Structure.from_file#

classmethod Structure.from_file(filename, keep_non_atom_records=False, filter_by_elements=None, filter_by_residues=None)[source]#

Reads an atomic structure file and into a Structure instance.

Parameters:

filenamestr

Input file. Supported extensions are:

.pdb	Reads a PDB file
.cif	Reads an mmCIF file

keep_non_atom_recordsbool, optional

Wheter to keep residues that are not labelled ATOM.

filter_by_elements: set, optional

Which elements to keep. Default corresponds to all elements.

filter_by_residues: set, optional

Which residues to keep. Default corresponds to all residues.

Returns:

Structure: Structure instance representing the read in file.

Raises:

ValueError: If the extension is not supported.

Examples

>>> from importlib_resources import files
>>> from tme import Structure
>>> fname = str(files("tests.data").joinpath("Structures/5khe.cif"))
>>> structure = Structure.from_file(filename=fname)
>>> structure
Unique Chains: A-B, Atom Range: 1-1564 [N = 1564], Residue Range: 142-239 [N = 1564]

We can include non ATOM entries and restrict the considered elements and residues

>>> structure = Structure.from_file(
>>>     filename=fname,
>>>     keep_non_atom_records=True,
>>>     filter_by_elements = {"C"},
>>>     filter_by_residues = {"GLY"},
>>> )
>>> structure
Unique Chains: A,B, Atom Range: 96-1461 [N = 44], Residue Range: 154-228 [N = 44]