2024-12-18 21:18:57

Focus on

  1. add Gromacs scripts
  2. fix code in interaction analysis

What's New

  • addon: lazydock\scripts\prepare_gmx.py: add prepare_protein and prepare_ligand
  • addon: lazydock\pml_plugin_init_.py: add open_vina_config_as_box: add function to visualize Vina config as box and improve plugin loading
  • addon: lazydock\scripts\run_gmx.py: add simple_complex implementation
  • addon: lazydock\scripts\distribute_file.py: add distribute_file.py for distributing files or directories
  • addon: lazydock\scripts\ana_gmx.py: add 'simple' command

Minor Addon

  • minor-addon: lazydock\scripts\gmx.py: prepare_complex: add max-step option to control processing steps
  • minor-addon: lazydock\pml\align_to_axis.py: add rotate method
  • minor-addon: lazydock\pml\align_to_axis.py: add move_name option
  • minor-addon: lazydock\scripts\prepare_gmx.py: (prepare_gmx): add option to specify N-Term type for gmx pdb2gmx
  • minor-addon: lazydock\scripts\prepare_gmx.py: add customizable arguments for pdb2gmx command
  • minor-addon: lazydock\scripts\run_gmx.py: protein: add auto box generation for Gromacs
  • minor-addon: lazydock\gmx\run.py: Gromacs: add log functionality for run_command_with_expect
  • minor-addon: lazydock\scripts\run_gmx.py: simple_protein: add auto-box and auto-box padding option
  • minor-addon: lazydock\gmx\run.py: Gromacs: gen_command: remove None values from kwargs in Gromacs class
  • minor-addon: lazydock\gmx\run.py: Gromacs: gen_command: add 'no' support

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
  • fix-bug: lazydock/scripts/prepare_gmx.py: update force field directory handling and add chain alteration
  • fix-bug: lazydock/scripts/prepare_gmx.py: ligand: use editconf insdead of pdb2gmx to get toplogy
  • fix-bug: lazydock\scripts\run_gmx.py: simplify complex class and update related functionality
  • fix-bug: lazydock\scripts\run_gmx.py: simple_protein: modify mdrun commands args for em, nvt, npt
  • fix-bug: lazydock\scripts\prepare_gmx.py: ligand: prepare_ligand: Fix type conversion of ff_dir to string when calling run_transform function
  • fix-code: lazydock\scripts\ana_interaction.py: deprecated excute_command
  • fix-bug: lazydock\scripts\ana_interaction.py: move error check for interactions to earlier position
  • fix-bug: lazydock\scripts\align_pose_to_axis.py: correct argument parsing for file types

CODE-FIX

  • fix-code: lazydock\scripts\gmx.py: prepare_complex: move some steps' code into staticmethod
  • fix-code: lazydock\config.py: add named_accounts for CGenFF and update config usage; Rename 'configs' instance to 'GlobalConfig' for better naming convention
  • fix-code: lazydock\web\cgenff.py: get_login_browser: change to headless browser
  • fix-code: lazydock\scripts\gmx.py: prepare_complex: implemente CGenFF spider call
  • fix-code: lazydock\pml_plugin_init_.py: align_pose_to_axis_warp: add quiet parameter to align_pose_to_axis_warp function, change default move_method to rotate
  • rename lazydock\scripts\gmx.py to lazydock\scripts\prepare_gmx.py
  • fix-code: lazydock\scripts\prepare_gmx.py: simplify subcommand names for GROMACS preparation
  • fix-code: lazydock\scripts\prepare_gmx.py: ligand: improve ff-dir handling and logging
  • fix-code: lazydock\gmx\run.py: Gromacs: run_command_with_expect: improve timeout handling in Gromacs class
  • fix-code: lazydock\scripts\run_gmx.py: simple_protein: add expected actions and visualization
  • fix-code: lazydock\storage\lazydock-cli-scripts-list.json: add run_gmx script support
  • fix-code: lazydock\scripts\prepare_gmx.py: protein: change output name to f'{protein_path.stem}.gro'
  • fix-code: lazydock\scripts\run_gmx.py: simple_protein: adjust simulation settings and improve data visualization
  • refactor(gmx): improve command log display in Gromacs class
  • fix-code: lazydock\scripts\run_gmx.py: simple_protein: correct box size and center for solvated protein
  • fix-code: lazydock\scripts\run_gmx.py: simple_protein: do not dicrease box size if sol box is bigger than protein box
  • fix-code: lazydock\scripts\run_gmx.py: simple_protein: organize main_process into functions for better readability and maintainability
  • fix-code: lazydock\pml\interaction_utils.py: handle TypeError in get_distance_info
  • fix-typo: lazydock\scripts\run_gmx.py： simple_protein: main_process: correct variable in error message

Remove

None or a little.

Other Changes

  • build(dependencies): add networkx
  • requirements.json: remove compas because it require numpy<2
  • fix-code: requirements.json: update requirements and add DuIvyTools dependency