mmLib.Structure

Package mmLib :: Module Structure

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Module mmLib.Structure

Classes for representing biological macromolecules.

Classes
`AlphaHelix`	Class containing information on a protein alpha helix.
`Altloc`	Container holding the same atom, but for different conformations and occupancies.
`AminoAcidResidue`	A subclass of Residue representing one amino acid residue in a polypeptide chain.
`Atom`	Class representing a single atom.
`AtomList`	Provides the functionallity of a Python list class for containing Atom instances.
`BetaSheet`	Class containing information on a protein beta sheet.
`Bond`	Indicates two atoms are bonded together.
`Chain`	Chain objects conatain a ordered list of Fragment objects.
`Fragment`	Fragment objects are a basic unit for organizing small groups of Atoms.
`FragmentID`	Stores a fragment_id as integer residue sequence number and a single-charactor insertion code.
`Model`	Multiple models support.
`NucleicAcidResidue`	A subclass of Residue representing one nuclic acid in a strand of DNA or RNA.
`Residue`	A subclass of Fragment representing one residue in a polymer chain.
`Segment`	Segment objects are a container for Fragment objects, but are disaccociated with the Structure object hierarch.
`Site`	List of Fragments within a structure involved in a SITE description.
`Strand`	One strand of a BetaSheet.
`Structure`	The Structure object is the parent container object for the entire macromolecular data structure.

Exceptions
`AtomOverwrite`	Raised by Structure.add_atom() or Fragment.add_atom() when a Atom added to a Structure or Fragment has the same chain_id, fragment_id, name, and alt_loc as a Atom already in the Structure or Fragment.
`ChainOverwrite`	Raised by Structure.add_chain() or by Model.add_chain() when a Chain added to a Structure has the same chain_id of a Chain already in the Structure.
`FragmentOverwrite`	Raised by Chain.add_fragment() when a Fragment added to a Chain has the same fragment_id as a Fragment already in the Chain.
`ModelOverwrite`	Raised by Structure.add_model() when a Model added to a Structure has the same model_id of a Model already in the Structure.
`StructureError`	Base class of errors raised by Structure objects.

Function Summary
	`fragment_id_cmp(frag_id1, frag_id2)` Compare two fragment ids.
	`fragment_id_eq(frag_id1, frag_id2)` Performs a proper equivelancy of frament_id strings according to their sequence number, then insertion code.
	`fragment_id_ge(frag_id1, frag_id2)` Performs a proper greator then or equal to comparison of frament_id strings according to their sequence number, then insertion code.
	`fragment_id_gt(frag_id1, frag_id2)` Performs a proper greator than comparison of frament_id strings according to their sequence number, then insertion code.
	`fragment_id_le(frag_id1, frag_id2)` Performs a proper less than or equal to comparison of frament_id strings according to their sequence number, then insertion code.
	`fragment_id_lt(frag_id1, frag_id2)` Performs a proper less than comparison of frament_id strings according to their sequence number, then insertion code.
	`fragment_id_split(frag_id)` Split a string fragment_id into a 2-tuple of: (sequence_num, insertion_code)
	`iter_fragments(fragiter, start_frag_id, stop_frag_id)` Given a fragment iterator and a start and end fragment id, return a iterator which yields only fragments within the range.
	`test_module()`

Function Details

Compare two fragment ids.

Performs a proper equivelancy of frament_id strings according to their sequence number, then insertion code.

Performs a proper greator then or equal to comparison of frament_id strings according to their sequence number, then insertion code.

Performs a proper greator than comparison of frament_id strings according to their sequence number, then insertion code.

Performs a proper less than or equal to comparison of frament_id strings according to their sequence number, then insertion code.

Performs a proper less than comparison of frament_id strings according to their sequence number, then insertion code.

Split a string fragment_id into a 2-tuple of: (sequence_num, insertion_code)

Given a fragment iterator and a start and end fragment id, return a iterator which yields only fragments within the range.

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