Changes in version 2.4.5 (2026-05-12)                  

Refactoring

  - Fully removed deprecated code based on "cryst1";
  - Changed order of arguments in the pdb-constructor;

New Functionality

  - Function connect.nucleic: Connect all atoms in nucleic acids;
  - Read secondary structure: Helix & Sheet;
      - Helper functions & Class (still hidden);
  - Extract names of Hetero-Molecules;
  - S3 method: crystal.pdb;
  - Function range.lattice is exported as well: finally found way to
    export it;
  - Function lattice.range: as alias for range.lattice.pdb;
  - Function mark.pdb: but still hidden;
  - Function drop.h: remove hydrogen (for NMR structures) - still
    hidden;
  - Functions to merge Hetero-Molecules & Secondary Structures;

Enhancement:

  - [fix] Model extraction in read.pdb;
  - Handle duplicate residues when connecting atoms/backbone;
  - Improvements to addAxes;
  - Keep the pdb fields Structure & Resolution after split;
  - Clever "[" for atoms object (potentially introducing very
    hard-to-debug bugs);

TODO

  - Extract all useful code and ideas from the discussion thread:
      - Root:
        https://stat.ethz.ch/pipermail/r-help/2023-October/478359.html
      - Example:
        https://stat.ethz.ch/pipermail/r-help/2023-October/478372.html

====

                 Changes in version 2.4.4 (2026-03-30)                  

Refactoring

  - Renaming "conect" -> "connect";
      - Renamed class to "connect";
      - Renamed function arguments to "connect";
      - Renamed functions to "connect";

New Functionality

  - Function chains: extract chain-codes;
  - Function select: Select groups of atoms;
  - Function residues: hidden/undocumented;
  - Function translate: shift observer;
  - Function addBBox: tight bounding box;
  - S3 method: distances.connect;

Enhancement:

  - PDB:
      - Properly import chemical symbols of elements (for newer PDB
        format);
      - Improved handling of atom names (older versions of PDB format);
      - Re-index ElementID (always);
  - Function addPBCBox:
      - new argument scale: includes also relative shift;
      - new argument col: set colour of box;
      - new argument alpha: set transparency;
      - x can be also a PDB molecule;
  - Visualization:
      - Improved: Protein backbone;
      - Improved: Nucleic acid backbone;
      - [fix] Nucleic acids: Detect both "X*" and "X'" codes;
      - Improved: Brute force connectivity;

=====

                 Changes in version 2.4.3 (2026-03-16)                  

  - Improved visualization:
      - Connect protein backbone: basic code;

Refactoring:

  - Rename: conect -> connect;
      - started some work;

                 Changes in version 2.4.1 (2025-09-15)                  

New Functions

  - dist.point: distances to a given point;
  - centres.ppRoll: centres computed using a rolling window over a
    peptide chain;

Updates to Existing Functions

  - Function read.pdb:
      - Bug fixed: process only FieldName CRYST1;
      - New arg: verbose = TRUE;
      - Warn if pdb is marked as obsolete;
      - Multi-line titles: import only the text;
      - Extract resolution from pdb;
      - Renaming arg CRYST1 to CRYSTAL;
  - Function is.crystal: as replacement to is.cryst1;
  - Function visualize.coords: starting some refactoring / optimization;
  - Function toSymbols: started refactoring;
  - [started] Renaming function cryst1 to crystal;

Deprecated

  - Class cryst1: replaced by class crystal;

                 Changes in version 2.3.4 (2023-09-28)                  

  - new maintainer;

Updates of Existing Functions

  - code updated to use rgl >= 1.1.3;

Documentation

  - corrected various bugs with Roxygen2;
  - improved compliance with CRAN-checks;