biopython v1.71.0 Bio.PDB.FragmentMapper
Classify protein backbone structure according to 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]Link to this section Summary
Functions
Dice up a peptide in fragments of length “length”
Map flist fragments to closest entry in reflist (PRIVATE)
Read a fragment spec file (PRIVATE)
Link to this section Functions
Dice up a peptide in fragments of length “length”.
:param pp: a list of residues (part of one peptide) :type pp: [L{Residue}, L{Residue}, …]
:param length: fragment length :type length: int
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.
:param flist: list of protein fragments :type flist: [L{Fragment}, L{Fragment}, …]
:param reflist: list of reference (ie. library) fragments :type reflist: [L{Fragment}, L{Fragment}, …]
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.
:param size: number of fragments in the library :type size: int
:param length: length of the fragments :type length: int
:param dir: directory where the fragment spec files can be found :type dir: string