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Changelog

RELEASE 2.0.0 - Oct 1, 2026

Features

  • Added timeout argument to compare_molecules in the PARITY method to control the MCS calculation time (default 40 seconds)
  • Added validate_ligand_cif_categories and validate_mm_cif_categories to validate ligand and macromolecule CIF files before reading
  • Errors raised during sanitisation are now reported in the errors of the reader results
  • CIP labels are assigned to molecules after sanitisation (#36)

Bug fixes

  • Stereochemistry is assigned from the Ideal conformer when it is valid, falling back to the Model conformer only when the Ideal one is degenerate
  • Physicochemical properties are calculated on the molecule without hydrogens, so bonds to terminal hydrogens are no longer counted as rotatable bonds
  • RDKit logging no longer redirects the global standard error output

Breaking changes

  • Added errors field to SanitisationResult, a list of "<error type>: <message>" strings
  • sanitize no longer converts bonds between metals and other atoms to dative bonds to fix valence issues
  • Ligand CIF readers raise CCDUtilsError when _chem_comp. or _chem_comp_atom. categories are missing, or when a macromolecule mmCIF file is provided
  • Bound molecule reader raises CCDUtilsError when _entry., _atom_site. or _chem_comp_bond. categories are missing
  • Missing optional categories are reported as a single warning (missing: ...) instead of one warning per category
  • compare_molecules raises TimeoutError when the MCS calculation times out
  • Physicochemical property values (e.g. NumRotatableBonds) differ from previous versions
  • Removed preprocessable_categories from ccd_reader, clc_reader and prd_reader

RELEASE 1.0.0 - Sep 4, 2025

Features

  • Support for RDKit 2025 and NumPy 2.0
  • Uses both coordgen library and the default RDKit functionality to generate 2D depictions

RELEASE 0.8.6 - Oct 28, 2024

Features

  • Enable parsing of a subset of CCDs from the Chemical Component Dictionary
  • Added CCDC to UniChem resources

RELEASE 0.8.5 - May 26, 2024

Features

  • Updated for RDKit 2023.09.6
  • Removed the formal charge adjustment for valence issues, instead uses Dative bonds
  • Uses Zero bond type (dotted lines) for depiction of coordinate bonds
  • Changes Dative bonds to single bonds for inchi calculation
  • Corrected the format of PDB files
  • Corrected the header of SDF file

Breaking changes

  • Removed smile from SubstructureMapping and added mol

RELEASE 0.8.0 - July 26, 2023

Features

  • Added clc_reader and clc_writer to read and write Covalently Linked Components (CLCs)
  • Added prd_reader and prd_writer to read and write Protein Reference Dictionarys (PRDs)
  • Added boundmolecule_cli, a pipeline to infer CLCs from PDB model files

RELEASE 0.7.0 - February 26, 2023

Features

  • Replaced pdbecif with gemmi for mmcif parsing
  • Support for rdkit 2022.09.x
  • Component representation of Covalently Linked Components (complex multi-component ligands typically represented as individual components represented by individual CCDs)

Breaking changes

  • Removed ccd_cif_dict (dict) property of Component. Please use ccd_cif_block (gemmi.cif.Block) to access data from mmcif file

RELEASE 0.6 - April 26, 2021

Features

  • A lot of minor bug fixes and code improvements
  • New templates for 2D layouts
  • Support for rdkit 2021.03.x

RELEASE 0.5 - May 15, 2019

Features

  • Add support for UniChem mapping.
  • Add bond information to the SVG decomposition.
  • Allow PARITY method to be atom/bond specific.
  • Improve and extend physchem properties.
  • Enhanced CIF export (physchem, scaffolds, fragments, 2D, mapping).
  • Few improvements to match newest RDKit version (breaking changes).

RELEASE 0.4 - January 12, 2019

Features

  • Add SVG decomposition in the SVG format.
  • Protein-ligand interaction pipeline moved to separate repository.
  • Add basic properties calculation (Abhik).
  • Extension and improvements of the Fragment library.

RELEASE 0.3 - October 12, 2018

Features

  • Introduce CoordGen from RDKit.
  • Refactored pdbeccdutils.core (breaking changes).
  • Scaffolding (Abhik).
  • Add protein-ligand interaction pipeline.

RELEASE 0.2 - June 14, 2018

Features

  • PDBeChem pipeline.
  • Support for PARITY method.
  • Introduce EKTGv2() method for 3D conformer generation.