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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. | |
| """Chain class, used in Structure objects.""" | |
| from Bio.PDB.Entity import Entity | |
| from Bio.PDB.internal_coords import IC_Chain | |
| from typing import Optional | |
| class Chain(Entity): | |
| """Define Chain class. | |
| Chain is an object of type Entity, stores residues and includes a method to | |
| access atoms from residues. | |
| """ | |
| def __init__(self, id): | |
| """Initialize the class.""" | |
| self.level = "C" | |
| self.internal_coord = None | |
| Entity.__init__(self, id) | |
| # Sorting methods: empty chain IDs come last. | |
| def __gt__(self, other): | |
| """Validate if id is greater than other.id.""" | |
| if isinstance(other, Chain): | |
| if self.id == " " and other.id != " ": | |
| return 0 | |
| elif self.id != " " and other.id == " ": | |
| return 1 | |
| else: | |
| return self.id > other.id | |
| else: | |
| return NotImplemented | |
| def __ge__(self, other): | |
| """Validate if id is greater or equal than other.id.""" | |
| if isinstance(other, Chain): | |
| if self.id == " " and other.id != " ": | |
| return 0 | |
| elif self.id != " " and other.id == " ": | |
| return 1 | |
| else: | |
| return self.id >= other.id | |
| else: | |
| return NotImplemented | |
| def __lt__(self, other): | |
| """Validate if id is less than other.id.""" | |
| if isinstance(other, Chain): | |
| if self.id == " " and other.id != " ": | |
| return 0 | |
| elif self.id != " " and other.id == " ": | |
| return 1 | |
| else: | |
| return self.id < other.id | |
| else: | |
| return NotImplemented | |
| def __le__(self, other): | |
| """Validate if id is less or equal than other id.""" | |
| if isinstance(other, Chain): | |
| if self.id == " " and other.id != " ": | |
| return 0 | |
| elif self.id != " " and other.id == " ": | |
| return 1 | |
| else: | |
| return self.id <= other.id | |
| else: | |
| return NotImplemented | |
| def _translate_id(self, id): | |
| """Translate sequence identifier to tuple form (PRIVATE). | |
| A residue id is normally a tuple (hetero flag, sequence identifier, | |
| insertion code). Since for most residues the hetero flag and the | |
| insertion code are blank (i.e. " "), you can just use the sequence | |
| identifier to index a residue in a chain. The _translate_id method | |
| translates the sequence identifier to the (" ", sequence identifier, | |
| " ") tuple. | |
| Arguments: | |
| - id - int, residue resseq | |
| """ | |
| if isinstance(id, int): | |
| id = (" ", id, " ") | |
| return id | |
| def __getitem__(self, id): | |
| """Return the residue with given id. | |
| The id of a residue is (hetero flag, sequence identifier, insertion code). | |
| If id is an int, it is translated to (" ", id, " ") by the _translate_id | |
| method. | |
| Arguments: | |
| - id - (string, int, string) or int | |
| """ | |
| id = self._translate_id(id) | |
| return Entity.__getitem__(self, id) | |
| def __contains__(self, id): | |
| """Check if a residue with given id is present in this chain. | |
| Arguments: | |
| - id - (string, int, string) or int | |
| """ | |
| id = self._translate_id(id) | |
| return Entity.__contains__(self, id) | |
| def __delitem__(self, id): | |
| """Delete item. | |
| Arguments: | |
| - id - (string, int, string) or int | |
| """ | |
| id = self._translate_id(id) | |
| return Entity.__delitem__(self, id) | |
| def __repr__(self): | |
| """Return the chain identifier.""" | |
| return f"<Chain id={self.get_id()}>" | |
| # Public methods | |
| def get_unpacked_list(self): | |
| """Return a list of undisordered residues. | |
| Some Residue objects hide several disordered residues | |
| (DisorderedResidue objects). This method unpacks them, | |
| ie. it returns a list of simple Residue objects. | |
| """ | |
| unpacked_list = [] | |
| for residue in self.get_list(): | |
| if residue.is_disordered() == 2: | |
| for dresidue in residue.disordered_get_list(): | |
| unpacked_list.append(dresidue) | |
| else: | |
| unpacked_list.append(residue) | |
| return unpacked_list | |
| def has_id(self, id): | |
| """Return 1 if a residue with given id is present. | |
| The id of a residue is (hetero flag, sequence identifier, insertion code). | |
| If id is an int, it is translated to (" ", id, " ") by the _translate_id | |
| method. | |
| Arguments: | |
| - id - (string, int, string) or int | |
| """ | |
| id = self._translate_id(id) | |
| return Entity.has_id(self, id) | |
| # Public | |
| def get_residues(self): | |
| """Return residues.""" | |
| yield from self | |
| def get_atoms(self): | |
| """Return atoms from residues.""" | |
| for r in self.get_residues(): | |
| yield from r | |
| def atom_to_internal_coordinates(self, verbose: bool = False) -> None: | |
| """Create/update internal coordinates from Atom X,Y,Z coordinates. | |
| Internal coordinates are bond length, angle and dihedral angles. | |
| :param verbose bool: default False | |
| describe runtime problems | |
| """ | |
| if not self.internal_coord: | |
| self.internal_coord = IC_Chain(self, verbose) | |
| self.internal_coord.atom_to_internal_coordinates(verbose=verbose) | |
| def internal_to_atom_coordinates( | |
| self, | |
| verbose: bool = False, | |
| start: Optional[int] = None, | |
| fin: Optional[int] = None, | |
| ): | |
| """Create/update atom coordinates from internal coordinates. | |
| :param verbose bool: default False | |
| describe runtime problems | |
| :param: start, fin integers | |
| optional sequence positions for begin, end of subregion to process. | |
| N.B. this activates serial residue assembly, <start> residue CA will | |
| be at origin | |
| :raises Exception: if any chain does not have .internal_coord attribute | |
| """ | |
| if self.internal_coord: | |
| self.internal_coord.internal_to_atom_coordinates( | |
| verbose=verbose, start=start, fin=fin | |
| ) | |
| else: | |
| raise Exception( | |
| "Structure %s Chain %s does not have internal coordinates set" | |
| % (self.parent.parent, self) | |
| ) | |