Lazydock

2024-11-06 22:06:27

2024-11-06 22:06:27


Focus on
1. fix interaction functionality's code to make pymol, PLIP and LigPlus as ONE.
2. add RMSD functionality to pymol-plugin.


What's New
- addon: setup.py: add entry point for lazydock_pymol_plugin.main:exec_from_cli in setup.py.
- addon: lazydock_pymol_plugin\main.py: Add exec_from_cli function to GUILauncher for command line interface execution.
- addon: lazydock_pymol_plugin\main.py: add LazyPml page and uni_load button
- add: lazydock_pymol_plugin\_nicegui\local_file_picker.py
- add: lazydock_pymol_plugin\lazy_pml.py
- addon: add lazydock\pml\ligplus_interaction.py
- addon: add lazydock\config.py
- minor-addon: lazydock\pml\interaction_utils.py: add string mode
- addon: lazydock\pml\autodock_utils.py: DlgFile: add method get_top_k_pose
- addon: lazydock_pymol_plugin\lazy_dlg.py: add RMSD functionality


Minor Addon
- minor-addon: lazydock_pymol_plugin\lazy_dlg.py: LazyPose: load_dlg_file: add path parameter
- minor-addon: lazydock\pml\plip_interaction.py: add mode param in string format
- minor-addon: lazydock_pymol_plugin\main.py: add upload for aonther uni-load
- minor-addon: lazydock_pymol_plugin\main.py: GUILauncher: add a taskpool in threads mode tab_panel style fix


BUG-FIX
- fix-bug: lazydock\pml\plip_interaction.py: calcu_receptor_poses_interaction: fix parameter passing for merge_interaction_df


CODE-FIX
- fix-code: lazydock\pml\ligplus_interaction.py: Fix comment clarification in ligplus interaction function.
- fix-code: lazydock\pml\interaction_utils.py: add a string mode 'all'
- fx-code: lazydock_pymol_plugin\lazy_dlg.py: InteractionPage: change mode from int for pymol to string for all methods


Remove
None or a little.


Other Changes
- Add "openbabel-wheel" to requirements.

**Full Changelog**: https://github.com/BHM-Bob/LazyDock/compare/v0.5.0...v0.6.0

2024-10-31 16:54:37


Focus on
1. add pocket utils
2. add RRCS calculation
3. add RMSD calculation for AutoDock result


What's New
- addon: add lazydock\web\gen_pocket.py
- addon: add lazydock\pml\thirdparty\__init__.py
- addon: add lazydock\pml\thirdparty\draw_bounding_box.py
- addon: add lazydock/pml/plip_interaction.py
- addon: lazydock_pymol_plugin\lazy_dlg.py: LazyDLG: add ResultPage
- addon: lazydock\pml\autodock_utils.py: add calcu_RMSD
- addon: lazydock\pyrt\relax.py: add RelaxPDBChain
- addon: lazydock\pyrt\energy_utils.py: add calcu_interface_energy
- addon: lazydock\pml\autodock_utils.py: add calcu_rmsd_by_coords and rmsd_cluster functionality


Minor Addon
- minor-addon: lazydock\web\gen_pocket.py: parse_pocket_box_from_ProteinPlus: add method: mean
- minor-addon: lazydock/pml/autodock_utils.py: ADModel: add default_chain option
- minor-addon: lazydock_pymol_plugin/lazy_dlg.py: InteractionPage: add PLIP calculate
- minor-addon: lazydock\pml\rrcs.py: add _cmd arg
- minor-addon: lazydock\pml\autodock_utils.py: ADModel: add run_idx attribute
- minor-addon: lazydock\pml\autodock_utils.py: DlgFile: rmsd


BUG-FIX
- fix-bug: lazydock_pymol_plugin\lazy_dlg.py: LazyPose: ui_update_ui: remove update for missing self.ui_dlg
- fix-bug: lazydock/pml/plip_interaction.py: get_atom_level_interactions: check receptor and ligand chain


CODE-FIX
- fix-code: lazydock\pml\interaction_utils.py: move sort function to module level for better accessibility
Moved the `sort_func` from within `calcu_receptor_poses_interaction` to the module level
Added type annotations to the `sort_func` for improved code clarity
Updated the `sort_func` to return a list of tuples with str, int, and str types
- fix-code: lazydock\web\gen_pocket.py: get_pocket_box_from_ProteinPlus: specify download path
- fix-code: lazydock\web\gen_pocket.py: add docs-string
- fix-code: setup.py: add lazydock_pymol_plugin as package
- fix-code: lazydock_pymol_plugin\lazy_dlg.py: remove RMSD because too slow


Remove
None or a little.


Other Changes
- use mbapy_lite instead of mbapy
- fix-code: requirements.json: Update mbapy version in requirements.json from 0.7.9 to 0.10.0.

**Full Changelog**: https://github.com/BHM-Bob/LazyDock/compare/v0.4.0...v0.5.0

2024-10-09 20:59:29


Focus on
1. Fix dlg-pdb parse in pml.autodock_utils
2. Add RRCS calcu in pml.rrcs


What's New
- addon: lazydock\pml\rrcs.py


Minor Addon
- minor-addon: lazydock_pymol_plugin\lazy_dlg.py: LazyPose: add parse2std and save_lig_with_HETATM option
- minor-addon: lazydock_pymol_plugin\lazy_dlg.py: LazyPose: ui_update_ui: excpt ligands in self.ui_molecule


BUG-FIX
- fix-bug: lazydock\pml\autodock_utils.py: fix PDB_PATTERN, avoid parsing error in ADModel: parse_content
- fix-bug: lazydock\pml\autodock_utils.py: remove q colum in PDB_PATTERN
- fix-bug: lazydock\pml\rrcs.py: back to for-loop calculation, correct calculation


CODE-FIX
- fix-code: lazydock\pml\autodock_utils.py: ADModel: parse_content: remove logic to force sort pdb lines if _parse2std is enabled
- fix-code: lazydock\pml\rrcs.py: optimize calcu_RRCS performance by using matrix calculation


Remove
None or a little.


Other Changes
None or a little.

**Full Changelog**: https://github.com/BHM-Bob/LazyDock/compare/v0.2.0...v0.4.0

**Full Changelog**: https://github.com/BHM-Bob/LazyDock/compare/v0.1.0...v0.2.0