Spaces:
No application file
No application file
| # 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. | |
| """Residue class, used by Structure objects.""" | |
| from Bio.PDB.PDBExceptions import PDBConstructionException | |
| from Bio.PDB.Entity import Entity, DisorderedEntityWrapper | |
| _atom_name_dict = {} | |
| _atom_name_dict["N"] = 1 | |
| _atom_name_dict["CA"] = 2 | |
| _atom_name_dict["C"] = 3 | |
| _atom_name_dict["O"] = 4 | |
| class Residue(Entity): | |
| """Represents a residue. A Residue object stores atoms.""" | |
| def __init__(self, id, resname, segid): | |
| """Initialize the class.""" | |
| self.level = "R" | |
| self.disordered = 0 | |
| self.resname = resname | |
| self.segid = segid | |
| self.internal_coord = None | |
| Entity.__init__(self, id) | |
| def __repr__(self): | |
| """Return the residue full id.""" | |
| resname = self.get_resname() | |
| hetflag, resseq, icode = self.get_id() | |
| full_id = (resname, hetflag, resseq, icode) | |
| return "<Residue %s het=%s resseq=%s icode=%s>" % full_id | |
| def add(self, atom): | |
| """Add an Atom object. | |
| Checks for adding duplicate atoms, and raises a | |
| PDBConstructionException if so. | |
| """ | |
| atom_id = atom.get_id() | |
| if self.has_id(atom_id): | |
| raise PDBConstructionException( | |
| f"Atom {atom_id} defined twice in residue {self}" | |
| ) | |
| Entity.add(self, atom) | |
| def flag_disordered(self): | |
| """Set the disordered flag.""" | |
| self.disordered = 1 | |
| def is_disordered(self): | |
| """Return 1 if the residue contains disordered atoms.""" | |
| return self.disordered | |
| def get_resname(self): | |
| """Return the residue name.""" | |
| return self.resname | |
| def get_unpacked_list(self): | |
| """Return the list of all atoms, unpack DisorderedAtoms.""" | |
| atom_list = self.get_list() | |
| undisordered_atom_list = [] | |
| for atom in atom_list: | |
| if atom.is_disordered(): | |
| undisordered_atom_list += atom.disordered_get_list() | |
| else: | |
| undisordered_atom_list.append(atom) | |
| return undisordered_atom_list | |
| def get_segid(self): | |
| """Return the segment identifier.""" | |
| return self.segid | |
| def get_atoms(self): | |
| """Return atoms.""" | |
| yield from self | |
| class DisorderedResidue(DisorderedEntityWrapper): | |
| """DisorderedResidue is a wrapper around two or more Residue objects. | |
| It is used to represent point mutations (e.g. there is a Ser 60 and a Cys 60 | |
| residue, each with 50 % occupancy). | |
| """ | |
| def __init__(self, id): | |
| """Initialize the class.""" | |
| DisorderedEntityWrapper.__init__(self, id) | |
| def __repr__(self): | |
| """Return disordered residue full identifier.""" | |
| if self.child_dict: | |
| resname = self.get_resname() | |
| hetflag, resseq, icode = self.get_id() | |
| full_id = (resname, hetflag, resseq, icode) | |
| return "<DisorderedResidue %s het=%s resseq=%i icode=%s>" % full_id | |
| else: | |
| return "<Empty DisorderedResidue>" | |
| def add(self, atom): | |
| """Add atom to residue.""" | |
| residue = self.disordered_get() | |
| if not atom.is_disordered() == 2: | |
| # Atoms in disordered residues should have non-blank | |
| # altlocs, and are thus represented by DisorderedAtom objects. | |
| resname = residue.get_resname() | |
| het, resseq, icode = residue.get_id() | |
| # add atom anyway, if PDBParser ignores exception the atom will be part of the residue | |
| residue.add(atom) | |
| raise PDBConstructionException( | |
| "Blank altlocs in duplicate residue %s (%s, %i, %s)" | |
| % (resname, het, resseq, icode) | |
| ) | |
| residue.add(atom) | |
| def sort(self): | |
| """Sort the atoms in the child Residue objects.""" | |
| for residue in self.disordered_get_list(): | |
| residue.sort() | |
| def disordered_add(self, residue): | |
| """Add a residue object and use its resname as key. | |
| Arguments: | |
| - residue - Residue object | |
| """ | |
| resname = residue.get_resname() | |
| # add chain parent to residue | |
| chain = self.get_parent() | |
| residue.set_parent(chain) | |
| assert not self.disordered_has_id(resname) | |
| self[resname] = residue | |
| self.disordered_select(resname) | |
| def disordered_remove(self, resname): | |
| """Remove a child residue from the DisorderedResidue. | |
| Arguments: | |
| - resname - name of the child residue to remove, as a string. | |
| """ | |
| # Get child residue | |
| residue = self.child_dict[resname] | |
| is_selected = self.selected_child is residue | |
| # Detach | |
| del self.child_dict[resname] | |
| residue.detach_parent() | |
| if is_selected and self.child_dict: # pick another selected_child | |
| child = next(iter(self.child_dict)) | |
| self.disordered_select(child) | |
| elif not self.child_dict: # no more children | |
| self.selected_child = None | |