Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / openbiosim/biosimspace issues and pull requests

#293 - Backport fixes from PR #292

Pull Request - State: open - Opened by lohedges 7 months ago
Labels: bug, cresset

#292 - Fix issue #291

Pull Request - State: closed - Opened by lohedges 7 months ago - 1 comment
Labels: bug, cresset

#291 - [BUG] prepareFEP.py calls `BSS.IO.saveMolecules` with an missing `match_water` parameter

Issue - State: closed - Opened by nigel-palmer-cresset 7 months ago - 2 comments
Labels: bug, cresset

#290 - Backport fixes from PR #287 and #289

Pull Request - State: closed - Opened by lohedges 7 months ago

#289 - Fix issue #288

Pull Request - State: closed - Opened by lohedges 7 months ago

#287 - Fix issue #284

Pull Request - State: closed - Opened by lohedges 7 months ago
Labels: bug

#286 - Backport fix from PR #281 into main

Pull Request - State: closed - Opened by lohedges 7 months ago
Labels: bug, exscientia

#283 - Fix Trajectory object cannot handle system generated from file

Pull Request - State: closed - Opened by xiki-tempula 7 months ago
Labels: accidental pr

#282 - [BUG] Trajectory.getFrames assumes system fileformat property is iterable

Issue - State: closed - Opened by lohedges 7 months ago
Labels: bug, exscientia

#281 - Fix issue #280

Pull Request - State: closed - Opened by lohedges 7 months ago - 13 comments
Labels: bug, exscientia

#280 - [BUG] getFrame space check incorrecty uses self

Issue - State: closed - Opened by lohedges 7 months ago
Labels: bug, exscientia

#279 - Fix the issue where position restraint cannot coexist with ABFE restraint

Pull Request - State: closed - Opened by xiki-tempula 7 months ago
Labels: accidental pr

#278 - Release 2024.1.0

Pull Request - State: closed - Opened by lohedges 8 months ago

#277 - Sync with Exscientia remote

Pull Request - State: closed - Opened by lohedges 8 months ago - 1 comment

#276 - Final fixes for the 2024.1.0 release

Pull Request - State: closed - Opened by lohedges 8 months ago - 1 comment
Labels: bug, enhancement

#274 - [BUG] The base Protocol should return None for getRestraint

Issue - State: closed - Opened by lohedges 8 months ago
Labels: bug

#272 - Add support for AMBER as a free-energy perturbation engine

Pull Request - State: closed - Opened by lohedges 8 months ago - 6 comments
Labels: enhancement

#271 - Fix issue #270

Pull Request - State: closed - Opened by lohedges 8 months ago - 2 comments
Labels: bug

#270 - [BUG] Non-reproducible search for restraint atoms

Issue - State: closed - Opened by lohedges 8 months ago
Labels: bug

#269 - Make handling of base units more robust

Pull Request - State: closed - Opened by fjclark 8 months ago - 6 comments

#267 - Add support for openff-nagl for generation of partial charges

Pull Request - State: closed - Opened by lohedges 8 months ago - 6 comments
Labels: enhancement, exscientia

#266 - Add support for clearing and disabling the file cache

Pull Request - State: closed - Opened by lohedges 8 months ago
Labels: enhancement

#265 - [BUG] Potential memory leak when saving systems

Issue - State: closed - Opened by noahharrison64 8 months ago - 5 comments
Labels: bug

#264 - Use Langevin integrator for free-energy simulations

Pull Request - State: closed - Opened by lohedges 8 months ago
Labels: bug, exscientia

#263 - Backport 2023.5.1

Pull Request - State: closed - Opened by lohedges 8 months ago
Labels: bug, exscientia

#262 - Support for openff-bespokefit

Issue - State: open - Opened by jmichel80 9 months ago
Labels: enhancement

#261 - 'is_crystal' prevents setup for GROMACS Relative Free Energy files

Issue - State: closed - Opened by annamherz 9 months ago - 3 comments
Labels: bug

#260 - Fix issues #258 and #259

Pull Request - State: closed - Opened by lohedges 9 months ago - 4 comments
Labels: bug, exscientia

#258 - [BUG] Ions should be excluded in AMBER position restraint mask

Issue - State: closed - Opened by lohedges 9 months ago
Labels: bug, exscientia

#257 - Only convert to end state if this isn't a FreeEnergy protocol.

Pull Request - State: closed - Opened by lohedges 9 months ago
Labels: bug, exscientia

#256 - [BUG] GROMACS hybrid topology file is lost when protocol used position restraints

Issue - State: closed - Opened by lohedges 9 months ago
Labels: bug, exscientia

#255 - Only write couple molecule when the decoupled mol is not perturbable

Pull Request - State: closed - Opened by xiki-tempula 9 months ago
Labels: accidental pr

#254 - Backport fixes from PR #251 and #253

Pull Request - State: closed - Opened by lohedges 9 months ago
Labels: bug, exscientia

#253 - Avoid setting all end-state properties when decoupling

Pull Request - State: closed - Opened by fjclark 9 months ago - 6 comments

#251 - Improve error mesage when attempting to extract all dummy selection.

Pull Request - State: closed - Opened by lohedges 9 months ago
Labels: bug, documentation, exscientia

#250 - [BUG] Improve error message when attempting to extract selection that only contains dummies

Issue - State: closed - Opened by lohedges 9 months ago
Labels: bug, exscientia

#249 - Backport fixes from PR #247

Pull Request - State: closed - Opened by lohedges 9 months ago
Labels: bug, exscientia

#247 - Fix issues #240 and #246

Pull Request - State: closed - Opened by lohedges 9 months ago - 3 comments
Labels: bug

#245 - Backport fixes from PR #244

Pull Request - State: closed - Opened by lohedges 9 months ago

#244 - Fix issues #241, #242, and #243

Pull Request - State: closed - Opened by lohedges 9 months ago

#243 - [BUG] Expose FreeEnergyMixin protocols for GROMACS

Issue - State: closed - Opened by lohedges 9 months ago
Labels: bug

#242 - [BUG] OpenFF parameterisation error reports the incorrect file name.

Issue - State: closed - Opened by lohedges 9 months ago
Labels: bug

#241 - [BUG] readPerturbableSystem needs to remove shared system properties

Issue - State: closed - Opened by lohedges 9 months ago
Labels: bug

#240 - Unable to parameterise with OFF2

Issue - State: closed - Opened by fjclark 10 months ago - 8 comments
Labels: bug

#239 - Backport fix from PR #237

Pull Request - State: closed - Opened by lohedges 10 months ago
Labels: bug

#238 - reduceBoxVectors does not prevent RuntimeError: Periodic box vectors must be in reduced form

Issue - State: closed - Opened by fjclark 10 months ago - 14 comments
Labels: bug

#237 - Fix issue #236

Pull Request - State: closed - Opened by lohedges 10 months ago - 9 comments
Labels: bug

#235 - Update makeCompatibleWith to use the new AtomCoordMatcher

Pull Request - State: closed - Opened by lohedges 10 months ago
Labels: enhancement, exscientia

#234 - Backport fixes from PR #233 into main

Pull Request - State: closed - Opened by lohedges 10 months ago
Labels: bug

#233 - Fix issues 231 and 232

Pull Request - State: closed - Opened by lohedges 10 months ago - 3 comments
Labels: bug

#232 - [BUG] Strange logging behaviour

Issue - State: closed - Opened by noahharrison64 11 months ago - 6 comments
Labels: bug

#231 - [BUG] generateNetwork raises TypeError when links_file is supplied

Issue - State: closed - Opened by jasmin-guven 11 months ago - 3 comments
Labels: bug

#229 - Conda Installation of Dev Version Fails

Issue - State: closed - Opened by fjclark 11 months ago - 5 comments
Labels: bug

#228 - Release 2023.5.0

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

#227 - Synchronise with Exscientia remote

Pull Request - State: closed - Opened by lohedges 12 months ago
Labels: exscientia

#226 - Fix issue #225

Pull Request - State: closed - Opened by lohedges 12 months ago - 4 comments
Labels: bug, exscientia

#225 - [BUG] custom_parameters option not exposed via AMBER protein force field generator

Issue - State: closed - Opened by lohedges 12 months ago - 1 comment
Labels: bug

#224 - Make sure disulphide search is converted to a SelectorBond.

Pull Request - State: closed - Opened by lohedges 12 months ago - 1 comment
Labels: bug

#223 - [BUG] Disulphide bond code fails when a single bond is present

Issue - State: closed - Opened by lohedges 12 months ago - 1 comment
Labels: bug

#222 - Fix issue #221

Pull Request - State: closed - Opened by lohedges 12 months ago
Labels: bug, exscientia

#221 - [BUG] AMBER restraint mask needs to match all hydrogens, not just those named H

Issue - State: closed - Opened by lohedges 12 months ago
Labels: bug, exscientia

#220 - bugfix: addtoconfig is not a function in _amber.py, add to protocol d…

Pull Request - State: closed - Opened by annamherz 12 months ago
Labels: bug

#219 - Fix issue #218

Pull Request - State: closed - Opened by lohedges 12 months ago
Labels: bug

#217 - Fix issues #215 and #216

Pull Request - State: closed - Opened by lohedges 12 months ago
Labels: bug

#216 - [BUG] Funnel metadynamics tutorial fails due to duplicate default force constants

Issue - State: closed - Opened by lohedges 12 months ago - 5 comments
Labels: bug

#215 - [BUG] OpenMM metadyanmics driver script not self contained

Issue - State: closed - Opened by lohedges 12 months ago
Labels: bug

#214 - Backport fixes from PR #210.

Pull Request - State: closed - Opened by lohedges 12 months ago - 13 comments
Labels: bug

#211 - _check_box_size Fails for rhombicDodecahedronHexagon Box with Reasonable Padding

Issue - State: closed - Opened by fjclark about 1 year ago - 6 comments
Labels: bug

#210 - Fix #208

Pull Request - State: closed - Opened by lohedges about 1 year ago
Labels: bug

#209 - Fix a typo introduced in PR #198

Pull Request - State: closed - Opened by lohedges about 1 year ago
Labels: bug, exscientia

#208 - [BUG] BioSImSpace._SireWrappers.Molecule.extract changes MolNum

Issue - State: closed - Opened by lohedges about 1 year ago
Labels: bug

#206 - Backport fix from PR #204

Pull Request - State: closed - Opened by lohedges about 1 year ago
Labels: bug

#205 - Backport fixes from PR #203

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

#203 - Internal updates due to Sire API fixes

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

#202 - Backport fix from PR #201

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

#201 - Fix issue #200

Pull Request - State: closed - Opened by lohedges about 1 year ago
Labels: bug, exscientia

#200 - [BUG] Remove redundant __neq__ operator for BioSImSpace.Types.Type

Issue - State: closed - Opened by lohedges about 1 year ago
Labels: bug, exscientia

#198 - Backport fixes from PR #197

Pull Request - State: closed - Opened by lohedges about 1 year ago
Labels: bug

#197 - Fix issue #196

Pull Request - State: closed - Opened by lohedges about 1 year ago - 1 comment
Labels: bug

#195 - [BUG] GROMACS MD Simulation resulting in unexpected pressure scaling warning

Issue - State: closed - Opened by portmanrk about 1 year ago - 3 comments
Labels: bug

#194 - Backport fix from PR #193

Pull Request - State: closed - Opened by lohedges about 1 year ago
Labels: bug, exscientia

#193 - Fix issue #192

Pull Request - State: closed - Opened by lohedges about 1 year ago
Labels: bug, exscientia