General Concepts

1. This PDB parser is organized as a text handler. This comes since its aim is to provide easy access to methods such as residue/atom selection, concatenation of data, etc. It was not primarily designed for numeric calculation using PDB data.
2. The different levels of data organization are:
   1. PDB: The top level. It corresponds to the level of one PDB file that is seen as a collection a residues (amino-acids, nucleic-acids, etc)
   2. residue: The level of one residue, and the information associated.
   3. atmList: A collection of ATOM or HETATM lines.
   4. atmLine: One line of a PDB file, one of the ATOM or HETATM lines.
   5. PDBLine: One line of a PDB file, supposingly matching the PDB file format.
   6. The other PDB lines such as the REMARK lines, despite loaded are only partly managed.

The navigation through the different levels should be rather intuitive:

Selecting a set of residues (or loading a file) will result in a PDB instance whereas selecting one residue will result in a residue instance. Selecting a subset of a residue will result in an atmList instance, and finally selecting one atom of a residue will result in an atmLine instance.