Package mmLib :: Module Structure
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Module Structure

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Classes for representing biological macromolecules.

Classes [hide private]
  StructureError
Base class of errors raised by Structure objects.
  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.
  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.
  AtomOverwrite
Raised by Structure.add_atom() or Fragment.add_atom() when an Atom added to a Structure or Fragment has the same chain_id, fragment_id, name, and alt_loc as an Atom already in the Structure or Fragment.
  Structure
The Structure object is the parent container object for the entire macromolecular data structure.
  Model
Multiple models support.
  Segment
Segment objects are a container for Fragment objects, but are disassociated with the Structure object hierarch.
  Chain
Chain objects contain an ordered list of Fragment objects.
  Fragment
Fragment objects are a basic unit for organizing small groups of Atoms.
  Residue
A subclass of Fragment representing one residue in a polymer chain.
  AminoAcidResidue
A subclass of Residue representing one amino acid residue in a polypeptide chain.
  NucleicAcidResidue
A subclass of Residue representing one nuclic acid in a strand of DNA or RNA.
  Altloc
Container holding the same atom, but for different conformations and occupancies.
  Atom
Class representing a single atom.
  Bond
Indicates two atoms are bonded together.
  AlphaHelix
Class containing information on a protein alpha helix.
  Strand
One strand of a BetaSheet.
  BetaSheet
Class containing information on a protein beta sheet.
  Site
List of Fragments within a structure involved in a SITE description.
  FragmentID
Stores a fragment_id as integer residue sequence number and a single-character insertion code.
  AtomList
Provides the functionality of a Python list class for containing Atom instances.
Functions [hide private]
 
fragment_id_split(frag_id)
Split a string fragment_id into a 2-tuple of: (sequence_num, insertion_code)
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fragment_id_eq(frag_id1, frag_id2)
Performs a proper equivalency of fragment_id strings according to their sequence number, then insertion code.
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fragment_id_lt(frag_id1, frag_id2)
Performs a proper less than comparison of fragment_id strings according to their sequence number, then insertion code.
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fragment_id_le(frag_id1, frag_id2)
Performs a proper less than or equal to comparison of fragment_id strings according to their sequence number, then insertion code.
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fragment_id_gt(frag_id1, frag_id2)
Performs a proper greater than comparison of fragment_id strings according to their sequence number, then insertion code.
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fragment_id_ge(frag_id1, frag_id2)
Performs a proper greater than or equal to comparison of fragment_id strings according to their sequence number, then insertion code.
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fragment_id_cmp(frag_id1, frag_id2)
Compare two fragment ids.
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iter_fragments(fragiter, start_frag_id=None, stop_frag_id=None)
Given a fragment iterator and a start and end fragment id, return an iterator which yields only fragments within the range.
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test_module() source code
Variables [hide private]
  __package__ = 'mmLib'