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

v0.8.0

2024-12-10 11:25:58

Focus on

1. add scripts (get_pocket, ana_interaction, dock)
2. fix-bugs in interaction analysis functionality

What's New

• addon: lazydock\scripts\get_pocket.py
• addon: add get_pocket and ana_interaction
• addon: lazydock\pml\autodock_utils.py: implement DLG file merging functionality
• addon: lazydock\scripts\ana_interaction.py: add simple analysis script for docking results
• addon: lazydock\scripts\dock.py: add dock script for molecular docking
• addon: lazydock\scripts\dock.py: add convert-result command for docking result conversion
• addon: add lazydock\web\lig_eval.py: add get_score_from_SwissADME and get_score_from_SwissTargetPrediction
• addon: add lazydock\web\hdock.py: add HDOCK docking functionality
• addon: lazydock\scripts\dock.py: add HDOCK docking support
• addon: lazydock\web\hdock.py: add support for HPEPDOCK docking
• addon: lazydock\scripts\dock.py: add HPEPDOCK docking command-line tool

Minor Addon

• minor-addon: lazydock\web\gen_pocket.py: make ligand_path parameter optional in get_pocket_box_from_ProteinPlus function
• minor-addon: lazydock\pml\ligplus_interaction.py: add force_cwd option to make sure the cwd works in Windows
• minor-addon: lazydock\pml\ligplus_interaction.py: add w_dir option
• addon: lazydock\pml\interaction_utils.py: add hydrogen_atom_only option
• addon: lazydock\scripts\ana_interaction.py: add hydrogen_atom_only option
• minor-addon: lazydock\scripts\ana_interaction.py: simple_analysis: output_fromater_receptor: sort interactions by residue number and improve output formatting
• minor-addon: lazydock\scripts\dock.py: hdock: support docking with receptor and ligand files directly

BUG-FIX

• fix-bug: lazydock\pml\plip_interaction.py: calcu_receptor_poses_interaction: avoid merge error when taskpool is None
• fix-bug: lazydock\scripts\get_pocket.py: improve pocket detection and output organization
• fix-bug: lazydock/scripts/dock.py: hdock: run_hdock_web: make right w_dir parsing when config_path is tuple
• fix-bug: lazydock\scripts\dock.py: hpepdock: update argument parser by change attributes
• fix-bug: lazydock\scripts\dock.py: add result_prefix argument to hdock_run_fn_warpper to specify the HDOCK and HPEPDOCK

CODE-FIX

• fix-code: lazydock\pml\ligplus_interaction.py: replace ValueError with put_err for better error handling
• fix-code: lazydock\pml\plip_interaction.py: handle unsupported mode and PLIP analysis errors
• fix-code: lazydock\pml\autodock_utils.py: update PDB pattern to match more case
• fix-code: lazydock\web\lig_eval.py: rename lig_eval.py output files with prefix
• fix-code: lazydock\web\lig_eval.py: handle "too large" error for lig_SMILES in SwissADME and SwissTargetPrediction
• fix-code: lazydock\scripts\dock.py: vina: change config file handling to directory-based
• fix-code: lazydock\web\hdock.py: add page refresh for HDOCK and HPEPDOCK result checking

Remove

None or a little.

Other Changes

• build(dependencies): update mbapy to version 0.10.2
• Upgrade mbapy from version 0.10.0 to 0.10.2 in requirements.json

v0.6.1

2024-11-06 22:06:27

Hotfix for v0.6.0

Focus on

1. fix interaction functionality's bug

What's New

None or a little.

Minor Addon

• minor-addon: lazydock\config.py: Config: add load and dump method

BUG-FIX

• fix-bug: lazydock\pml\interaction_utils.py: calcu_receptor_poses_interaction: add only_return_inter param to control the return part of interactions dict
• fix-bug: lazydock\pml\ligplus_interaction.py: _run_ligplus_for_complex: change logic for linux platform recognition from equal to startswith

CODE-FIX

None or a little.

Remove

None or a little.

Other Changes

None or a little.

v0.6.0

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: v0.5.0...v0.6.0

v0.5.0

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: v0.4.0...v0.5.0

v0.4.0

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: v0.2.0...v0.4.0

v0.2.0

2024/9/4 21:31:18

Focus on

1. Add pml.shader and pml.server sub-module

What's New

• addon: add lazydock\pml\shader.py
• addon: lazydock\pml\server.py
• addon: add lazydock_pymol_plugin\lazy_plot.py
• addon: lazydock_pymol_plugin_init_.py: extend new cmd: start_lazydock_server
• addon: lazydock\pml\shader.py: ShaderValues: add method from_interaction_df
• addon: lazydock\pml\shader.py: Shader: add repr method
• addon: lazydock\pml\shader.py: Shader: add method auto_scale_norm, apply_shader_values_to_selection, apply_shader_values_to_sele

Minor Addon

• minor-addon: lazydock\pml\shader.py: Shader: apply_shader_values: add alpha_mode argument
• minor-addon: lazydock\pml\shader.py: Shader: support global_name2col and norm
• minor-addon: lazydock\pml\server.py: add data-length to enssure server can read all data
• minor-addon: lazydock\pml\shader.py: add _cmd option
• minor-addon: lazydock\pml\server.py: VClient: send_action: support return the return value of an action
• minor-addon: lazydock_pymol_plugin_init_.py: start_lazydock_server: add start log

BUG-FIX

• fix-bug: lazydock\pml\shader.py: from_interaction_df: skip first row now
• fix-bug: lazydock\pml\shader.py: fix _cmd argument passing

CODE-FIX

• fix-code: lazydock\pml\interaction_utils.py: add all
• fix-code: lazydock_pymol_plugin\main.py: GUILauncher: add lazy_plot_tab
• fix-code: lazydock_pymol_plugin\lazy_plot.py: move pymol import to dev code

Remove

None or a little.

Other Changes

None or a little.

Details

完整的更新日志: https://gitee.com/bhm-bob/LazyDock/commits/v0.2.0
Full Changelog: v0.1.0...v0.2.0

v0.1.0

v0.1.0