Package Bio :: Package PDB :: Module FragmentMapper'
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Module FragmentMapper'

source code

Classify protein backbone structure with Kolodny et al's fragment libraries.

It can be regarded as a form of objective secondary structure classification. Only fragments of length 5 or 7 are supported (ie. there is a 'central' residue).

Full reference:

Kolodny R, Koehl P, Guibas L, Levitt M. Small libraries of protein fragments model native protein structures accurately. J Mol Biol. 2002 323(2):297-307.

The definition files of the fragments can be obtained from:

http://github.com/csblab/fragments/

You need these files to use this module.

The following example uses the library with 10 fragments of length 5. The library files can be found in directory 'fragment_data'.

>>> model = structure[0]
>>> fm = FragmentMapper(model, lsize=10, flength=5, dir="fragment_data")
>>> fragment = fm[residue]
Classes [hide private]
  Fragment
Represent a polypeptide C-alpha fragment.
  FragmentMapper
Map polypeptides in a model to lists of representative fragments.
Functions [hide private]
 
_make_fragment_list(pp, length)
Dice up a peptide in fragments of length "length" (PRIVATE).
source code
 
_map_fragment_list(flist, reflist)
Map flist fragments to closest entry in reflist (PRIVATE).
source code
 
_read_fragments(size, length, dir='.')
Read a fragment spec file (PRIVATE).
source code
Variables [hide private]
  _FRAGMENT_FILE = 'lib_%s_z_%s.txt'
  __package__ = 'Bio.PDB'
Function Details [hide private]

_make_fragment_list(pp, length)

source code 
Dice up a peptide in fragments of length "length" (PRIVATE).
Parameters:
  • pp ([L{Residue}, L{Residue}, ...]) - a list of residues (part of one peptide)
  • length (int) - fragment length

_map_fragment_list(flist, reflist)

source code 

Map flist fragments to closest entry in reflist (PRIVATE).

Map all frgaments in flist to the closest (in RMSD) fragment in reflist.

Returns a list of reflist indices.

Parameters:
  • flist ([L{Fragment}, L{Fragment}, ...]) - list of protein fragments
  • reflist ([L{Fragment}, L{Fragment}, ...]) - list of reference (ie. library) fragments

_read_fragments(size, length, dir='.')

source code 

Read a fragment spec file (PRIVATE).

Read a fragment spec file available from http://github.com/csblab/fragments/ and return a list of Fragment objects.

Parameters:
  • size (int) - number of fragments in the library
  • length (int) - length of the fragments
  • dir (string) - directory where the fragment spec files can be found