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.

__init__(ID: str, download_dir: PathLike | None = None, overwrite: bool = False)

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

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