Lazydock

**1. scripts/ana_gmx**

**New Features**
- **Added method selection feature for GROMACS analysis**:
- Implemented the `--methods` command line argument to allow users to select specific analysis methods.
- Added conditional execution of analysis methods based on user selection.
- Updated the help message to include the new method selection feature.
- Rearranged import statements for better organization.
- **Commit Hash**: `386c6e63a2f6df9e4c679fa7a8e1ee5d6057e2f2`
- **Added DSSP analysis functionality**:
- Implemented DSSP (Dictionary of Secondary Structure of Proteins) analysis.
- **Commit Hash**: `6ca1bd54c9feb05ad6d85e9477e315e8d3b0bc78`
- **Added porcupine plot analysis for GROMACS simulation**:
- Implemented porcupine plot analysis for visualizing GROMACS simulation results.
- **Commit Hash**: `4e15c43cfb3b0f4025da2cf280785f6f5e7af705`
- **Added RRCS (Residue-Restraint Cumulative Score) analysis**:
- Implemented RRCS analysis functionality.
- Added new class `RRCS` to handle RRCS calculations.
- Updated `str2func` dictionary to include RRCS analysis.
- Modified `main_process` method to support RRCS calculations.
- Added support for numpy, torch, and cuda backends for RRCS calculation.
- **Commit Hash**: `84e1812a97c20fd4946b233319c19f372d58801c`

**Improvements**
- **Improved interaction analysis plot visualization**:
- Added y-axis tick interval and figure size arguments.
- Enhanced heatmap visualization with custom color map and labels.
- Set default beginning frame to 1 for analysis.
- **Commit Hash**: `4420b86957f68b478fadcf8f6cc481ed63f5a4bb`
- **Updated axis label for residue interaction plots**:
- Changed the xlabel from 'Residue' to 'Residues (aa)' for residue interaction plots.
- **Commit Hash**: `98d5de3a76a7a3964e750eff93192402bc7ac87c`
- **Added options to skip plot and limit max residues to plot**:
- Added options to skip plot generation and limit the number of residues plotted.
- **Commit Hash**: `da19a37539dee10d9671e1c1f53eeca9447515ad`
- **Added option to clear DSSP calculation**:
- Added an option to clear DSSP calculation results.
- **Commit Hash**: `ea81430ac3fe94bc857c3e39dd954d9a42955fd1`
- **Added ur option for trjconv and updated related commands**:
- Added '-ur' argument to trjconv class for unit cell shape selection.
- Updated trjconv command execution to include ur option.
- **Commit Hash**: `807e6eb74790f4c01fb1215733ed164ae5427c0c`

**Bug Fixes**
- **Prevent plotting empty dataframe**:
- Added a check to ensure the plot_df DataFrame is not empty before plotting.
- **Commit Hash**: `1a8df6f2e53e04677e60ba7788d2196a23c528b4`
- **Sort interaction columns by residue number**:
- Fixed the sorting of interaction columns by residue number.
- **Commit Hash**: `b90363cd601480b31d0616f1669b6e10b52b7cc1`
- **Check support mode for plip interaction analysis**:
- Fixed the support mode check for plip interaction analysis.
- **Commit Hash**: `2ea167371dcab7e5e11f21e86675e79883f81267`
- **Optimize plip interaction processing**:
- Fixed and optimized plip interaction processing.
- **Commit Hash**: `815615fe47c523c08e52582d90a63666e3d7278d`

**2. scripts/md_task**

**New Features**
- **Added PRS (Perturbation Response Scanning) functionality**:
- Implemented PRS analysis in the md_task module.
- Added `prs_main` function import from `lazydock_md_task.scripts.prs`.
- Created `prs` class with `calcu_network` and `save_results` methods.
- Updated `_str2func` dictionary to include 'prs' option.
- **Commit Hash**: `8185e16b6510bf45ae676e99dd299d512ff47636`
- **Added chain selection for network analysis**:
- Removed ligand selection option from network and correlation classes.
- Added chain selection option (-c, --chain).
- Updated atom selection logic to use chainID when chain is specified.
- Improved code readability and flexibility for different molecular systems.
- **Commit Hash**: `cc3eb892a02bc8ccb14b2f4ec2618df58f86a2db`

**Improvements**
- **Improved network analysis visuals and output**:
- Enhanced the visualization and output of network analysis results.
- **Commit Hash**: `3c5b34603ddc994ecfb637098eee700f2ec1dc5b`
- **Fixed atom selection for parallel calculation**:
- Fixed the atom selection logic for parallel calculation.
- **Commit Hash**: `cc85e9c65d6702a51caccb8e934d38c1f851c7dc`

**3. lazydock**

**Bug Fixes**
- **Fixed typo in distribute_file script name**:
- Fixed typo in script name from 'distrbute_file' to 'distribute_file'.
- Updated corresponding exec_names and detailed description.
- **Commit Hash**: `0b0054713d07bfd99a5262a02af224040ab0d9b7`
- **Fixed typo in 'choices' parameter for mode argument parser**:
- Fixed typo in 'choices' parameter for mode argument parser.
- **Commit Hash**: `b5a23c334251a2a80cdc4a9724932c5fb72e35e8`

**Improvements**
- **Updated RMSD calculation module location**:
- Updated the location of the RMSD calculation module.
- **Commit Hash**: `1b68912a72edb73444a89398d4f163e2bdb9ce34`
- **Added fit_to fix-bug: lazydock/gmx/mda/rms.py: fix rmsd and rotation calculation**:
- Fixed RMSD and rotation calculation bugs.
- **Commit Hash**: `17b6ff0ec165c3945bad59d7b769db0737ef7dbd`

**4. pml Module**

**New Features**
- **Added exception handling and debugging information**:
- Added exception handling and debugging information to plip interaction analysis.
- **Commit Hash**: `9404e5220d0a630d7cf5aa0a782d9dd77657a28a`
- **Added modevectors function for visualizing protein movements**:
- Added `modevectors` function for visualizing protein movements.
- **Commit Hash**: `f3ea93eb30fff7741d6511f24483e1b32e5b66fa`

**Improvements**
- **Improved interaction calculation with mode support**:
- Improved interaction calculation with mode support.
- **Commit Hash**: `92dac5995b5c80d51256c0f3d2f05b5e5621eb48`

**5. gmx/mda Module**

**New Features**
- **Implemented GNM analysis functions**:
- Added GNM (Gaussian Network Model) analysis functions.
- **Commit Hash**: `e2dfe6cebb8239d1df8a4f5fe8853855507f5382`
- **Implemented RMSD calculation functions**:
- Added RMSD (Root Mean Square Deviation) calculation functions.
- **Commit Hash**: `a4a962ba2ea2db4e88ed4c576284ae198b6b857c`

**Improvements**
- **Optimized PDB file writing in mdanalysis converter**:
- Optimized PDB file writing in the mdanalysis converter.
- **Commit Hash**: `c670fd8e63015d3c3b3daa34504be0d02e86fc27`
- **Added chain-based record type alteration in PDB conversion**:
- Added chain-based record type alteration in PDB conversion.
- **Commit Hash**: `a44250dda87c30c235a782b97b29a5e7d81e25a7`

**6. Scripts Module**

**New Features**
- **Added MDTraj CLI tools**:
- Added MDTraj CLI tools for molecular dynamics trajectory analysis.
- **Commit Hash**: `b2d8e52dd5bff7ee83b7c2a7565c7480e157984f`
- **Added MDAnalysis analysis script**:
- Added MDAnalysis analysis script for molecular dynamics analysis.
- **Commit Hash**: `4a35c9e6a898a4d7250e7da84cedcf69356cea22`

**Improvements**
- **Optimized import structure and order in script files**:
- Reorganized import statements in script files for better readability and organization.
- **Commit Hash**: `db9a468d1e6a04a02bf521082d47b2156e176c0c`

**7. Documentation and Build**

**Documentation**
- **Updated installation guide and added Python env compatibility info**:
- Updated the installation guide and added information about Python environment compatibility.
- **Commit Hash**: `2f34c37df0ed34c7d30b2e1c8ab16823df5408d0`
- **Moved lazydock_md_task from default to all dependencies**:
- Moved `lazydock_md_task` from default dependencies to all dependencies to support the Windows platform.
- **Commit Hash**: `1872cf52f2803b695a35df0c448813b638a068af`

**Build**
- **Added toml package to requirements**:
- Added `toml` package to the list of requirements to support the use of TOML files in the project.
- **Commit Hash**: `ac8f53887c9bfe2820fd170e7d2b4fa40c2fcc6f`

2025-02-06 16:08:21

Focus on
1. fix bugs in lazydock/scripts/prepare_gmx.py, run_gmx.py, ana_gmx.py


What's New
- addon: lazydock\pml_plugin\_init_.py: add RRCS calculation and shader application features
- addon: lazydock\web\dinc.py: add DINC ensemble docking functionality
- addon: lazydock\scripts\dock.py: add DINC-Ensemble docking command tool
- addon: lazydock\scripts\dock.py: add cluster_result: add cluster analysis for docking results
- addon: add lazydock/scripts/md_task.py: add optimized CLI tools for MD-TASK
- addon: lazydock/scripts/md_task.py: add contact map analysis for MD-TASK
- addon: lazydock/gmx/mda/convert.py: add PDB string converter


Minor Addon
- minor-addon: lazydock\scripts\ana_interaction.py: simple_analysis: add reference residue analysis
- minor-addon: lazydock\scripts\dock.py: vina: add customization options for config file name and Vina arguments
- minor-addon: lazydock\scripts\run_gmx.py: simple_protein: add em-args to run_gmx.py
- minor-addon: lazydock\pml\autodock_utils.py: DlgFile: add max_iter parameter to rmsd_cluster method
- minor-addon: lazydock\scripts\run_gmx.py: simple-protein: add start time argument and sleep until start
- minor-addon: lazydock\scripts\prepare_gmx.py: add C-terminal option and modify N-terminal logic
- minor-addon: lazydock\scripts\ana_gmx.py: simple: add customizable group and xmax options for analysis
- minor-addon: lazydock\scripts\prepare_gmx.py: protein: support multiple chains in protein
- minor-addon: lazydock\scripts\run_gmx.py: add check for existing md.tpr file
- minor-addon: lazydock/scripts/ana_gmx.py: simple: add -ns option to xvg_compare and xvg_show
- minor-addon: lazydock/scripts/run_gmx.py: simple_protein: add maxwarn option to grompp commands
- minor-addon: lazydock/scripts/ana_gmx.py: simple: add free energy landscape analysis by md-davis


BUG-FIX
- fix-bug: scripts/ana_interaction.py: pass ref_res to calc_interaction_from_dlg, add reference residues sorting and formatting
- fix-bug: My_Progs/LazyDock/lazydock/web/dinc.py: run_dock_on_DINC_ensemble: fix waiting logic and result file extraction process
- fix-bug: lazydock\scripts\ana_gmx.py: simple: correct SASA calculation in Gromacs
- fix-bug: lazydock\scripts\ana_gmx.py: simple: add -c 1 option to dit xvg_compare for consistency
- fix-bug: lazydock\scripts\run_gmx.py: simple-protein: optimize start time functionality
- fix-bug: lazydock\gmx\thirdparty\cgenff_charmm2gmx.py: use only file names for prm and itp inclusions for fit run_gmx: simple_complex: equilibration: STEP 2
- fix-bug: lazydock\web\cgenff.py: get_result_from_CGenFF: correct function name and update LastEditTime
- fix-bug: lazydock\scripts\prepare_gmx.py: ligand: prepare_ligand: improve ff-dir handling logic to avoid not copy abs ff-dir
- fix-bug: lazydock\scripts\run_gmx.py: update prompt matching
- fix-bug: lazydock\scripts\prepare_gmx.py: complex:prepare_complex_topol: add newline at the end of topol file in prepare_gmx.py
- fix-bug: lazydock\scripts\run_gmx.py: add genion_groups argument and adjust related functionality
- fix-bug: lazydock\scripts\prepare_gmx.py: ligand: fix_name_in_mol2: update mol2 file parsing
- fix-bug: lazydock\scripts\ana_gmx.py: simple: gyrate: remove parameter from gyrate function for compatibility
- fix-bug: lazydock/scripts/run_gmx.py: simple_protein: main_process: add continue statement for md.tpr check in simple_protein command
- fix-bug: lazydock/gmx/run.py: Gromacs: run_command_with_expect: add quotes around bash_path in expect script to avoid path parsing issues
- fix-bug: lazydock/scripts/_script_utils_.py: excute_command: update to mbapy 870aaf003c380a1172ca4bb84c676a1c32bcce27


CODE-FIX
- fix-code: lazydock/pml/ligplus_interaction.py: improve path handling in ligplus_interaction
- fix-code: lazydock\pml\align_to_axis.py: change dss option to be False in default, avoiding ss change
- fix(scripts): correct SASA and covar analysis in ana_gmx.py
- fix-code: lazydock\scripts\ana_gmx.py: simple: enhance data visualization and analysis
- fix-code: lazydock\scripts\run_gmx.py: simple-protein: make mdp file arguments required and improve missing file warning
- fix-code: lazydock\scripts\ana_gmx.py: simple: modify RMSF and covariance analysis in Gromacs script
- fix-code: lazydock\scripts\prepare_gmx.py: ligand: avoid using pymol to disorder the lig_ini.pdb lines; add copy for topol.top
- fix-code: lazydock\scripts\run_gmx.py: simple_ligand: add group selection for energy analysis and improve ligand handling
- fix-code: My_Progs/LazyDock/lazydock/web/dinc.py: run_dock_on_DINC_ensemble: improve DINC browser automation with logging and screenshot
- fix-code: lazydock\web\cgenff.py: get_result_from_CGenFF: improve CGenFF result generation and download process
- fix-code: lazydock\scripts\prepare_gmx.py: ligand: prepare_ligand: handle CGenFF download failure and improve error logging
- fix-code: lazydock\scripts\prepare_gmx.py: refactor force field directory handling
- fix-code: lazydock/scripts/prepare_gmx.py: protein: improve handling of termini for multi-chain proteins in prepare_gmx.py
- fix-code: lazydock/scripts/run_gmx.py: simple_protein: update visualization commands
- fix-code: lazydock/gmx/run.py: update expect script timeout setting
- fix-code: lazydock/scripts/ana_gmx.py: simple: add timeout handling for Gromacs commands to fit different Gromacs versions
- fix-code: lazydock/scripts/md_task.py: network: add more info in argument parser
- fix-code: lazydock/scripts/md_task.py: fix import


Remove
None or a little.


Other Changes
- fix-code: requirements.json: add compas as an optional dependency
- build: add lazydock_md_task as a new dependency
- build(requirements): add md-davis package
- build: add plip as a new dependency
- build: update mbapy dependency to version 0.11.0

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

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

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