4.1.1.1.1.1.1.3. datanator.api.lib.metabolite package

4.1.1.1.1.1.1.3.1. Submodules

4.1.1.1.1.1.1.3.2. datanator.api.lib.metabolite.manager module

Author:Jonathan Karr <jonrkarr@gmail.com> Author:Saahith Pochiraju <saahith116@gmail.com> Date:2017-05-16 Copyright:2017, Karr Lab License:MIT

class datanator.api.lib.metabolite.manager.MetaboliteManager(cache_dirname='/root/.wc/data/datanator')

Bases: datanator.api.lib.data_manager.BaseManager

Manages metabolite information for API

get_concentration_by_structure(inchi, only_formula_and_connectivity=True, select=<class 'datanator.core.models.Concentration'>)

Parameters:inchi (str) – inchi structure to find concentrations Returns:List of models.Concentration Objects Return type:list

get_metabolite_by_id(id)

get_metabolite_by_structure(inchi, only_formula_and_connectivity=False, select=<class 'datanator.core.models.Metabolite'>)

Get metabolites with the same structure. Optionally, get metabolites which only have the same core empirical formula and core atom connecticity (i.e. same InChI formula and connectivity layers).

Parameters:

• inchi (str) – molecule structure in InChI format
• only_formula_and_connectivity (bool, optional) – if True, get metabolites which only have the same core empirical formula and core atom connecticity. if False, get metabolites with the identical structure.

Returns:

query for matching metabolites

Return type:

sqlalchemy.orm.query.Query

get_observed_concentrations(metabolite)

Find observed concentrations for the metabolite or similar metabolites

Parameters:metabolite (models.Metabolite) – metabolite to find data for Returns:list of relevant observations Return type:list of data_model.ObservedValue

4.1.1.1.1.1.1.3.3. Module contents