marsi.io package

Submodules

marsi.io.bigg module

marsi.io.build_database module

marsi.io.build_database.build_database(data, data_dir, with_zinc=True, session=<sqlalchemy.orm.session.Session object>)

Builds then Molecules database. It requires that the input files have been downloaded.

See also

Initialization()

Parameters:

• data (module) – The marsi.io.data module
• data_dir (str) – The path to where data is stored.

marsi.io.build_database.upload_chebi_entries(chebi_structures_file, chebi_data, i=0, session=<sqlalchemy.orm.session.Session object>, keys=None)

Import ChEBI data

marsi.io.build_database.upload_drugbank_entries(drugbank_structures_file, drugbank_data, i=0, session=<sqlalchemy.orm.session.Session object>, keys=None)

Import DrugBank

marsi.io.build_database.upload_kegg_entries(kegg_mol_files_dir, kegg_data, i=0, session=<sqlalchemy.orm.session.Session object>, keys=None)

Import KEGG

marsi.io.build_database.upload_pubchem_entries(pubchem_sdf_files_dir, pubchem_data, i=0, session=<sqlalchemy.orm.session.Session object>, keys=None)

Import PubChem

marsi.io.build_database.upload_zinc_entries(zinc_data_file, i=0, session=<sqlalchemy.orm.session.Session object>, keys=None)

Add ZINC

marsi.io.data module

marsi.io.db module

class marsi.io.db.Reference(**kwargs)

Bases: sqlalchemy.ext.declarative.api.Base

Methods

add_reference(database, accession[, session])
get(database, accession[, session])
to_dict()

id

database

accession

classmethod get(database, accession, session=<sqlalchemy.orm.session.Session object>)

classmethod add_reference(database, accession, session=<sqlalchemy.orm.session.Session object>)

to_dict()

class marsi.io.db.Metabolite(**kwargs)

Bases: sqlalchemy.ext.declarative.api.Base

Attributes

volume

Methods

calc_solubility()
dump()
fingerprint([fingerprint_format])
from_molecule(molecule, references, synonyms)
from_references(references[, session])
get(inchi_key[, session])	Retrieves a metabolite using the InChI Key.
molecule([library, get3d])
restore(dump[, session])
to_dict()
validate_inchi_key(key, inchi_key)

id

inchi_key

inchi

analog

formula

num_atoms

num_bonds

num_rings

sdf

references

synonyms

fingerprints

A descriptor that presents a read/write view of an object attribute.

validate_inchi_key(key, inchi_key)

classmethod get(inchi_key, session=<sqlalchemy.orm.session.Session object>)

Retrieves a metabolite using the InChI Key.

Parameters:

• inchi_key (str) – A valid InChi Key.
• session (sqlalchemy.orm.session.Session) – A database session.

Returns:

Return type:

Metabolite

Raises:

KeyError – If the InChI Key is not available.

classmethod from_references(references, session=<sqlalchemy.orm.session.Session object>)

classmethod from_molecule(molecule, references, synonyms, analog=False, session=<sqlalchemy.orm.session.Session object>, first_time=False)

calc_solubility()

volume

molecule(library='openbabel', get3d=True)

fingerprint(fingerprint_format='maccs')

to_dict()

dump()

classmethod restore(dump, session=<sqlalchemy.orm.session.Session object>)

class marsi.io.db.Database

Bases: object

metabolites = <marsi.io.db.CollectionWrapper object>

marsi.io.enrichment module

marsi.io.enrichment.map_uniprot_from_pdb_ids(pdb_ids)

marsi.io.enrichment.find_chebi_id(metabolite)

Queries ChEBI using InChI Key.

Parameters:metabolite (Metabolite) – Returns:With tuples of (id, name) Return type:list

marsi.io.enrichment.find_pubchem_id(metabolite)

Queries PubChem Compound using InChI Key.

Parameters:metabolite (Metabolite) – Returns:With tuples of (id, name) Return type:list

marsi.io.enrichment.find_best_chebi_structure(entity)

marsi.io.parsers module

marsi.io.parsers.parse_kegg_brite(brite_file)

marsi.io.parsers.parse_chebi_data(chebi_names_file, chebi_vertice_file, chebi_relation_file)

marsi.io.parsers.parse_pubchem(summary_file)

marsi.io.plots module

marsi.io.plots.summary_plot(summary, dbs=['chebi', 'kegg', 'drugbank', 'pubchem'])

marsi.io.plots.venn_plot(summary, dbs=['chebi', 'kegg', 'drugbank', 'pubchem'])

marsi.io.retriaval module

marsi.io.retriaval.retrieve_bigg_reactions(dest='/home/travis/.marsi/data/bigg_models_reactions.txt')

Retrieves bigg reactions file

marsi.io.retriaval.retrieve_bigg_metabolites(dest='/home/travis/.marsi/data/bigg_models_metabolites.txt')

Retrieves bigg metabolites file

marsi.io.retriaval.retrieve_drugbank_open_structures(db_version='5.0.3', dest='/home/travis/.marsi/data/drugbank_open_structures.sdf')

Retrieves Drugbank Open Structures.

Parameters:db_version (str) – The version of drugbank to retrieve

marsi.io.retriaval.retrieve_drugbank_open_vocabulary(db_version='5.0.3', dest='/home/travis/.marsi/data/drugbank_open_vocabulary.csv')

Retrieves Drugbank Open Vocabulary.

Parameters:db_version (str) – The version of drugbank to retrieve

marsi.io.retriaval.retrieve_chebi_structures(dest='/home/travis/.marsi/data/chebi_lite_3star.sdf')

Retrieves ChEBI sdf (lite version).

marsi.io.retriaval.retrieve_chebi_names(dest='/home/travis/.marsi/data/chebi_names_3star.txt')

Retrieves ChEBI names.

marsi.io.retriaval.retrieve_chebi_relation(dest='/home/travis/.marsi/data/chebi_relation_3star.tsv')

Retrieves ChEBI relation data.

marsi.io.retriaval.retrieve_chebi_vertice(dest='/home/travis/.marsi/data/chebi_vertice_3star.tsv')

Retrieves ChEBI vertice data.

marsi.io.retriaval.retrieve_kegg_brite(dest='/home/travis/.marsi/data/kegg_brite_08310.keg')

Retrieves KEGG Brite 08310 (Target-based Classification of Drugs)

marsi.io.retriaval.retrieve_pubchem_mol_files(pubchem_ids, dest='/home/travis/.marsi/data')

Retrieves SDF Files from PubChem.

marsi.io.retriaval.retrieve_kegg_mol_files(kegg, dest='/home/travis/.marsi/data')

Retrieves KEGG MOL Files using KEGG REST API.

marsi.io.retriaval.retrieve_zinc_properties(dest='/home/travis/.marsi/data/zinc_16_prop.tsv')

Retrieves ZINC properties file: “All Clean As Subset #6, but without ‘yuck’ compounds”

marsi.io.retriaval.retrieve_zinc_structures(dest='/home/travis/.marsi/data/zinc_16.sdf.gz')

Retrieves ZINC structures file: “All Clean As Subset #6, but without ‘yuck’ compounds”

Module contents

marsi.io.write_excel_file(data_frame, path, molecules)