Rpdb 2.4.5

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

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Rpdb 2.4.4

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;

=====

Rpdb 2.4.3

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

Refactoring:

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

Rpdb 2.4.1

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;

Rpdb 2.3.4

• 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;