crystals.PDBParser
- class crystals.PDBParser(ID: str, download_dir: PathLike | None = None, overwrite: bool = False)
Collection of methods that parses Protein DataBank (PDB) files. This object should be used as a context manager.
- Parameters:
ID (str) – Protein DataBank identification. The correct .pdb file will be downloaded, cached and parsed.
download_dir (path-like object or None, optional) – Directory where to save the PDB file.
overwrite (bool, optional) – Whether or not to overwrite files in cache if they exist. If no revision number is provided, files will always be overwritten.
Methods
__delattr__
(name, /)Implement delattr(self, name).
__dir__
()Default dir() implementation.
__enter__
()Return self upon entering the runtime context.
__eq__
(value, /)Return self==value.
__exit__
(*args, **kwargs)Raise any exception triggered within the runtime context.
__format__
(format_spec, /)Default object formatter.
__ge__
(value, /)Return self>=value.
__getattribute__
(name, /)Return getattr(self, name).
__gt__
(value, /)Return self>value.
__hash__
()Return hash(self).
__init__
(ID[, download_dir, overwrite])__init_subclass__
This method is called when a class is subclassed.
__le__
(value, /)Return self<=value.
__lt__
(value, /)Return self<value.
__ne__
(value, /)Return self!=value.
__new__
(**kwargs)__reduce__
()Helper for pickle.
__reduce_ex__
(protocol, /)Helper for pickle.
__repr__
()Return repr(self).
__setattr__
(name, value, /)Implement setattr(self, name, value).
__sizeof__
()Size of object in memory, in bytes.
__str__
()Return str(self).
__subclasshook__
(C)Abstract classes can override this to customize issubclass().
atoms
()Returns a list of atoms associated with a PDB structure in fractional coordinates.
download_pdb_file
(pdb_code[, download_dir, ...])Retrieves a PDB structure file from a PDB server and stores it in a local file tree.
helices
([ignored])Returns an iterable of helices present in the protein.
lattice_vectors
()Returns the lattice vectors associated to a PDB structure.
residues
([ignored])Iterable of residues present in the structure.
secondary_structures
([ignored])Iterable of all secondary structures present in this file.
sheets
([ignored])Returns an iterable of sheets present in the protein.
symmetry_operators
()Returns the symmetry operators that map the atomic positions in a PDB file to the crystal unit cell.
Attributes
__abstractmethods__
__annotations__
__class_getitem__
__slots__
_abc_impl
filename