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Polypeptide.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.

"""Polypeptide-related classes (construction and representation).

Simple example with multiple chains,

    >>> from Bio.PDB.PDBParser import PDBParser
    >>> from Bio.PDB.Polypeptide import PPBuilder
    >>> structure = PDBParser().get_structure('2BEG', 'PDB/2BEG.pdb')
    >>> ppb=PPBuilder()
    >>> for pp in ppb.build_peptides(structure):
    ...     print pp.get_sequence()
    LVFFAEDVGSNKGAIIGLMVGGVVIA
    LVFFAEDVGSNKGAIIGLMVGGVVIA
    LVFFAEDVGSNKGAIIGLMVGGVVIA
    LVFFAEDVGSNKGAIIGLMVGGVVIA
    LVFFAEDVGSNKGAIIGLMVGGVVIA

Example with non-standard amino acids using HETATM lines in the PDB file,
in this case selenomethionine (MSE):

    >>> from Bio.PDB.PDBParser import PDBParser
    >>> from Bio.PDB.Polypeptide import PPBuilder
    >>> structure = PDBParser().get_structure('1A8O', 'PDB/1A8O.pdb')
    >>> ppb=PPBuilder()
    >>> for pp in ppb.build_peptides(structure):
    ...     print pp.get_sequence()
    DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW
    TETLLVQNANPDCKTILKALGPGATLEE
    TACQG

If you want to, you can include non-standard amino acids in the peptides:

    >>> for pp in ppb.build_peptides(structure, aa_only=False):
    ...     print pp.get_sequence()
    ...     print pp.get_sequence()[0], pp[0].get_resname()
    ...     print pp.get_sequence()[-7], pp[-7].get_resname()
    ...     print pp.get_sequence()[-6], pp[-6].get_resname()
    MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG
    M MSE
    M MSE
    M MSE

In this case the selenomethionines (the first and also seventh and sixth from
last residues) have been shown as M (methionine) by the get_sequence method.
"""

import warnings

from Bio.Alphabet import generic_protein
from Bio.Seq import Seq
from Bio.SCOP.Raf import to_one_letter_code
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.Residue import Residue, DisorderedResidue
from Bio.PDB.Vector import calc_dihedral, calc_angle


standard_aa_names=["ALA", "CYS", "ASP", "GLU", "PHE", "GLY", "HIS", "ILE", "LYS", 
                   "LEU", "MET", "ASN", "PRO", "GLN", "ARG", "SER", "THR", "VAL",
                   "TRP", "TYR"]


aa1="ACDEFGHIKLMNPQRSTVWY"
aa3=standard_aa_names

d1_to_index={}
dindex_to_1={}
d3_to_index={}
dindex_to_3={}

# Create some lookup tables
for i in range(0, 20):
    n1=aa1[i]
    n3=aa3[i]
    d1_to_index[n1]=i
    dindex_to_1[i]=n1
    d3_to_index[n3]=i
    dindex_to_3[i]=n3

def index_to_one(index):
    """Index to corresponding one letter amino acid name.
    
    >>> index_to_one(0)
    'A'
    >>> index_to_one(19)
    'Y'
    """
    return dindex_to_1[index]

def one_to_index(s):
    """One letter code to index.
    
    >>> one_to_index('A')
    0
    >>> one_to_index('Y')
    19
    """
    return d1_to_index[s]

def index_to_three(i):
    """Index to corresponding three letter amino acid name.
    
    >>> index_to_three(0)
    'ALA'
    >>> index_to_three(19)
    'TYR'
    """
    return dindex_to_3[i]

def three_to_index(s):
    """Three letter code to index.
    
    >>> three_to_index('ALA')
    0
    >>> three_to_index('TYR')
    19
    """
    return d3_to_index[s]

def three_to_one(s):
    """Three letter code to one letter code.
    
    >>> three_to_one('ALA')
    'A'
    >>> three_to_one('TYR')
    'Y'

    For non-standard amino acids, you get a KeyError:

    >>> three_to_one('MSE')
    Traceback (most recent call last):
       ...
    KeyError: 'MSE'
    """
    i=d3_to_index[s]
    return dindex_to_1[i]

def one_to_three(s):
    """One letter code to three letter code.
    
    >>> one_to_three('A')
    'ALA'
    >>> one_to_three('Y')
    'TYR'
    """
    i=d1_to_index[s]
    return dindex_to_3[i]

def is_aa(residue, standard=False):
    """Return True if residue object/string is an amino acid.

    @param residue: a L{Residue} object OR a three letter amino acid code
    @type residue: L{Residue} or string

    @param standard: flag to check for the 20 AA (default false) 
    @type standard: boolean

    >>> is_aa('ALA')
    True

    Known three letter codes for modified amino acids are supported,

    >>> is_aa('FME')
    True
    >>> is_aa('FME', standard=True)
    False
    """
    #TODO - What about special cases like XXX, can they appear in PDB files?
    if not isinstance(residue, basestring):
        residue=residue.get_resname()
    residue=residue.upper()
    if standard:
        return residue in d3_to_index
    else:
        return residue in to_one_letter_code


00181 class Polypeptide(list):
    """A polypeptide is simply a list of L{Residue} objects."""
00183     def get_ca_list(self):
        """Get list of C-alpha atoms in the polypeptide.
        
        @return: the list of C-alpha atoms
        @rtype: [L{Atom}, L{Atom}, ...]
        """
        ca_list=[]
        for res in self:
            ca=res["CA"]
            ca_list.append(ca)
        return ca_list

00195     def get_phi_psi_list(self):
        """Return the list of phi/psi dihedral angles."""
        ppl=[]
        lng=len(self)
        for i in range(0, lng):
            res=self[i]
            try:
                n=res['N'].get_vector()
                ca=res['CA'].get_vector()
                c=res['C'].get_vector()
            except:
                # Some atoms are missing
                # Phi/Psi cannot be calculated for this residue
                ppl.append((None, None))
                res.xtra["PHI"]=None
                res.xtra["PSI"]=None
                continue
            # Phi
            if i>0:
                rp=self[i-1]
                try:
                    cp=rp['C'].get_vector()
                    phi=calc_dihedral(cp, n, ca, c)
                except:
                    phi=None
            else:
                # No phi for residue 0!
                phi=None
            # Psi
            if i<(lng-1):
                rn=self[i+1]
                try:
                    nn=rn['N'].get_vector()
                    psi=calc_dihedral(n, ca, c, nn)
                except:
                    psi=None
            else:
                # No psi for last residue!
                psi=None
            ppl.append((phi, psi))
            # Add Phi/Psi to xtra dict of residue
            res.xtra["PHI"]=phi
            res.xtra["PSI"]=psi
        return ppl

00240     def get_tau_list(self):
        """List of tau torsions angles for all 4 consecutive Calpha atoms."""
        ca_list=self.get_ca_list()
        tau_list=[]
        for i in range(0, len(ca_list)-3):
            atom_list = (ca_list[i], ca_list[i+1], ca_list[i+2], ca_list[i+3])
            v1, v2, v3, v4 = [a.get_vector() for a in atom_list]
            tau=calc_dihedral(v1, v2, v3, v4)
            tau_list.append(tau)
            # Put tau in xtra dict of residue
            res=ca_list[i+2].get_parent()
            res.xtra["TAU"]=tau
        return tau_list

00254     def get_theta_list(self):
        """List of theta angles for all 3 consecutive Calpha atoms."""
        theta_list=[]
        ca_list=self.get_ca_list()
        for i in range(0, len(ca_list)-2):
            atom_list = (ca_list[i], ca_list[i+1], ca_list[i+2])
            v1, v2, v3 = [a.get_vector() for a in atom_list]
            theta=calc_angle(v1, v2, v3)
            theta_list.append(theta)
            # Put tau in xtra dict of residue
            res=ca_list[i+1].get_parent()
            res.xtra["THETA"]=theta
        return theta_list

00268     def get_sequence(self):
        """Return the AA sequence as a Seq object.

        @return: polypeptide sequence 
        @rtype: L{Seq}
        """
        s=""
        for res in self:
            s += to_one_letter_code.get(res.get_resname(), 'X')
        seq=Seq(s, generic_protein)
        return seq

00280     def __repr__(self):
        """Return string representation of the polypeptide.
        
        Return <Polypeptide start=START end=END>, where START
        and END are sequence identifiers of the outer residues.
        """
        start=self[0].get_id()[1]
        end=self[-1].get_id()[1]
        s="<Polypeptide start=%s end=%s>" % (start, end)
        return s

00291 class _PPBuilder:
    """Base class to extract polypeptides.
    
    It checks if two consecutive residues in a chain are connected.
    The connectivity test is implemented by a subclass.
    
    This assumes you want both standard and non-standard amino acids.
    """
00299     def __init__(self, radius):
        """
        @param radius: distance
        @type radius: float
        """
        self.radius=radius

00306     def _accept(self, residue, standard_aa_only):
        """Check if the residue is an amino acid (PRIVATE)."""
        if is_aa(residue, standard=standard_aa_only):
            return True
        elif not standard_aa_only and "CA" in residue.child_dict:
            #It has an alpha carbon...
            #We probably need to update the hard coded list of
            #non-standard residues, see function is_aa for details.
            warnings.warn("Assuming residue %s is an unknown modified "
                          "amino acid" % residue.get_resname())
            return True
        else:
            # not a standard AA so skip
            return False
    
00321     def build_peptides(self, entity, aa_only=1):
        """Build and return a list of Polypeptide objects.

        @param entity: polypeptides are searched for in this object
        @type entity: L{Structure}, L{Model} or L{Chain}

        @param aa_only: if 1, the residue needs to be a standard AA
        @type aa_only: int
        """
        is_connected=self._is_connected
        accept=self._accept
        level=entity.get_level()
        # Decide wich entity we are dealing with
        if level=="S":
            model=entity[0]
            chain_list=model.get_list()
        elif level=="M":
            chain_list=entity.get_list()
        elif level=="C":
            chain_list=[entity]
        else:
            raise PDBException("Entity should be Structure, Model or Chain.")
        pp_list=[]
        for chain in chain_list:
            chain_it=iter(chain)
            try:
                prev_res = chain_it.next()
                while not accept(prev_res, aa_only):
                    prev_res = chain_it.next()
            except StopIteration:
                #No interesting residues at all in this chain
                continue
            pp=None
            for next_res in chain_it:
                if accept(prev_res, aa_only) \
                and accept(next_res, aa_only) \
                and is_connected(prev_res, next_res):
                    if pp is None:
                        pp=Polypeptide()
                        pp.append(prev_res)
                        pp_list.append(pp)
                    pp.append(next_res)
                else:
                    #Either too far apart, or one of the residues is unwanted.
                    #End the current peptide
                    pp=None
                prev_res=next_res
        return pp_list


00371 class CaPPBuilder(_PPBuilder):
    """Use CA--CA distance to find polypeptides."""
00373     def __init__(self, radius=4.3):
        _PPBuilder.__init__(self, radius)

    def _is_connected(self, prev_res, next_res):
        for r in [prev_res, next_res]:
            if not r.has_id("CA"):
                return False
        n=next_res["CA"]
        p=prev_res["CA"]
        # Unpack disordered
        if n.is_disordered():
            nlist=n.disordered_get_list()
        else:
            nlist=[n]
        if p.is_disordered():
            plist=p.disordered_get_list()
        else:
            plist=[p]
        for nn in nlist:
            for pp in plist:
                if (nn-pp)<self.radius:
                    return True
        return False


00398 class PPBuilder(_PPBuilder):
    """Use C--N distance to find polypeptides."""
00400     def __init__(self, radius=1.8):
        _PPBuilder.__init__(self, radius)

    def _is_connected(self, prev_res, next_res):
        if not prev_res.has_id("C"):
            return False
        if not next_res.has_id("N"):
            return False
        test_dist=self._test_dist
        c=prev_res["C"]
        n=next_res["N"]
        # Test all disordered atom positions!
        if c.is_disordered():
            clist=c.disordered_get_list()
        else:
            clist=[c]
        if n.is_disordered():
            nlist=n.disordered_get_list()
        else:
            nlist=[n]
        for nn in nlist:
            for cc in clist:
                # To form a peptide bond, N and C must be 
                # within radius and have the same altloc
                # identifier or one altloc blank
                n_altloc=nn.get_altloc()
                c_altloc=cc.get_altloc()
                if n_altloc==c_altloc or n_altloc==" " or c_altloc==" ": 
                    if test_dist(nn, cc):
                        # Select the disordered atoms that
                        # are indeed bonded
                        if c.is_disordered():
                            c.disordered_select(c_altloc)
                        if n.is_disordered():
                            n.disordered_select(n_altloc)
                        return True
        return False

00438     def _test_dist(self, c, n):
        """Return 1 if distance between atoms<radius (PRIVATE)."""
        if (c-n)<self.radius:
            return 1
        else:
            return 0
    

if __name__=="__main__":
    import sys
    from Bio.PDB.PDBParser import PDBParser

    p=PDBParser(PERMISSIVE=1)

    s=p.get_structure("scr", sys.argv[1])

    ppb=PPBuilder()

    print "C-N"
    for pp in ppb.build_peptides(s):
        print pp.get_sequence()
    for pp in ppb.build_peptides(s[0]):
        print pp.get_sequence()
    for pp in ppb.build_peptides(s[0]["A"]):
        print pp.get_sequence()

    for pp in ppb.build_peptides(s):
        for phi, psi in pp.get_phi_psi_list():
            print phi, psi

    ppb=CaPPBuilder()

    print "CA-CA"
    for pp in ppb.build_peptides(s):
        print pp.get_sequence()
    for pp in ppb.build_peptides(s[0]):
        print pp.get_sequence()
    for pp in ppb.build_peptides(s[0]["A"]):
        print pp.get_sequence()


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