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: openjournals/joss-reviews#3951

What's Changed

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

Full Changelog: v1.0.0...v1.0.1

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.
• 🚧 io: read and write molecules from/to files.
• 🚧 structure.pocket: identification and analysis of protein (sub)pockets.
• 🚧 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) #107
  • structure conformations #108
  • modified residues in structures #110
• opencadd.databases.klifs: Add OpenCADD-KLIFS paper #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) #111 #116 #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 #109)

v0.2.2

Bug fixes

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

Minor changes

• Use matplotlib-base instead of matplotlib #101

v0.2.1

Changes

• Use matplotlib-base instead of matplotlib in environment #101

Fix bugs

• opencadd.databases.klifs: Fix parallelization issue with opencadd.databases.klifs.remote module #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 #104

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: #67
• Add test that syncs the KLIFS fields (remote) with the opencadd fields (if new fields available in KLIFS, CI will fail)

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

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.