Metabolite

As noted previously, both the get_metabolites() and mass_search() methods returns a list of Metabolite objects. If you already know the InChIKey of the metabolite you're interested in - it is possible to instantiate a Metabolite instantly using the from_inchikey method.

from dimedbpy import Metabolite

metabolite = Metabolite.from_inchikey("DOUMFZQKYFQNTF-WUTVXBCWSA-N")

Attributes

• name
• synonyms
• systematic_name
• smiles
• molecular_formula
• inchi
• clogP
• polar_surface_area
• secondary_amines
• ether_oxygens
• rings
• hydrogen_bond_acceptors
• hydrogen_bond_donors
• aromatic_rings
• formal_charge
• mr_values
• fraction_sp3_carbon
• carboxylc_acids
• molecular_weight
• rotatable_bonds
• chebi
• hmdb
• pubchem
• kegg
• cas
• wikidata
• biocyc
• chemspider
• kegg_pathways
• smpdb_pathways
• biocyc_pathways

Dictionary interface

For ease of access, Metabolite contains a _record property which represents a Python dictionary that contains all of the data about the Metabolite. Moreover, the to_dict() class method returns a simplified dictionary representation of the aforementioned data. Through this method it is also possible to list the desired properties to obtain, for example:

from dimedbpy import Metabolite

metabolite = Metabolite.from_inchikey("DOUMFZQKYFQNTF-WUTVXBCWSA-N")
metabolite.to_dict(properties=["Name", "Synonyms", "Molecular Formula"])