v0.9.1

2024-12-18 21:18:57

Focus on

1. add Gromacs scripts
2. add scripts and fix bug in docs

What's New

• addon: lazydock\scripts\eval_modeling.py: add eval_modeling script for protein modeling evaluation
• addon: lazydock\gmx\thirdparty\cgenff_charmm2gmx.py: Add new script cgenff_charmm2gmx.py to convert CHARMM parameters to GROMACS format, with compatibility with Networkx 3.X. THIS SCRIPT IS FROM https://github.com/Lemkul-Lab/cgenff_charmm2gmx
• addon: lazydock\storage\lazydock-cli-scripts-list.json: add gmx script
• addon: add lazydock\gmx\run.py: add Gromacs class for running GROMACS commands
• addon: lazydock\pml\utils.py: add get_seq function to get protein sequences
• addon: lazydock\scripts\gmx.py: add prepare_complex script for GROMACS

Minor Addon

• minor-addon: lazydock\scripts\dock.py: HDOCK and HPEPDOCK: add GUI option for browser and refactor docking process
• minor-addon: lazydock_pymol_plugin_init_.py: add align_pose_to_axis command to LazyDock Pymol Plugin
• minor-addon: lazydock\pml\align_to_axis.py: add 'alter' method to align pose to axis
• minor-addon: lazydock\pml\align_to_axis.py: add dss option to align_pose_to_axis function

BUG-FIX

• fix-bug: lazydock\pml\align_to_axis.py: sort_vertices: improve bounding box alignment algorithm
• fix-bug: lazydock\gmx\thirdparty_init_.py: create thirdparty init file

CODE-FIX

• fix-code: lazydock\scripts\eval_modeling.py: add QMEAN and QMEANDisCo support and improve result formatting
• fix-code: lazydock\scripts\dock.py: update run_vina task to include vina_name argument

Remove

None or a little.

Other Changes

• build(dependencies): add networkx
• requirements.json: remove compas because it require numpy<2