nuri.fmt

class nuri.fmt.MoleculeReader

__iter__(self: MoleculeReader) → MoleculeReader: Returns itself.

__next__(self: MoleculeReader) → Molecule: Returns the next molecule.

class nuri.fmt.CifBlock

property data

property is_global

property name

property save_frames

class nuri.fmt.CifFrame

prefix_search_first(self: CifFrame, prefix: str) → CifTable | None

Search for the first table containing a column starting with the given prefix.

Parameters:: prefix – The prefix to search for.
Returns:: The first table containing the given prefix, or None if not found.

property name

class nuri.fmt.CifParser

class nuri.fmt.CifTable

keys(self: CifTable) → list[str]

nuri.fmt.cif_ddl2_frame_as_dict(frame: CifFrame) → dict[str, list[dict[str, str | None]]]

Convert a CIF frame to a dictionary of lists of dictionaries.

Parameters:: frame – The CIF frame to convert.
Returns:: A dictionary of lists of dictionaries, where the keys are the parent keys and the values are the rows of the table.

nuri.fmt.mmcif_load_frame(frame: CifFrame) → list[Molecule]

Load a CIF frame as a list of molecules.

Parameters:: frame – The CIF frame to load.
Returns:: A list of molecules loaded from the frame.

nuri.fmt.read_cif(path: PathLike) → CifParser

Create a parser object from a CIF file path.

Parameters:: path – The path to the CIF file.
Returns:: A parser object that can be used to iterate over the blocks in the file.

nuri.fmt.to_pdb(mol: Molecule, conf: int | None = None) → str

Convert a molecule to PDB string.

Parameters:

mol – The molecule to convert.
conf – The conformation to convert. If not specified, writes all conformations. Ignored if the molecule has no conformations.

Raises:

IndexError – If the molecule has any conformations and conf is out of range.
ValueError – If the conversion fails.

Note

Unlike most other formats, PDB does not support writing multiple different molecules in a single file. Simply concatenating the results of this function will not produce a valid PDB file.