FIGrpcTable of Contents

all_compoundsall_mapsall_reactionscatalyzed_bycatalyzescomp2reactcurrent_FIGgenomesmap_to_ecsreversibleset_remoteset_remoteusage: $fig->set_remote($url)

Sets the remote version of FIG to the one given by $url.

current_FIGusage: $url = $fig->current_FIG

Returns the URL of the current FIG ("" for a local copy).

genomesusage: @genome_ids = $fig->genomes;

Genomes are assigned ids of the form X.Y where X is the taxonomic id maintained b NCBI for the species (not the specific strain), and Y is a sequence digit assigned t this particular genome (as one of a set with the same genus/species). Genomes als have versions, but that is a separate issue.

all_mapsusage: @maps = $fig->all_maps

Returns a list containing all of the KEGG maps that the system knows about (th maps need to be periodically updated).

map_to_ecsusage: @ecs = $fig->map_to_ecs($map)

Returns the set of functional roles (usually ECs) that are contained in the functionalit depicted by $map.

all_compoundsusage: @compounds = $fig->all_compounds

Returns a list containing all of the KEGG compounds.

comp2reactusage: @rids = $fig->comp2react($cid)

Returns a list containing all of the reaction IDs for reactions that take $ci as either a substrate or a product.

all_reactionsusage: @rids = $fig->all_reactions

Returns a list containing all of the KEGG reaction IDs.

reversibleusage: $rev = $fig->reversible($rid)

Returns true iff the reactions had a "main direction" designated as "<=>";

catalyzed_byusage: @ecs = $fig->catalyzed_by($rid)

Returns the ECs that are reputed to catalyze the reaction. Note that we are currentl just returning the ECs that KEGG gives. We need to handle the incompletely specified form (e.g., 1.1.1.-), but we do not do it yet.

catalyzesusage: @ecs = $fig->catalyzes($role)

Returns the rids of the reactions catalyzed by the "role" (normally an EC).