 - [DNM] hack to allow undefined stero when mapping

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 3 comments

#1166 - Include cloudpathlib as requirement in meta.yaml

Pull Request - State: closed - Opened by craabreu over 1 year ago - 2 comments

#1165 - only run dev with newest python version

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 5 comments

#1164 - Avoid testing non-examples in CI

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 2 comments

#1163 - fix issue with logic, add debug statements

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment
Labels: bug :bug:

#1162 - update release process

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment

#1161 - Mapping/parameterization issue

Issue - State: open - Opened by viktorbelay over 1 year ago - 9 comments
Labels: help wanted :raised_hand:, potential bug :thinking: :bug:

#1160 - Double check usage of `openmmtools` `FireMinimizer`

Issue - State: open - Opened by ijpulidos over 1 year ago

#1159 - remove outdated recipe

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment

#1158 - Use bootstrapping by default

Issue - State: open - Opened by ijpulidos over 1 year ago

#1157 - Serialized XML objects in small molecule pipeline have the wrong extension

Issue - State: closed - Opened by ijpulidos over 1 year ago - 3 comments
Labels: priority: low

#1156 - List of input smiles as input for `RelativeFEPSetup`

Pull Request - State: open - Opened by ijpulidos over 1 year ago

#1155 - `RelativeFEPSetup` cannot handle list of smiles as input ligands

Issue - State: open - Opened by ijpulidos over 1 year ago
Labels: bug :bug:, help wanted :raised_hand:, priority: high

#1154 - Overhaul perses writing of topology information

Issue - State: closed - Opened by jchodera over 1 year ago - 2 comments
Labels: enhancement :sparkles:

#1153 - Questions about mapping

Issue - State: closed - Opened by SZhang66 over 1 year ago - 6 comments
Labels: potential bug :thinking: :bug:, priority: high

#1152 - Expand GPU instances or pick new ones for GPU CI

Issue - State: closed - Opened by mikemhenry over 1 year ago - 4 comments
Labels: tests, priority: high

#1151 - resolves issue #1150

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment

#1150 - Fix resume tests

Issue - State: closed - Opened by ijpulidos over 1 year ago
Labels: tests, priority: low, effort: low

#1149 - Remove basic config

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 1 comment

#1148 - switch to using openmm rc

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 3 comments

#1147 - Test Newest OpenMM Release Candidate

Issue - State: closed - Opened by mikemhenry over 1 year ago - 2 comments
Labels: tests, priority: high

#1146 - Document Release Process

Issue - State: closed - Opened by mikemhenry over 1 year ago

#1145 - Add reproducible version of COVID Moonshot example anyone can run as an example

Pull Request - State: closed - Opened by jchodera over 1 year ago - 1 comment

#1144 - Fix CI

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 2 comments

#1143 - Githubs actions CI failing

Issue - State: closed - Opened by ijpulidos over 1 year ago - 1 comment
Labels: tests, priority: high

#1142 - Remove basicConfig

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 5 comments

#1141 - WIP -- intuitive handling of minimization steps kwarg

Pull Request - State: open - Opened by ijpulidos over 1 year ago - 1 comment

#1140 - Enable virtual bonds restraint between protein subunits by default

Issue - State: open - Opened by ijpulidos over 1 year ago - 1 comment

#1139 - feat(docker): Add opencontainers image-spec to `Dockerfile`

Pull Request - State: closed - Opened by SauravMaheshkar over 1 year ago - 1 comment

#1138 - Using the faster `LangevinDynamicsMove`

Pull Request - State: closed - Opened by ijpulidos over 1 year ago - 2 comments

#1137 - CLI repex should use `LangevinDynamicsMove`

Issue - State: closed - Opened by jchodera over 1 year ago
Labels: enhancement :sparkles:, optimization, priority: high, effort: low

#1136 - New CLI analysis tool

Issue - State: open - Opened by jchodera over 1 year ago - 7 comments
Labels: priority: high, analysis, effort: medium, feature

#1135 - Add tool to extract equilibrium pose from simulations

Issue - State: open - Opened by JenkeScheen over 1 year ago - 4 comments
Labels: priority: high, analysis, effort: medium, feature

#1134 - Ensure that perses calls `addHydrogens` on PDB files so we don't need fully protonated versions if OpenMM knows how to add the protons

Issue - State: open - Opened by jchodera over 1 year ago
Labels: enhancement :sparkles:, effort: low

GitHub / choderalab/perses issues and pull requests