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Recent Releases of OpenCADD-KLIFS

OpenCADD-KLIFS - v1.0.1

Summary

New release including the changes made during the OpenCADD-KLIFS JOSS manuscript review (full list below). Link to the JOSS review: https://github.com/openjournals/joss-reviews/issues/3951

What's Changed

  • Add zenodo badge by @dominiquesydow in https://github.com/volkamerlab/opencadd/pull/119
  • Move OpenCADD-KLIFS paper to paper folder by @dominiquesydow in https://github.com/volkamerlab/opencadd/pull/121
  • OpenCADD-KLIFS: Add statement of need by @dominiquesydow in https://github.com/volkamerlab/opencadd/pull/125
  • OpenCADD-KLIFS: Sync stat. of need in paper with docs (issue #124) by @dominiquesydow in https://github.com/volkamerlab/opencadd/pull/131
  • Docs: Extend installation instructions (add conda-forge channel note) by @dominiquesydow in https://github.com/volkamerlab/opencadd/pull/130
  • Update docstring for KLIFS RMSD values by @dominiquesydow in https://github.com/volkamerlab/opencadd/pull/122
  • Clarify OpenCADD installation (issue #127) by @dominiquesydow in https://github.com/volkamerlab/opencadd/pull/132
  • Revise OpenCADD-KLIFS manuscript (issues #133 and #134) by @dominiquesydow in https://github.com/volkamerlab/opencadd/pull/135

Full Changelog: https://github.com/volkamerlab/opencadd/compare/v1.0.0...v1.0.1

Scientific Software - Peer-reviewed - Python
Published by dominiquesydow over 4 years ago

OpenCADD-KLIFS - v1.0.0

This is the first official release of the opencadd package with the fully functional submodule opencadd.databases.klifs (OpenCADD-KLIFS) and several other work-in-progress submodules.

Overview

  • databases.klifs: utilities to query the KLIFS database, offline or online.
  • :construction: io: read and write molecules from/to files.
  • :construction: structure.pocket: identification and analysis of protein (sub)pockets.
  • :construction: structure.superposition (formerly superposer): superimpose macromolecules using sequence and structural information.

New

  • opencadd.databases.klifs: Add API for more data types provided by KLIFS:
    • drugs (including PKIDB drugs) https://github.com/volkamerlab/opencadd/pull/107
    • structure conformations https://github.com/volkamerlab/opencadd/pull/108
    • modified residues in structures https://github.com/volkamerlab/opencadd/pull/110
  • opencadd.databases.klifs: Add OpenCADD-KLIFS paper https://github.com/volkamerlab/opencadd/pull/112

Improvements

  • opencadd.databases.klifs: Define KLIFS data fields in CSV file instead of being part of the package code
  • opencadd.databases.klifs: Update documentation and instructions for installing OpenCADD-KLIFS only (instead of the full package and all its dependencies) https://github.com/volkamerlab/opencadd/pull/111 https://github.com/volkamerlab/opencadd/pull/116 https://github.com/volkamerlab/opencadd/pull/118

Fixes

  • Pin jsonschema to versions below 4.0.0 to work around version issues with bravado; once these issues are resolved remove this pin (more details in issue https://github.com/volkamerlab/opencadd/issues/109)

Scientific Software - Peer-reviewed - Python
Published by dominiquesydow over 4 years ago

OpenCADD-KLIFS - v0.2.2

Bug fixes

  • opencadd.databases.klifs: Fix parallelization in remote module + add dedicated test! https://github.com/volkamerlab/opencadd/pull/103
  • opencadd.databases.klifs: Drop remotely unavailable structures from local database in local module https://github.com/volkamerlab/opencadd/pull/106
  • opencadd.structure.pocket: Cast sphere center coordinates from numpy.float to float https://github.com/volkamerlab/opencadd/pull/104

Minor changes

  • Use matplotlib-base instead of matplotlib https://github.com/volkamerlab/opencadd/pull/101

Scientific Software - Peer-reviewed - Python
Published by dominiquesydow over 4 years ago

OpenCADD-KLIFS - v0.2.1

Changes

  • Use matplotlib-base instead of matplotlib in environment https://github.com/volkamerlab/opencadd/pull/101

Fix bugs

  • opencadd.databases.klifs: Fix parallelization issue with opencadd.databases.klifs.remote module https://github.com/volkamerlab/opencadd/pull/103
  • opencadd.structure.pocket: Fix problem with nglview usage: nglview throws TypeError for add_sphere because sphere center given as numpy.float but must be now float https://github.com/volkamerlab/opencadd/pull/104

Scientific Software - Peer-reviewed - Python
Published by dominiquesydow over 4 years ago

OpenCADD-KLIFS - v0.2.0

Updates the opencadd.databases.klifs module w.r.t. to changes and updates in the KLIFS database

  • Update KLIFS Swagger URL to development version https://dev.klifs.net/swagger_v2/
  • Move many globals in schema module that touch KLIFS field names/types to a new fields.Fields class (there was a bit too much redundancy here and the old setup was hard to maintain when new fields come in because we had to touch too many different globals in sync)
    • Cavet: Rename existing kinase.hgnc_name>kinase.gene_name
    • Cavet: Rename existing kinase.class > kinase.subfamily
    • Cavet: Change existing signature Kinases.all_kinase_families(group, species) to Kinases.all_kinase_families(groups, species)
    • Cavet: Change existing signature Kinases.all_kinases(group, family, species) to Kinases.all_kinases(groups, families, species) --- KLIFS allows for multiple inputs now
    • Update schema for kinases: Add kinase.klifs_name and kinase.uniprot
    • Update schema for bioactivities: Add kinase.chembl_id and ligand.chembl_id
    • Update schema for structures: Add ligand.klifs_id
  • Rerun opencadd.databases.klifs tutorial notebook!
  • Rerun notebook that saves all KLIFS IDs locally (after KLIFS fixed the "Some ligand PDB IDs mapped to mulitple ligand KLIFS IDs" problem)
  • Escape HTML encoding for all output DataFrames: https://github.com/volkamerlab/opencadd/issues/67
  • Add test that syncs the KLIFS fields (remote) with the opencadd fields (if new fields available in KLIFS, CI will fail)

Scientific Software - Peer-reviewed - Python
Published by dominiquesydow over 4 years ago

OpenCADD-KLIFS - v0.1.1

Pre-release of the opencadd package with the following patches - Check availability of theseus/mmligner executables; not available under Windows, thus raise informative error for users: PR - Use logger instead of print statements for module disclaimer (informing which modules are ready-to-use and which are still work-in-progress): PR

Scientific Software - Peer-reviewed - Python
Published by dominiquesydow almost 5 years ago

OpenCADD-KLIFS - v0.1.0

First pre-release of the opencadd package with the following submodules: - databases.klifs: utilities to query the KLIFS database, offline or online. - structure.pocket: identification and analysis of protein (sub)pockets. - [WIP] io: read and write molecules from/to files. - [WIP] structure.superposition (formerly superposer): superimpose macromolecules using sequence and structural information.

Scientific Software - Peer-reviewed - Python
Published by dominiquesydow almost 5 years ago