Ecosyste.ms: Issues

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

GitHub / 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

#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 almost 2 years 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 over 2 years ago - 1 comment

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

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

#146 - CI and Docs: Use mamba

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

#140 - minor changes in paper

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

#139 - Zenodo not linked to GitHub releases

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

#138 - Unpin `nbsphinx`

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

#137 - Fix docs CI fails

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

#136 - Unpin `setuptools`

Issue - State: open - Opened by dominiquesydow almost 3 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 about 3 years ago - 1 comment
Labels: module-databases-klifs

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

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

#120 - Update env (sync with cf recipe)

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

#119 - Add zenodo badge

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

#118 - Note WIP vs. finished modules

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

#117 - Base branch for `superposer` updates

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

#115 - Add selection option

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

#114 - Add clustal omega

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

#113 - TheseusAligner performs a wrong tranformation

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

#112 - Add first draft of OpenCADD-KLIFS paper

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

#111 - KLIFS: Update docs text!

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

#110 - Add KLIFS structures' modified residues

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

#109 - Remove `jsonschema` from environments

Issue - State: closed - Opened by dominiquesydow about 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

#106 - KLIFS: Drop remotely unavailable structures from local database

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

#105 - Different results from different KLIFS APIs

Issue - State: closed - Opened by schallerdavid about 3 years ago - 3 comments
Labels: module-databases-klifs

#104 - Pocket: Cast sphere center coordinates numpy.float > float

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago

#103 - KLIFS module: RecursionError with parallelization... again!

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

#102 - KLIFS module: RecursionError with parallelization

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

#101 - Update env with matplotlib-base

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

#100 - Update README + docs incl. conda installation

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

#99 - Check availability of theseus/mmligner executables

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

#98 - Module disclaimer: Use logger instead of print

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

#97 - opencadd conda package

Issue - State: closed - Opened by dominiquesydow about 3 years ago - 4 comments

#96 - Update README and environment file

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

#95 - Add disclaimer about dev stages for different submodules

Pull Request - State: closed - Opened by dominiquesydow about 3 years ago

#94 - Add coverage

Pull Request - State: closed - Opened by pipaj97 about 3 years ago - 3 comments
Labels: module-structure-superposition

#93 - MDAnalysis 2.0.0: Structures fetched by PDB code do not contain elements

Issue - State: open - Opened by dominiquesydow about 3 years ago - 1 comment
Labels: module-structure

#92 - Mda fix

Pull Request - State: closed - Opened by pipaj97 over 3 years ago - 1 comment

#91 - MmLigner fix

Pull Request - State: closed - Opened by pipaj97 over 3 years ago - 2 comments

#90 - Cli fix

Pull Request - State: closed - Opened by pipaj97 over 3 years ago - 3 comments
Labels: module-structure-superposition

#89 - io: DataFrame from PDB: Concat residue ID and insertion code

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

#88 - Add customized KLIFS exception classes

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

#87 - Raise exceptions for unexpected KLIFS pockets

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

#85 - Extend KLIFS API usage (drugs, conformations, modifications)

Issue - State: closed - Opened by dominiquesydow over 3 years ago
Labels: enhancement, module-databases-klifs

#84 - Pocket: Add pocket/sphere names to NGL GUI

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 3 comments
Labels: module-structure-pocket

#83 - Specific OpenCadd package and environment creation link

Issue - State: closed - Opened by Carlbullish over 3 years ago - 2 comments

#82 - Use redo to query KLIFS database

Issue - State: open - Opened by dominiquesydow over 3 years ago
Labels: module-databases-klifs

#81 - Automatize local KLIFS IDs copy (needed for local session)

Issue - State: open - Opened by dominiquesydow over 3 years ago
Labels: module-databases-klifs

#80 - Fetch local copy of KLIFS IDs for 20210701 status

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

#79 - Change logging level INFO to DEBUG

Issue - State: open - Opened by dominiquesydow over 3 years ago
Labels: module-structure-pocket

#78 - Read from zipped KLIFS download folder

Issue - State: closed - Opened by dominiquesydow over 3 years ago
Labels: module-databases-klifs

#77 - Extend comment on unexpected KLIFS API

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

#75 - Fetch information for multiple kinases with _one_ API call

Pull Request - State: closed - Opened by dominiquesydow over 3 years ago - 4 comments
Labels: module-databases-klifs

#74 - KLIFS multiprocessing

Issue - State: closed - Opened by schallerdavid over 3 years ago - 7 comments
Labels: module-databases-klifs

#73 - KLIFS corrections

Pull Request - State: closed - Opened by schallerdavid over 3 years ago - 11 comments
Labels: module-databases-klifs

#71 - UnboundLocalError in MMLigner

Issue - State: closed - Opened by jaimergp almost 4 years ago - 1 comment
Labels: module-structure-superposition

#70 - Initial Standardization module import

Pull Request - State: open - Opened by Allend95 almost 4 years ago - 5 comments
Labels: not-continued, module-compounds-standardization

#67 - databases.klifs: HTML-encoded entities in some strings

Issue - State: closed - Opened by jaimergp almost 4 years ago - 1 comment
Labels: module-databases-klifs

#66 - Refactor pocket module

Pull Request - State: closed - Opened by dominiquesydow almost 4 years ago - 1 comment

#65 - Pin parso to 0.8.1 for compartibility with jedi 0.18.0

Issue - State: closed - Opened by dominiquesydow almost 4 years ago - 2 comments

#63 - Pylint RecursionError

Issue - State: closed - Opened by dominiquesydow almost 4 years ago - 8 comments

#57 - Add some Jupyter utilities

Pull Request - State: closed - Opened by jaimergp almost 4 years ago - 2 comments
Labels: module-utils

#56 - superposer is insenstive to residues with insertion codes

Issue - State: open - Opened by dominiquesydow almost 4 years ago - 2 comments
Labels: module-structure-superposition

#55 - Add KLIFS Swagger API updates

Pull Request - State: closed - Opened by dominiquesydow about 4 years ago - 2 comments
Labels: module-databases-klifs

#52 - opencadd README: Add list of external resources

Issue - State: open - Opened by dominiquesydow about 4 years ago - 1 comment
Labels: documentation

#49 - opencadd.structure.pocket: Add features to nglview views

Issue - State: open - Opened by dominiquesydow about 4 years ago
Labels: module-structure-pocket

#48 - Update biopandas usage: Read pdb from list of strings

Issue - State: open - Opened by dominiquesydow about 4 years ago - 1 comment
Labels: module-io

#47 - Slow performance of atom selection with MDAnalysis

Issue - State: open - Opened by dominiquesydow about 4 years ago
Labels: module-structure-superposition

#46 - Unpin biopython and update Bio.Alphabet usage

Issue - State: open - Opened by jaimergp about 4 years ago
Labels: module-structure-superposition

#42 - Parsing molecules

Issue - State: open - Opened by dominiquesydow about 4 years ago - 3 comments
Labels: module-io

#35 - ASCONA

Issue - State: open - Opened by jaimergp over 4 years ago - 1 comment
Labels: enhancement, module-structure-superposition