FragmentMapper.py

# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""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:

U{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(model, lsize=10, flength=5, dir="fragment_data")
    >>> fragment = fm[residue]
"""

from __future__ import print_function

import numpy

from Bio.SVDSuperimposer import SVDSuperimposer

from Bio.PDB import Selection
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Polypeptide import PPBuilder

__docformat__ = "restructuredtext en"

# 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 (available from
    U{http://csb.stanford.edu/rachel/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, "r") as fp:
        flist=[]
        # ID of fragment=rank in spec file
        fid=0
        for l in fp.readlines():
                    # skip comment and blank lines
            if l[0]=="*" or l[0]=="\n":
                continue
            sl=l.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(object):
    """
    Represent a polypeptide C-alpha fragment.
    """
    def __init__(self, length, fid):
        """
        @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):
        """
        @return: the residue names
        @rtype: [string, string,...]
        """
        return self.resname_list

    def get_id(self):
        """
        @return: id for the fragment
        @rtype: int
        """
        return self.fid

    def get_coords(self):
        """
        @return: the CA coords in the fragment
        @rtype: Numeric (Nx3) array
        """
        return self.coords_ca

    def add_residue(self, resname, ca_coord):
        """
        @param resname: residue name (eg. GLY).
        @type resname: string

        @param ca_coord: the c-alpha coorinates 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 fragment
        @rtype: int
        """
        return self.length

    def __sub__(self, other):
        """
        Return rmsd between two fragments.

        Example:
            >>> rmsd=fragment1-fragment2

        @return: rmsd between fragments
        @rtype: float
        """
        sup=SVDSuperimposer()
        sup.set(self.coords_ca, other.coords_ca)
        sup.run()
        return sup.get_rms()

    def __repr__(self):
        """
        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".

    @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 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(object):
    """
    Map polypeptides in a model to lists of representative fragments.
    """
    def __init__(self, model, lsize=20, flength=5, fdir="."):
        """
        ::
        
            @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):
        """
        @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)
        return fd

    def has_key(self, res):
        """(Obsolete)

        @type res: L{Residue}
        """
        import warnings
        from Bio import BiopythonDeprecationWarning
        warnings.warn("has_key is deprecated; use 'res in object' instead", BiopythonDeprecationWarning)
        return (res in self)

    def __contains__(self, res):
        """True if the given residue is in any of the mapped fragments.

        @type res: L{Residue}
        """
        return (res in self.fd)

    def __getitem__(self, res):
        """
        @type res: L{Residue}

        @return: fragment classification
        @rtype: L{Fragment}
        """
        return self.fd[res]


if __name__=="__main__":

    import sys

    p = PDBParser()
    s = p.get_structure("X", sys.argv[1])
    m = s[0]
    fm = FragmentMapper(m, 10, 5, "levitt_data")

    for r in Selection.unfold_entities(m, "R"):
        print("%s:" % r)
        if r in fm:
            print(fm[r])