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