Source code for MMTK.Biopolymers

# This module implements the base classes for proteins and
# nucleic acid chains.
#
# Written by Konrad Hinsen
#

"""
Base classes for proteins and nucleic acids
"""

from MMTK import Bonds, ChemicalObjects, Collections, Database, PDB
import Scientific.IO.PDB

[docs]class Residue(ChemicalObjects.Group): """ Base class for aminoacid and nucleic acid residues """ def __setstate__(self, state): self.__dict__.update(state) try: self.model = self.hydrogens except AttributeError: pass self._init() def _init(self): # construct PDB map and alternative names type = self.type if not hasattr(type, 'pdbmap'): pdb_dict = {} type.pdbmap = [(type.symbol, pdb_dict)] offset = 0 for g in type.groups: for name, atom in g.pdbmap[0][1].items(): pdb_dict[name] = Database.AtomReference(atom.number + \ offset) offset = offset + len(g.atoms) if not hasattr(type, 'pdb_alternative'): alt_dict = {} for g in type.groups: if hasattr(g, 'pdb_alternative'): for key, value in g.pdb_alternative.items(): alt_dict[key] = value setattr(type, 'pdb_alternative', alt_dict) def _residueThroughLinkAtom(self, link_atom): if link_atom is None: return None levels = 0 obj = link_atom while obj is not None and obj != self: obj = obj.parent levels += 1 for atom in link_atom.bondedTo(): if atom.parent is not link_atom.parent: obj = atom while levels > 0: obj = obj.parent levels -= 1 return obj return None
[docs] def precedingResidue(self): """ :returns the preceding residue in the chain """ return self._residueThroughLinkAtom(self.chain_links[0])
[docs] def nextResidue(self): """ :returns the next residue in the chain """ return self._residueThroughLinkAtom(self.chain_links[1])
[docs]class ResidueChain(ChemicalObjects.Molecule): """ Chain of residues Base class for peptide chains and nucleotide chains """ is_chain = 1 def _setupChain(self, circular, properties, conf): self.atoms = [] self.bonds = [] for g in self.groups: self.atoms.extend(g.atoms) self.bonds.extend(g.bonds) for i in range(len(self.groups)-1): link1 = self.groups[i].chain_links[1] link2 = self.groups[i+1].chain_links[0] self.bonds.append(Bonds.Bond((link1, link2))) if circular: link1 = self.groups[-1].chain_links[1] link2 = self.groups[0].chain_links[0] self.bonds.append(Bonds.Bond((link1, link2))) self.bonds = Bonds.BondList(self.bonds) self.parent = None self.type = None self.configurations = {} try: self.name = properties['name'] del properties['name'] except KeyError: self.name = '' if conf: conf.applyTo(self) try: self.translateTo(properties['position']) del properties['position'] except KeyError: pass self.addProperties(properties) def __len__(self): return len(self.groups) def __getitem__(self, item): return self.groups[item] def __setitem__(self, item, value): self.replaceResidue(self.groups[item], value)
[docs] def residuesOfType(self, *types): """ :param types: residue type codes :type types: str :returns: a collection that contains all residues whose type (residue code) is contained in types :rtype: :class:`~MMTK.Collections.Collection` """ types = [t.lower() for t in types] rlist = [r for r in self.groups if r.type.symbol.lower() in types] return Collections.Collection(rlist)
[docs] def residues(self): """ :returns: a collection containing all residues :rtype: :class:`~MMTK.Collections.Collection` """ return Collections.Collection(self.groups)
[docs] def sequence(self): """ :returns: the residue sequence as a list of residue codes :rtype: list of str """ return [r.type.symbol.lower() for r in self.groups] # # Find the full name of a residue #
def _fullName(residue): residue = residue.lower() try: return _aa_residue_names[residue] except KeyError: return _na_residue_names[residue] _aa_residue_names = {'ala': 'alanine', 'a': 'alanine', 'arg': 'arginine', 'r': 'arginine', 'asn': 'asparagine', 'n': 'asparagine', 'asp': 'aspartic_acid', 'd': 'aspartic_acid', 'cys': 'cysteine', 'c': 'cysteine', 'gln': 'glutamine', 'q': 'glutamine', 'glu': 'glutamic_acid', 'e': 'glutamic_acid', 'gly': 'glycine', 'g': 'glycine', 'his': 'histidine', 'h': 'histidine', 'ile': 'isoleucine', 'i': 'isoleucine', 'leu': 'leucine', 'l': 'leucine', 'lys': 'lysine', 'k': 'lysine', 'met': 'methionine', 'm': 'methionine', 'phe': 'phenylalanine', 'f': 'phenylalanine', 'pro': 'proline', 'p': 'proline', 'ser': 'serine', 's': 'serine', 'thr': 'threonine', 't': 'threonine', 'trp': 'tryptophan', 'w': 'tryptophan', 'tyr': 'tyrosine', 'y': 'tyrosine', 'val': 'valine', 'v': 'valine', 'cyx': 'cystine_ss', 'cym': 'cysteine_with_negative_charge', 'app': 'aspartic_acid_neutral', 'glp': 'glutamic_acid_neutral', 'hsd': 'histidine_deltah', 'hse': 'histidine_epsilonh', 'hsp': 'histidine_plus', 'hid': 'histidine_deltah', 'hie': 'histidine_epsilonh', 'hip': 'histidine_plus', 'lyp': 'lysine_neutral', 'ace': 'ace_beginning', 'nme': 'nmethyl', 'nhe': 'amide', } _na_residue_names = {'da': 'd-adenosine', 'da5': 'd-adenosine_5ter', 'da3': 'd-adenosine_3ter', 'dan': 'd-adenosine_5ter_3ter', 'dc': 'd-cytosine', 'dc5': 'd-cytosine_5ter', 'dc3': 'd-cytosine_3ter', 'dcn': 'd-cytosine_5ter_3ter', 'dg': 'd-guanosine', 'dg5': 'd-guanosine_5ter', 'dg3': 'd-guanosine_3ter', 'dgn': 'd-guanosine_5ter_3ter', 'dt': 'd-thymine', 'dt5': 'd-thymine_5ter', 'dt3': 'd-thymine_3ter', 'dtn': 'd-thymine_5ter_3ter', 'ra': 'r-adenosine', 'ra5': 'r-adenosine_5ter', 'ra3': 'r-adenosine_3ter', 'ran': 'r-adenosine_5ter_3ter', 'rc': 'r-cytosine', 'rc5': 'r-cytosine_5ter', 'rc3': 'r-cytosine_3ter', 'rcn': 'r-cytosine_5ter_3ter', 'rg': 'r-guanosine', 'rg5': 'r-guanosine_5ter', 'rg3': 'r-guanosine_3ter', 'rgn': 'r-guanosine_5ter_3ter', 'ru': 'r-uracil', 'ru5': 'r-uracil_5ter', 'ru3': 'r-uracil_3ter', 'run': 'r-uracil_5ter_3ter', } for code in _aa_residue_names: if len(code) == 3: Scientific.IO.PDB.defineAminoAcidResidue(code) for code in _na_residue_names: Scientific.IO.PDB.defineNucleicAcidResidue(code) # # Add a residue to the residue list #
[docs]def defineAminoAcidResidue(full_name, code3, code1 = None): """ Add a non-standard amino acid residue to the internal residue table. Once added to the residue table, the new residue can be used like any of the standard residues in the creation of peptide chains. :param full_name: the name of the group definition in the chemical database :type full_name: str :param code3: the three-letter residue code :type code3: str :param code1: an optionel one-letter residue code :type code1: str """ code3 = code3.lower() if code1 is not None: code1 = code1.lower() if _aa_residue_names.has_key(code3) or _na_residue_names.has_key(code3): raise ValueError("residue name " + code3 + " already used") if _aa_residue_names.has_key(code1): raise ValueError("residue name " + code1 + " already used") _aa_residue_names[code3] = full_name if code1 is not None: _aa_residue_names[code1] = full_name Scientific.IO.PDB.defineAminoAcidResidue(code3)
[docs]def defineNucleicAcidResidue(full_name, code): """ Add a non-standard nucleic acid residue to the internal residue table. Once added to the residue table, the new residue can be used like any of the standard residues in the creation of nucleotide chains. :param full_name: the name of the group definition in the chemical database :type full_name: str :param code: the residue code :type code3: str """ code = code.lower() if _aa_residue_names.has_key(code) or _na_residue_names.has_key(code): raise ValueError("residue name " + code + " already used") _na_residue_names[code] = full_name Scientific.IO.PDB.defineNucleicAcidResidue(code)