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:

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


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

Link to this function _make_fragment_list()

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

Link to this function _map_fragment_list()

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}, …]

Link to this function _read_fragments()

Read a fragment spec file (PRIVATE).

Read a fragment spec file available from 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