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

#191 - Backport fix from PR #190

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

#190 - Pass match_water parameter to specialised solvation functions

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

#189 - Feature Nucleic Acid Backbone

Pull Request - State: closed - Opened by fjclark about 1 year ago - 10 comments
Labels: enhancement

#188 - [BUG] Solvating a system containing an externally merged molecule

Issue - State: closed - Opened by noahharrison64 about 1 year ago - 7 comments
Labels: bug

#186 - Pass match_water parameter to specialised solvation functions

Pull Request - State: closed - Opened by lohedges about 1 year ago - 8 comments
Labels: invalid

#185 - [BUG] match_water parameter not passed through to solvation function

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

#184 - Release 2023.4.0

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

#183 - Synchronise with Exscientia remote

Pull Request - State: closed - Opened by lohedges about 1 year ago - 6 comments
Labels: exscientia

#182 - review small fixes

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

#181 - Fix issue #180

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

#180 - [BUG] BSS.FreeEnergy.Relative() automatically sets GPU index in somd.cfg

Issue - State: closed - Opened by jasmin-guven about 1 year ago - 11 comments
Labels: bug

#179 - Allow unit-based protocol options to be passed as strings

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

#178 - Feature Multiple Distance Restraints

Pull Request - State: closed - Opened by fjclark about 1 year ago - 15 comments
Labels: enhancement

#177 - ValueError: setting an array element with a sequence.

Issue - State: closed - Opened by velocirraptor23 about 1 year ago - 3 comments
Labels: invalid

#175 - Feature reduce

Pull Request - State: closed - Opened by lohedges about 1 year ago - 5 comments
Labels: enhancement

#174 - Backport fix from PR #173

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

#173 - Fix issue #172

Pull Request - State: closed - Opened by lohedges about 1 year ago - 3 comments
Labels: bug

#172 - [BUG] getSystem might replace space with an infinite Cartesian box

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

#171 - Backport fix from PR #169

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

#170 - Decouple custom parameters and additional LEaP commands

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

#169 - Fix #168

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

#168 - [BUG] Gromacs process throws an error when a checkpoint file is given

Issue - State: closed - Opened by jasmin-guven about 1 year ago - 1 comment
Labels: bug

#167 - Allow user commands to reference molecule in LEaP script

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

#166 - Fix user commands that reference mol error:

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

#165 - Backport fix from PR #164

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

#164 - Ensure that SOMD ABFE pert files are always correct

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

#163 - Fix issue #162

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

#162 - [BUG] SOMD ABFE tests are incorrectly skipped when GROMACS isn't installed

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

#161 - Backport fix from PR #160

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

#160 - Fix issue #159

Pull Request - State: closed - Opened by lohedges over 1 year ago - 2 comments
Labels: bug, exscientia

#159 - [BUG] Missing space and time shared_property for wrapped Sire system

Issue - State: closed - Opened by lohedges over 1 year ago - 4 comments
Labels: bug

#158 - Backport fix from PR #157

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

#157 - Fix handling of connectivity changes during molecular perturbations

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

#156 - [BUG] OpenMM position restraints can lead to steric clashes when no simulation box is present

Issue - State: closed - Opened by xiki-tempula over 1 year ago - 17 comments
Labels: bug, exscientia

#155 - Add unified FEP analysis using alchemlyb

Pull Request - State: closed - Opened by lohedges over 1 year ago - 5 comments
Labels: enhancement

#154 - Add support for crystal waters

Pull Request - State: closed - Opened by lohedges over 1 year ago - 2 comments
Labels: enhancement

#153 - Backport fix from PR #151

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

#152 - Add support for computing trajectory RMSDs using Sire

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

#151 - Fix issue #150

Pull Request - State: closed - Opened by lohedges over 1 year ago - 2 comments
Labels: bug

#149 - Fix issue #148

Pull Request - State: closed - Opened by lohedges over 1 year ago - 2 comments
Labels: bug

#148 - [BUG] Water molecule coordinates are setting to (0,0,0) (reposting)

Issue - State: closed - Opened by ale94mleon over 1 year ago - 4 comments
Labels: bug

#147 - Backport fix from PR #146

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

#146 - Fix issue #145

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

#145 - [BUG] Incorrect use totalSteps in OpenMM StateDataReporter

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

#144 - Update _openmm.py

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

#143 - Add support for aligning principal axes of system to solvent box

Pull Request - State: closed - Opened by lohedges over 1 year ago
Labels: enhancement

#141 - [BUG] genion fails with crystallographic water in a protein-ligand system

Issue - State: closed - Opened by cespos over 1 year ago - 6 comments
Labels: bug

#139 - Align Principal Axes of the system to the coordinate axes prior to solvation

Issue - State: closed - Opened by cespos over 1 year ago - 1 comment
Labels: enhancement

#138 - Fixed OpenMM compatibility in BSSEqBoundNode.ipynb.

Pull Request - State: closed - Opened by mb2055 over 1 year ago
Labels: bug

#137 - [BUG] BSSEqBoundNode.ipynb fails to run using OpenMM

Issue - State: closed - Opened by mb2055 over 1 year ago
Labels: bug

#136 - Backport fixes from PRs #133 and #135

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

#135 - Fix issue #134

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

#134 - [BUG] ParmEd box vectors are occasionally incompatible with OpenMM

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

#133 - Fix issue #132

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

#132 - [BUG] Incorrect alchemlyb extract function imported

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

#131 - Feat 2023.3

Pull Request - State: closed - Opened by xiki-tempula over 1 year ago
Labels: accidental pr

#130 - [BUG] Unable to save to RST7 file

Issue - State: closed - Opened by xiki-tempula over 1 year ago - 8 comments
Labels: exscientia

#129 - Backport fixes from PR #128

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

#128 - Fix issues caught by BioSimSpaceTutorials

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

#127 - Issue reading in PDB/top file

Issue - State: closed - Opened by noahharrison64 over 1 year ago - 7 comments

#126 - Backport fix from PR #125

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

#125 - Fix issue #124

Pull Request - State: closed - Opened by lohedges over 1 year ago - 4 comments
Labels: bug

#124 - [BUG] Check for non-periodic Cartesian space in process setup

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

#123 - Release 2023.3.0

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

#122 - Synchronise with Exscientia remote

Pull Request - State: closed - Opened by lohedges over 1 year ago - 8 comments
Labels: exscientia

#121 - Add support for Sire as a trajectory backend

Pull Request - State: closed - Opened by lohedges over 1 year ago
Labels: enhancement

#120 - Fixed an exception raised if a system has a cartesian space.

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

#119 - Bugfix Somd Analysis

Pull Request - State: closed - Opened by fjclark over 1 year ago - 2 comments
Labels: bug

#118 - [BUG] Trajectory.getFrames returns system before updating original system

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

#117 - Fix issue #116

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

#116 - [BUG] Invalid selector in conda recipe for py39

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

#115 - Fix issue #114

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

#113 - Correctly handle PLUMED version number

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

#112 - [BUG] Crystallographic waters could be removed during solvation

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

#111 - Fix issue #84

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

#110 - Expose Sire "make whole" functionality

Pull Request - State: closed - Opened by lohedges over 1 year ago
Labels: bug, enhancement

#109 - Improve unit parsing using Sire unit grammar

Pull Request - State: closed - Opened by lohedges over 1 year ago - 1 comment
Labels: enhancement, exscientia

#108 - This fixes the Gro87/GRO87 and GroTop/GROTOP issues.

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

#107 - Feature Improve Plotting

Pull Request - State: closed - Opened by fjclark over 1 year ago - 13 comments

#106 - Backport fix from PR #105

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

#105 - Fix issue #92

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

#104 - Feature ABFE SOMD

Pull Request - State: closed - Opened by fjclark over 1 year ago - 47 comments
Labels: enhancement

#103 - Matching atoms and merging ring systems (fused rings, different hybridisation states) - issues

Issue - State: open - Opened by annamherz over 1 year ago - 8 comments
Labels: enhancement

#102 - Details of BSS parallelisation options / schemes

Issue - State: closed - Opened by DreamCykl over 1 year ago - 4 comments
Labels: question

#101 - Backport fixes from PR #95 and #99 into main

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

#100 - Confusion over FEP protocol

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

#99 - Fix issue #98

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

#97 - Backport fixes from PR #89 and #90

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

#96 - Allow saveMetric to be executed at the end of the simulation

Pull Request - State: closed - Opened by xiki-tempula over 1 year ago
Labels: accidental pr

#95 - Fix issue #86

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

#94 - Backport fix from PR #79

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

#93 - [BUG] Unable to save BSS mol as PDB

Issue - State: closed - Opened by noahharrison64 over 1 year ago - 9 comments
Labels: bug

#92 - [BUG] Sire file caching breaking process.getSystem() when used interactively

Issue - State: closed - Opened by lohedges over 1 year ago - 6 comments
Labels: bug

#91 - Fix OpenMM restraints

Pull Request - State: closed - Opened by janjoswig over 1 year ago - 2 comments
Labels: accidental pr

#90 - Fix issue #88

Pull Request - State: closed - Opened by lohedges over 1 year ago
Labels: bug, documentation

#89 - Fix issue #81

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