volkamerlab/opencadd issues and pull requests

#157 - Biopython update

Pull Request - State: open - Opened by pipaj97 over 1 year ago
Labels: enhancement, module-structure-superposition

#156 - Upgrade package and repo infrastructure

Pull Request - State: open - Opened by AAriam over 1 year ago - 4 comments
Labels: enhancement

#155 - Why might the aligner be failing on these PDB files?

Issue - State: open - Opened by noahharrison64 over 1 year ago

#154 - Only MDAnalysis superpose alghorithms worked while MMLigner and TheseusAligner did not.

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

#153 - Update formatting (black version 23.3.0)

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

#152 - Update GHA CI configs

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

#151 - V2

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

#150 - Move OpenCADD-KLIFS paper to papers/ folder

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

#149 - Superposition: Cast universes w and w/o models to atom groups

Pull Request - State: closed - Opened by dominiquesydow about 2 years ago - 1 comment

#148 - Docs: Set sphinx language from None to en

Pull Request - State: closed - Opened by dominiquesydow about 2 years ago - 1 comment

#147 - Superposition align function fails when no models available in MDA Universe

Issue - State: closed - Opened by noahharrison64 about 2 years ago - 5 comments

#146 - CI and Docs: Use mamba

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

#145 - Add CITATION.cff

Issue - State: open - Opened by dominiquesydow over 2 years ago

#144 - Run CI weekly (not daily)

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

#143 - Mmligner improvements

Pull Request - State: open - Opened by pipaj97 over 2 years ago - 3 comments
Labels: enhancement, module-structure-superposition

#142 - Fix CI (pylint)

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

#141 - Add JOSS publication to README

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

#140 - minor changes in paper

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

#139 - Zenodo not linked to GitHub releases

Issue - State: closed - Opened by dominiquesydow over 2 years ago - 1 comment

#138 - Unpin `nbsphinx`

Issue - State: open - Opened by dominiquesydow over 2 years ago

#137 - Fix docs CI fails

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

#136 - Unpin `setuptools`

Issue - State: open - Opened by dominiquesydow over 2 years ago

#135 - Revise OpenCADD-KLIFS manuscript (issues #133 and #134)

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago - 2 comments

#134 - State of the field missing in JOSS paper

Issue - State: closed - Opened by ojeda-e almost 3 years ago - 3 comments
Labels: joss-review

#133 - Comments on JOSS manuscript

Issue - State: closed - Opened by andrewtarzia almost 3 years ago - 4 comments
Labels: joss-review

#132 - Clarify OpenCADD installation (issue #127)

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago - 1 comment
Labels: joss-review

#131 - OpenCADD-KLIFS: Sync stat. of need in paper with docs (issue #124)

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago
Labels: joss-review

#130 - Docs: Extend installation instructions (add `conda-forge` channel note)

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago - 1 comment
Labels: joss-review

#129 - An alternative to conda/mamba-based installation

Issue - State: closed - Opened by andrewtarzia almost 3 years ago - 3 comments
Labels: joss-review

#128 - Get PDF compiled for JOSS review

Issue - State: closed - Opened by andrewtarzia almost 3 years ago - 3 comments
Labels: joss-review

#127 - List of minimum dependencies missing (plus questions about installation instructions)

Issue - State: closed - Opened by ojeda-e almost 3 years ago - 11 comments
Labels: joss-review

#126 - Installation docs assume conda-forge channel already in conda config

Issue - State: closed - Opened by mcs07 almost 3 years ago - 1 comment
Labels: joss-review

#125 - OpenCADD-KLIFS: Add statement of need

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago - 2 comments
Labels: documentation, joss-review

#124 - Statement of need not found in documentation

Issue - State: closed - Opened by ojeda-e almost 3 years ago - 2 comments
Labels: joss-review

#123 - `superposer` cli referening commented-out args

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

#122 - Update docstring for KLIFS RMSD values

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago - 1 comment
Labels: module-databases-klifs

#121 - Move OpenCADD-KLIFS paper to `paper` folder

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

#120 - Update env (sync with cf recipe)

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

#119 - Add zenodo badge

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago
Labels: documentation

#118 - Note WIP vs. finished modules

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago
Labels: documentation

#117 - Base branch for `superposer` updates

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago - 9 comments
Labels: module-structure-superposition

#116 - Remove io init imports (to enable OpenCADD-KLIFS only deps)

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago - 1 comment
Labels: module-io

#115 - Add selection option

Pull Request - State: closed - Opened by pipaj97 almost 3 years ago - 1 comment
Labels: enhancement, module-structure-superposition

#114 - Add clustal omega

Pull Request - State: closed - Opened by pipaj97 almost 3 years ago - 2 comments
Labels: enhancement, module-structure-superposition

#113 - TheseusAligner performs a wrong tranformation

Issue - State: open - Opened by pipaj97 almost 3 years ago
Labels: module-structure-superposition

#112 - Add first draft of OpenCADD-KLIFS paper

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago - 2 comments
Labels: module-databases-klifs

#111 - KLIFS: Update docs text!

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago
Labels: documentation, module-databases-klifs

#110 - Add KLIFS structures' modified residues

Pull Request - State: closed - Opened by dominiquesydow almost 3 years ago
Labels: enhancement, module-databases-klifs

#109 - Remove `jsonschema` from environments

Issue - State: closed - Opened by dominiquesydow almost 3 years ago

#108 - Add KLIFS structure conformation data

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago - 1 comment
Labels: enhancement, module-databases-klifs

#107 - Add KLIFS drugs data

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago - 1 comment
Labels: module-databases-klifs