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# Copyright (C) 2002, Thomas Hamelryck ([email protected])
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""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'.
>>> from Bio.PDB.PDBParser import PDBParser
>>> from Bio.PDB.FragmentMapper import FragmentMapper
>>> parser = PDBParser()
>>> structure = parser.get_structure("1a8o", "PDB/1A8O.pdb")
>>> model = structure[0]
>>> fm = FragmentMapper(model, lsize=10, flength=5, fdir="PDB")
>>> chain = model['A']
>>> res152 = chain[152]
>>> res157 = chain[157]
>>> res152 in fm # is res152 mapped? (fragment of a C-alpha polypeptide)
False
>>> res157 in fm # is res157 mapped? (fragment of a C-alpha polypeptide)
True
"""
import numpy
from Bio.SVDSuperimposer import SVDSuperimposer
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.Polypeptide import PPBuilder
# fragment file (lib_SIZE_z_LENGTH.txt)
# SIZE=number of fragments
# LENGTH=length of fragment (4,5,6,7)
_FRAGMENT_FILE = "lib_%s_z_%s.txt"
def _read_fragments(size, length, dir="."):
"""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
"""
filename = (dir + "/" + _FRAGMENT_FILE) % (size, length)
with open(filename) as fp:
flist = []
# ID of fragment=rank in spec file
fid = 0
for line in fp:
# skip comment and blank lines
if line[0] == "*" or line[0] == "\n":
continue
sl = line.split()
if sl[1] == "------":
# Start of fragment definition
f = Fragment(length, fid)
flist.append(f)
# increase fragment id (rank)
fid += 1
continue
# Add CA coord to Fragment
coord = numpy.array([float(x) for x in sl[0:3]])
# XXX= dummy residue name
f.add_residue("XXX", coord)
return flist
class Fragment:
"""Represent a polypeptide C-alpha fragment."""
def __init__(self, length, fid):
"""Initialize fragment object.
:param length: length of the fragment
:type length: int
:param fid: id for the fragment
:type fid: int
"""
# nr of residues in fragment
self.length = length
# nr of residues added
self.counter = 0
self.resname_list = []
# CA coordinate matrix
self.coords_ca = numpy.zeros((length, 3), "d")
self.fid = fid
def get_resname_list(self):
"""Get residue list.
:return: the residue names
:rtype: [string, string,...]
"""
return self.resname_list
def get_id(self):
"""Get identifier for the fragment.
:return: id for the fragment
:rtype: int
"""
return self.fid
def get_coords(self):
"""Get the CA coordinates in the fragment.
:return: the CA coords in the fragment
:rtype: Numeric (Nx3) array
"""
return self.coords_ca
def add_residue(self, resname, ca_coord):
"""Add a residue.
:param resname: residue name (eg. GLY).
:type resname: string
:param ca_coord: the c-alpha coordinates of the residues
:type ca_coord: Numeric array with length 3
"""
if self.counter >= self.length:
raise PDBException("Fragment boundary exceeded.")
self.resname_list.append(resname)
self.coords_ca[self.counter] = ca_coord
self.counter = self.counter + 1
def __len__(self):
"""Return length of the fragment."""
return self.length
def __sub__(self, other):
"""Return rmsd between two fragments.
:return: rmsd between fragments
:rtype: float
Examples
--------
This is an incomplete but illustrative example::
rmsd = fragment1 - fragment2
"""
sup = SVDSuperimposer()
sup.set(self.coords_ca, other.coords_ca)
sup.run()
return sup.get_rms()
def __repr__(self):
"""Represent the fragment object as a string.
Returns <Fragment length=L id=ID> where L=length of fragment
and ID the identifier (rank in the library).
"""
return "<Fragment length=%i id=%i>" % (self.length, self.fid)
def _make_fragment_list(pp, length):
"""Dice up a peptide in fragments of length "length" (PRIVATE).
:param pp: a list of residues (part of one peptide)
:type pp: [L{Residue}, L{Residue}, ...]
:param length: fragment length
:type length: int
"""
frag_list = []
for i in range(0, len(pp) - length + 1):
f = Fragment(length, -1)
for j in range(0, length):
residue = pp[i + j]
resname = residue.get_resname()
if residue.has_id("CA"):
ca = residue["CA"]
else:
raise PDBException("CHAINBREAK")
if ca.is_disordered():
raise PDBException("CHAINBREAK")
ca_coord = ca.get_coord()
f.add_residue(resname, ca_coord)
frag_list.append(f)
return frag_list
def _map_fragment_list(flist, reflist):
"""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}, ...]
"""
mapped = []
for f in flist:
rank = []
for i in range(0, len(reflist)):
rf = reflist[i]
rms = f - rf
rank.append((rms, rf))
rank.sort()
fragment = rank[0][1]
mapped.append(fragment)
return mapped
class FragmentMapper:
"""Map polypeptides in a model to lists of representative fragments."""
def __init__(self, model, lsize=20, flength=5, fdir="."):
"""Create instance of FragmentMapper.
:param model: the model that will be mapped
:type model: L{Model}
:param lsize: number of fragments in the library
:type lsize: int
:param flength: length of fragments in the library
:type flength: int
:param fdir: directory where the definition files are
found (default=".")
:type fdir: string
"""
if flength == 5:
self.edge = 2
elif flength == 7:
self.edge = 3
else:
raise PDBException("Fragment length should be 5 or 7.")
self.flength = flength
self.lsize = lsize
self.reflist = _read_fragments(lsize, flength, fdir)
self.model = model
self.fd = self._map(self.model)
def _map(self, model):
"""Map (PRIVATE).
:param model: the model that will be mapped
:type model: L{Model}
"""
ppb = PPBuilder()
ppl = ppb.build_peptides(model)
fd = {}
for pp in ppl:
try:
# make fragments
flist = _make_fragment_list(pp, self.flength)
# classify fragments
mflist = _map_fragment_list(flist, self.reflist)
for i in range(0, len(pp)):
res = pp[i]
if i < self.edge:
# start residues
continue
elif i >= (len(pp) - self.edge):
# end residues
continue
else:
# fragment
index = i - self.edge
assert index >= 0
fd[res] = mflist[index]
except PDBException as why:
if why == "CHAINBREAK":
# Funny polypeptide - skip
pass
else:
raise PDBException(why) from None
return fd
def __contains__(self, res):
"""Check if the given residue is in any of the mapped fragments.
:type res: L{Residue}
"""
return res in self.fd
def __getitem__(self, res):
"""Get an entry.
:type res: L{Residue}
:return: fragment classification
:rtype: L{Fragment}
"""
return self.fd[res]
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