fpocketR v1.3.4

fix typo pyproject.toml

fpocketR v1.3.3

pymol-open-source not available on pypi

fpocketR 1.3.2

Fix pypi requirements.

fpocketR 1.3.1

Update installation.

fpocketR 1.3.0

New features

• Add the --align-ligand feature to align apo and holo structures to visualize the alignment of pockets and ligand binding sites.
• Add the --knownnt argument to classify known pockets in apo RNA structures
• Added pocket density figures for mutlistate analysis
• Added demonstration workflows for bash, snakemake, and modeled RNA structures from CASP16
• Integrated testing on commit for MacOS 13 (x86_64) and Ubuntu:latest (x86_64)

Fixes

• Fixed conda executable path (issue #2). fpocketR >= 1.3.0 should support conda/miniconda/microconda
• Rewrote documentation and added READTHEDOCS
• Improved installation process. The recommended installation in now conda + pip
• Replaced rcsb.org (RETIRED) with www.ebi.ac.uk for ligand .sdf file requests

fpocketR 1.1.0

New features:

• --pdb excepts a PDB code input in addition to a file path (auto fetch from the PDB)
• Update to 2D figures using RNAviagte v1.0.0
• Calculates ligand: npr1, npr2, geometry, and QED score
• --chain default value changed to automatically detect the first RNA chain in the structure
• Integrated essential RNAvigate features to streamline installation

Bug fixes

• Improved error messaging
• Fixed ligand bugs
• #1 fixed offset bug

fpocketR 1.0.0

The original version released with the publication of "Ligand-binding pockets in RNA, and where to find them."