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Changelog

All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

None.

2.0.0 - 2023-10-12

🎉 LABODOCK v2.0.0 is here!

This update focuses on improving the code base, implementing informational molecular visualization, and fixing post-installation conda environment corruptions.

Most functions have been refactored and improved, and previous molecular visualization options have been reduced with new being added to provide informative visual inspection 👀.

The conda environment is no longer corrupted by MGLTools package installation, and you can now install any other packages that require Python 3.10 or higher 🐍.

The native ligand preparation step is now optional by default. Should you proceed without this phase, skip the 03 | Preparing the Native Ligand (optional) section ✨.

Added

  • PKG : Add meeko 0.5.0 to replace MGLTools 1.5.7 for preparing .pdbqt files
  • PKG : Add sPyRMSD 0.6.0 to include Hungarian's algorithm and symmetry corrected RMSD calculations
  • SRC : Add basic function type hints and annotations for better code understanding
  • PRE : Add bond order assignment for native ligand with RDKit AllChem.AssignBondOrdersFromTemplate() function
  • ENM : Add gradient option to select from conjugate (default) or steepest **
  • ENM : Add convergence criteria option to specify termination endpoint
  • ENM : Add maximum steps option to specify allowed iteration step
  • ENM : Add logging into _obmin.log file to store ligand EGM record
  • GBX : Add residues-defined gird box option (defined-by-res() method) using LaBOX method and list of user-inpt residues
  • RMS : Add maximum common substructrure PNG generation in ComputeRMSD() class
  • ANL : Add result clustring mode option to select from Best-Pose and LABO-RMSD **
  • ANL : Add ranking option for docking result ** (Sort_by, Order, Top, Maximum_RMSD)
  • ANL : Add ranking option for binding interactions with frequency bar chart ** (Sort_by, Order, Hide_hydrophobic, Show_barchart)
  • VIS : Add 8 new built-in py3Dmol stylings focusing on providing informational visualisation
  • VIS : Add 2 new protein surface representations with built-in colour scales (hydrophobicity, isoelectric points)
  • VIS : Add colour bar for displaying colour scale of surface representation with Matplotlib pyplot.colorbar() function
  • VIS : Add slab view option to display sagittal section of molecules
  • VIS : Add filter option to specify displaying binding interactions

Changed

  • PKG : Update Autodock Vina from 1.2.0 to 1.2.5
  • PKG : Update PLIP from 2.0.0 to 2.2.2
  • SRC : Update source code to improve logic, clarity and compliance to PEP 8, PEP 3107
  • DSC : Rewrite cell description and form fields to improve clarity, accuracy and specificity
  • PRE : Enable native ligand preparation step as optional #3
  • PRE : Replace molecule structure extraction code with vanilla extract_entity() function
  • PRE : Replace separate_chain() function with vanilla extract_chains() function
  • GBX : Encapsulate all grid box calculation functions into GridBox() class
  • DCK : Change --exhaustiveness default value to 16
  • INT : Update _cmpx.pdb file generation code with generate_cmpx_pdb() function
  • INT : Refactor interaction_profiler() into nested function
  • RMS : Replace get_RMSD() function with labo_RMSD() method under ComputeRMSD() class to generate MCS-based RMSD
  • RMS : Replace get_score() function with vina_report() function and rmsd_report() method to generate docking report
  • VIS : Replace VIEW() function with LaboSpace() class to consolidate all visualisation functions

Fixed

  • ENV : Conda base environment no longer corrupted from MGLTools installation
  • SRC : Replace non-standard for loop with pythonic-style for loop

Removed

  • SRC : Remove {'run': 'auto'} options
  • DCK : Remove SDF generation step for docked ligand output file in Process output file cell

Deprecated

  • PKG : Remove MGLTools, Pybel, Biopython, xlswritter

** Exclusively for virtual screening protocol.

1.2.2 - 2023-08-14

Changed

  • SRC : Update DataFrame merging method from append() to concat()
  • RMS : Rename labogrid() function to labox() as per version 1.2.1
  • VIS : Reset count to 0 in all VIEW_****() functions

Fixed

  • VIS : Correct input arguments for py3Dmol.view() function call in all VIEW_****() functions

1.2.1 - 2023-08-12

Added

  • DCK : Add os.cpu_count() to determine number of cpu cores available for --cpu parameter
  • DCK : Add --cpu parameter in %vina to maximise CPU resource

Changed

  • DSC : Rename LABOGRID to LaBOX
  • PKG : Update packages: py3Dmol 2.0.3, rdkit-pypi 2022.9.5, biopython 1.80, openbabel 3.1.1, zlib 1.2.13
  • SRC : Update mamba installation process

Fixed

  • VIS : Fix incomplete visualisation of binding interactions in VIEW_PILE() function

Removed

  • SRC : Remove unused space characters to improve PEP8 compliance

1.2.0 - 2023-02-12

This update primarily focuses on improvements to virtual_screening.ipynb

Added

  • GBX : Add 5 new methods for defining grid box
  • VIS : Add showHs argument in VIEW_LIG()

Fixed

  • DSC : Correct several spellings mistake

Removed

  • VIS : Remove AllChem.MMFFOptimizeMolecule() in VIEW_LIG()

1.1.0 - 2023-02-12

This update primarily focuses on improvements to basic_molecular_docking.ipynb

Added

  • GBX : Add 5 new methods for defining grid box
  • VIS : Add showHs argument in VIEW_LIG()

Removed

  • VIS : Remove AllChem.MMFFOptimizeMolecule() in VIEW_LIG()
  • VIS : Remove showBestPose argument in VIEW_PILE()

1.0.0 - 2023-02-08

Added

Deprecated

0.0.0 - 2022-09-21

Initial commit.

Abbreviations

PKG : Packages, ENV : Environment, SRC : Source code, DSC : Description, PRE : Preparation, ENM : Energy minimisation, GBX : Grid box , DCK : Docking, INT : Binding interactions, RMS : RMSD, ANL : Analysis, VIS : Visualisation