Module FragmentMapper'
source code
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://csb.stanford.edu/~rachel/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(lsize=10, flength=5, dir="fragment_data")
>>> fm.map(model)
>>> fragment=fm[residue]
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Fragment
Represent a polypeptide C-alpha fragment.
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FragmentMapper
Map polypeptides in a model to lists of representative fragments.
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Dice up a peptide in fragments of length "length".
- Parameters:
pp ([Residue,
Residue,
...]) - a list of residues (part of one peptide)
length (int) - fragment length
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Map all frgaments in flist to the closest (in RMSD) fragment in
reflist.
Returns a list of reflist indices.
- Parameters:
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Read a fragment spec file (available from http://csb.stanford.edu/rachel/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
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standard_aa_names
- Value:
[ ' ALA ' ,
' CYS ' ,
' ASP ' ,
' GLU ' ,
' PHE ' ,
' GLY ' ,
' HIS ' ,
' ILE ' ,
...
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to_one_letter_code
- Value:
{ ' 2AS ' : ' D ' ,
' 3AH ' : ' H ' ,
' 5HP ' : ' E ' ,
' ACL ' : ' R ' ,
' AGM ' : ' R ' ,
' AIB ' : ' A ' ,
' ALA ' : ' A ' ,
' ALM ' : ' A ' ,
...
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