pyproteonet.data.molecule_set.MoleculeSet

class pyproteonet.data.molecule_set.MoleculeSet(molecules: Dict[str, DataFrame], mappings: Dict[str, DataFrame | MoleculeMapping])

A set of molecules and their relations/mapping. E.g. a set of proteins and peptides with every peptide belonging to one or many proteins

__init__(molecules: Dict[str, DataFrame], mappings: Dict[str, DataFrame | MoleculeMapping])

A set of molecules and their relations/mapping.

Parameters:

• molecules (Dict[str, pd.DataFrame]) – Relevant molecules as dictionay of molecule name and dataframe containing at least the molecule indices

• mappings (Dict[str, pd.DataFrame]) – Every mapping has a multi-index, where every item consists of the ids of the two molecues that are mapped

Methods

__init__(molecules, mappings)	A set of molecules and their relations/mapping.
add_mapping_pairs(name, pairs[, ...])
add_molecules(molecule, df)
clear_cache()
copy([molecule_ids])
drop_mapping(mapping)
drop_molecule_data(columns[, molecule, inplace])
get_mapped(mapping[, molecule, ...])
get_mapped_pairs(mapping[, molecule_a, ...])
get_mapping(mapping_name[, molecule, ...])
get_mapping_degrees(molecule, mapping[, ...])	Returns the node degrees for the given molecule type according to the given mapping.
get_mapping_partner(molecule, mapping)	Infer the partner molecule type for a molecule type and mapping
get_mapping_unique_molecules(molecule[, ...])
get_node_values_for_graph(graph[, ...])
infer_mapping(molecule, mapping)	Infer a mapping name from a molecule type and a mapping string.
infer_mapping_name(molecule, mapping_name)
load(path)
number_molecules(molecule)
rename_mapping(mapping, new_name)
rename_molecule(molecule, new_name)	Rename a molecule type.
rename_molecule_data(columns[, molecule, ...])
save(path[, overwrite])
set_molecule_data(molecule, column, data[, ...])

Attributes

molecule_names

get_mapping_degrees(molecule: str, mapping: str, result_column: str | None = None, partner_molecule: str | None = None, only_unique: bool = False) → Series

Returns the node degrees for the given molecule type according to the given mapping.

E.g. can be used to get the number of peptides per protein.

Parameters:

• molecule (str) – The molecule type to get the degrees for.

• mapping (str) – The mapping to use to generate the graph for the degree calculation.

• result_column (Optional[str], optional) – If given stores the results as a molecule column in the molecule set. Defaults to None.

• partner_molecule (str, optional) – _description_. Defaults to None.

• only_unique (bool, optional) – _description_. Defaults to False.

Raises:

AttributeError – _description_

Returns:

_description_

Return type:

pd.Series

get_mapping_partner(molecule: str, mapping: str) → str

Infer the partner molecule type for a molecule type and mapping

Parameters:

• molecule (str) – The one molecule type of the mapping

• mapping (str) – The mapping name.

Returns:

The other molecule type of the mapping.

Return type:

str

infer_mapping(molecule: str, mapping: str) → Tuple[str, str, str]

Infer a mapping name from a molecule type and a mapping string.

Parameters:

• molecule (str) – Molecule type like protein, peptide …

• mapping (str) – If the name of a molecule type is given it is tried to infer the mapping name connecting both molecule types. If a mapping name is given it is returned as is.

Returns:

The from molecule type, the mapping name, and the to molecule type.

Return type:

Tuple[str, str, str]

rename_molecule(molecule: str, new_name: str)

Rename a molecule type.

Parameters:

• molecule (str) – The current name.

• new_name (str) – The new name.

Raises:

KeyError – Raised when the new name already exists.