Biomolecule Toolkit 0.8.1

Biomolecule Toolkit project is an Open Source library for the structural modeling of biological macromolecules. The toolkit provides a C++ interface for common tasks in computational structural biology, to facilitate the development of molecular modeling, design, and analysis tools.
Enhancements:
Documentation updates
- Addition of an extensive discussion of the leastsquares_superposition and RMSD-calculation methods, including a description of the mathematical theory behind their operation.
- Fully documented the rotation/translation methods
- Addition of a documented example program ("gyration_radius.cpp")
Bug fixes
- Fixed copy construction bug in PDBAtomDecorator that caused compilation errors in rare situations.
- Fixed a bug in PDBFileParser that caused a compilation error in the PDBSystem copy constructor.
- Fixed a const-conversion bug in GroupedElementIterator which prevented proper interoperation of const and non-const iterator types.
- Fixed a crash-producing bug in stream output for the TypeID class.
- Fixed a math error in RMSD and superposition methods that would corrupt molecule coordinates.
- Fixed a bug that caused all default-constructed PDBAtom objects to be treated as HETATMs.
Feature additions
- Added operator[] to AtomicStructure and PolymerStructure-derived classes.
- Added protected increment() and decrement() operators to TypeID class.
- PDBFileParser can now handle PDB files with ill-formed residue numbering (i.e. Files where residue numbers are repeated in successive chains).