DB

class pathomx.db.Compound(**entries)

as_csv()

type = u'compound'

type_name = u'Compound'

url

class pathomx.db.Gene(**entries)

as_csv()

type = u'gene'

type_name = u'Gene'

url

class pathomx.db.Pathway(**entries)

as_csv()

type = u'pathway'

type_name = u'Pathway'

url

class pathomx.db.Protein(**entries)

as_csv()

type = u'protein'

type_name = u'Protein'

url

class pathomx.db.Reaction(**entries)

as_csv()

compounds

secondary_compounds

type = u'reaction'

type_name = u'Reaction'

url

class pathomx.db.ReactionIntermediate(**entries)

name = u'n/a'

type = u'dummy'

type_name = u'n/a'

class pathomx.db.databaseManager

add_compound(id, attr)

add_db_synonyms(id, databases)

add_gene(id, attr)

add_identity(id, identity)

add_pathway(id, attr)

add_protein(id, attr)

add_reaction(id, attr)

add_synonym(id, synonym)

add_synonyms(id, synonyms)

extract_db_unification(db_unification)

get_via_synonym(id)

get_via_unification(database, id)

load_compounds()

load_genes()

load_gibbs()

load_identities()

load_pathways()

load_proteins()

load_reactions()

load_synonyms(filename=u'/home/docs/checkouts/readthedocs.org/user_builds/pathomx/checkouts/stable/pathomx/database/synonyms')

load_xrefs()

save_compounds()

save_genes()

save_pathways()

save_proteins()

save_reactions()

save_synonyms()