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.

PDB Format Support

from nuri.fmt import pdb

PDB format-specific handlers and utilities.

class nuri.fmt.pdb.Atom

property element

property formal_charge

property hetero

property name

property res_id

property sites

class nuri.fmt.pdb.AtomSite

property altloc

property occupancy

property pos

property tempfactor

class nuri.fmt.pdb.Chain

property id

property res_idxs

class nuri.fmt.pdb.Model

as_dict(self: Model) → dict: Convert the PDB model to a dictionary.

property atoms

property chains

property major_conf

property props

property residues

class nuri.fmt.pdb.Residue

property atom_idxs

property id

property name

class nuri.fmt.pdb.ResidueId

property chain_id

property ins_code

property res_seq

nuri.fmt.pdb.read_models(path: PathLike, skip_on_error: bool = False) → list[Model]

Read PDB models from a file.

Parameters:

path – The path to the PDB file.
skip_on_error – Whether to skip a model if an error occurs, instead of raising an exception.

Raises:

OSError – If any file-related error occurs.
ValueError – If reading a model fails, unless skip_on_error is set.