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