Changelog

0.2.0

Added

  • output_format="atlas" writes one resumable results folder per run, with Parquet tables and one pose file per protein. Several jobs can write into the same folder (Results format).

  • execute_docking() shows the best scores at the end. best_scores(), show() and select() work on the run, and Results gives the same methods for an earlier run (Getting started).

  • show() draws the results like the protein page of the PocketVina Atlas (3D views).

  • PoseBusters checks of selected poses, of a whole run, or during docking (PoseBusters checks).

  • Several engines per GPU, and several GPUs in one run (GPUs and GPU sharing).

  • The pocketvina command with dock, bust, show, export, info, query, import-legacy, setup p2rank and bench gpu (Command line reference).

  • Seeded runs: the same seed gives the same poses again.

  • top_pockets and pockets choose the pockets. pockets_dir docks into pockets that P2Rank found before.

  • mmCIF and PDBQT structures, also gzipped.

  • A Colab notebook, these pages and a conda recipe.

Changed

  • PocketVina is on PyPI: pip install pocketvina installs everything and compiles nothing. P2Rank is downloaded at the first run, and no environment variables need to be set (Installation).

  • The pip package is now pocketvina. Uninstall pocketvina-gpu first (Migrating from PocketVina 0.1).

  • Ligands are docked from their largest fragment. ligand_prep="legacy" restores the preparation of 0.1.

  • The engine compiles its GPU code on first use into ~/.cache/pocketvina and never writes into the installation.

  • Importing pocketvina no longer changes environment variables.