Ecosyste.ms: Issues

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

GitHub / GilsonLabUCSD/pAPRika issues and pull requests

#195 - [DNM] Test Python 3.11

Pull Request - State: open - Opened by jeff231li over 1 year ago

#194 - Fix bug in calculating center of mass with zero masses

Pull Request - State: closed - Opened by jeff231li over 1 year ago - 1 comment

#193 - Fix bug in `Analysis` module -- saving and loading results

Pull Request - State: closed - Opened by jeff231li over 1 year ago - 1 comment

#192 - Improve QOL for Restraints Modules

Pull Request - State: closed - Opened by jeff231li over 1 year ago - 1 comment

#191 - Fix bugs in restraint modules

Pull Request - State: closed - Opened by jeff231li almost 2 years ago - 1 comment

#190 - Refactor Analysis Modules

Pull Request - State: closed - Opened by jeff231li almost 2 years ago - 1 comment

#189 - Update read_yaml module for taproom

Pull Request - State: closed - Opened by jeff231li almost 2 years ago - 1 comment

#188 - Remove LGTM yaml file

Pull Request - State: closed - Opened by jeff231li almost 2 years ago - 1 comment

#187 - update readme

Pull Request - State: closed - Opened by jeff231li almost 2 years ago

#186 - Update CI.yaml -- include python 3.10 in unit tests

Pull Request - State: closed - Opened by jeff231li almost 2 years ago - 1 comment

#185 - error in paprika tutorial cb6-but

Issue - State: closed - Opened by mauramalinka01 about 2 years ago - 4 comments

#184 - Update pin on OpenFF-Units

Pull Request - State: closed - Opened by jeff231li about 2 years ago

#183 - [WIP] Update Evaluator modules

Pull Request - State: open - Opened by jeff231li over 2 years ago - 1 comment

#182 - Update conda and readme

Pull Request - State: closed - Opened by jeff231li over 2 years ago

#181 - Update README and docs for new release

Pull Request - State: closed - Opened by jeff231li over 2 years ago - 1 comment

#180 - Update URLS after transfer

Pull Request - State: closed - Opened by jeff231li over 2 years ago - 1 comment

#179 - Implement centroid-based anchor atoms in openmm

Pull Request - State: closed - Opened by jeff231li over 2 years ago - 3 comments
Labels: enhancement

#178 - Update tests and GA

Pull Request - State: closed - Opened by jeff231li over 2 years ago - 2 comments

#177 - Update for OpenFF-Units v0.1.7

Pull Request - State: closed - Opened by jeff231li over 2 years ago - 2 comments

#176 - Fix analysis units

Pull Request - State: closed - Opened by jeff231li over 2 years ago
Labels: bug

#175 - Pymbar update

Pull Request - State: closed - Opened by jeff231li over 2 years ago

#174 - Colab support

Pull Request - State: open - Opened by jaketanderson almost 3 years ago - 7 comments

#173 - Added prmtop to openmm tutorial

Pull Request - State: closed - Opened by jaketanderson almost 3 years ago - 4 comments

#172 - Progress bars

Pull Request - State: closed - Opened by jaketanderson almost 3 years ago - 5 comments

#171 - Quality of life time estimation

Issue - State: open - Opened by jaketanderson almost 3 years ago - 7 comments
Labels: enhancement

#170 - Add option to calculate `ref_state_work` for DDM.

Pull Request - State: closed - Opened by jeff231li almost 3 years ago - 1 comment

#169 - Logger.info output during alignment exception

Pull Request - State: closed - Opened by jaketanderson almost 3 years ago - 14 comments

#168 - Update dependencies for docs

Pull Request - State: closed - Opened by jeff231li almost 3 years ago

#167 - Add CITATION.cff to repo

Pull Request - State: closed - Opened by jeff231li over 3 years ago - 1 comment
Labels: enhancement

#166 - Update import namespace for OpenMM and add unit tests for restraints modules

Pull Request - State: closed - Opened by jeff231li over 3 years ago - 1 comment

#165 - Tleap not work properly

Issue - State: closed - Opened by rehan1988 over 3 years ago - 16 comments

#164 - Add Pint units to pAPRika

Pull Request - State: closed - Opened by jeff231li over 3 years ago - 5 comments

#163 - pAPRika error

Issue - State: closed - Opened by rehan1988 over 3 years ago - 25 comments

#162 - Update docs for v1.1.0 release

Pull Request - State: closed - Opened by jeff231li almost 4 years ago

#161 - Add osx-arm64 builds to conda-forge recipe

Issue - State: closed - Opened by slochower almost 4 years ago - 1 comment

#160 - module build not found

Issue - State: closed - Opened by 2young-2simple-sometimes-naive almost 4 years ago - 7 comments

#159 - Add Bind3P as an option in TLeap module

Pull Request - State: closed - Opened by jeff231li almost 4 years ago - 3 comments

#158 - Can I perform a antibody-antigen binding free energy calculation on pAPRika?

Issue - State: closed - Opened by MeetXinZhang almost 4 years ago - 3 comments

#157 - Refactor build related modules

Pull Request - State: closed - Opened by jeff231li about 4 years ago - 3 comments

#156 - Refactor build-related modules into one common namespace?

Issue - State: closed - Opened by jeff231li about 4 years ago - 1 comment
Labels: enhancement

#155 - Bump setup_miniconda to v2 so we don't have to allow unsafe GHA commands

Pull Request - State: closed - Opened by j-wags about 4 years ago - 1 comment

#154 - CI update -> use miniconda v2

Pull Request - State: closed - Opened by jeff231li about 4 years ago

#153 - Refactor Evaluator related module

Pull Request - State: closed - Opened by jeff231li about 4 years ago

#152 - Fix bug in tleap when solvating a single ion.

Pull Request - State: closed - Opened by jeff231li about 4 years ago - 1 comment

#151 - Set up GitHub Actions CI

Pull Request - State: closed - Opened by mattwthompson about 4 years ago - 1 comment

#150 - Migrate to Github Actions

Issue - State: closed - Opened by jeff231li about 4 years ago - 1 comment
Labels: enhancement

#149 - Remove redundant conda channel

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 2 comments

#148 - Fix bug with temperature setter in Analysis class

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 1 comment

#147 - Add a function to rotate a system around an axis

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 1 comment

#146 - Tleap InterMol support

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 5 comments

#145 - NAMD+Colvars support and improvement for all simulation classes

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 7 comments

#144 - Update README.md

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 2 comments

#143 - Fixes bug in #140 where additional PDB files were suppressed by filter_template

Pull Request - State: closed - Opened by slochower over 4 years ago - 1 comment

#142 - Images in README.md are missing

Issue - State: closed - Opened by slochower over 4 years ago - 4 comments
Labels: bug

#141 - filter_template function makes loading multiple PDB files impossible

Issue - State: closed - Opened by tuckerburgin over 4 years ago - 4 comments

#140 - Refactor wrapper and add Gromacs support

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 9 comments

#139 - Change documentation badge

Pull Request - State: closed - Opened by slochower over 4 years ago - 1 comment

#138 - Update documentation

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 5 comments

#137 - Remove last vestiges of codecov

Pull Request - State: closed - Opened by slochower over 4 years ago - 1 comment

#136 - Remove codeclimate and use lint

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 17 comments

#135 - Integrate Pint units into pAPRika

Issue - State: closed - Opened by jeff231li over 4 years ago - 3 comments
Labels: enhancement

#134 - Blackify code base

Issue - State: closed - Opened by slochower over 4 years ago - 1 comment

#133 - Add support for Plumed-based restraints

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 39 comments

#132 - Fix RTD by removing `m2r` package

Pull Request - State: closed - Opened by slochower over 4 years ago - 3 comments

#131 - Update tutorials

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 3 comments

#130 - Refactor Evaluator Setup and Analysis Modules

Pull Request - State: closed - Opened by SimonBoothroyd over 4 years ago - 7 comments

#129 - Add new utility functions

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 5 comments

#128 - update install requirements to include Ambertools v20

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 1 comment

#127 - Fix setup for evaluator

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 2 comments

#126 - Fix missing import of parmed in tleap.py

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 2 comments

#125 - Tleap HMR support

Pull Request - State: closed - Opened by jeff231li over 4 years ago - 3 comments

#124 - Update miniconda URL from continuum.io to anaconda.com

Pull Request - State: closed - Opened by mattwthompson almost 5 years ago - 1 comment

#123 - Update README with contributors

Pull Request - State: closed - Opened by slochower almost 5 years ago - 1 comment

#122 - optimize distance restraint calculations

Pull Request - State: closed - Opened by wwilla7 almost 5 years ago - 1 comment

#121 - Pymbar fix

Pull Request - State: closed - Opened by jeff231li about 5 years ago - 2 comments

#120 - Updates for `pymbar 3.0.4`

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

#119 - Fix CUDA_VISIBLE_DEVICES function

Pull Request - State: closed - Opened by wwilla7 about 5 years ago - 9 comments

#118 - fix CUDA_VISIBLE_DEVICES function

Pull Request - State: closed - Opened by wwilla7 about 5 years ago - 1 comment

#117 - Update documentation

Pull Request - State: closed - Opened by slochower about 5 years ago

#116 - Update documentation (for RTD) and also update docstrings

Pull Request - State: closed - Opened by slochower over 5 years ago - 7 comments

#115 - Update documentation build procedure

Pull Request - State: closed - Opened by slochower over 5 years ago

#114 - Add example on running pAPRika through PropertyEstimator via Dask

Issue - State: closed - Opened by slochower over 5 years ago - 1 comment
Labels: documentation

#113 - Consider migrating to Data Classes

Issue - State: open - Opened by slochower over 5 years ago
Labels: enhancement

#111 - Code cleanup

Pull Request - State: closed - Opened by SimonBoothroyd over 5 years ago - 2 comments

#110 - Minor cleanup & test fixes

Pull Request - State: closed - Opened by slochower over 5 years ago - 2 comments

#109 - Minor clean-ups

Pull Request - State: closed - Opened by slochower over 5 years ago - 3 comments

#105 - [WIP] Additional test cases

Issue - State: open - Opened by slochower over 5 years ago
Labels: openff

#99 - Update formatting with isort, autoflake, and black

Pull Request - State: closed - Opened by slochower almost 6 years ago - 2 comments

#98 - K cl

Pull Request - State: closed - Opened by slochower almost 6 years ago - 1 comment

#97 - [TODO] Evaluate center of mass restraints

Issue - State: closed - Opened by slochower almost 6 years ago - 1 comment
Labels: question

#96 - [TODO] Split `analysis.py`

Issue - State: open - Opened by slochower almost 6 years ago - 2 comments
Labels: enhancement

#94 - Update all docstrings to NumPy style

Issue - State: closed - Opened by slochower almost 6 years ago - 1 comment
Labels: enhancement, openff

#87 - Possible issue with `mbar-block` and `fractions`

Issue - State: open - Opened by slochower almost 6 years ago - 2 comments
Labels: bug

#85 - Comment about "6.6 is wrong"

Issue - State: closed - Opened by nhenriksen almost 6 years ago

#73 - Problem with letting through invalid restraints

Issue - State: closed - Opened by jlomibao over 6 years ago - 1 comment
Labels: bug

#54 - Index should not be win_idx

Issue - State: closed - Opened by nhenriksen almost 7 years ago - 1 comment

#53 - Simplify checking if a restraint is changing

Issue - State: closed - Opened by slochower almost 7 years ago

#52 - Should `_identify_active_rest` be method of the restraint class?

Issue - State: closed - Opened by slochower almost 7 years ago - 1 comment