//!enzyme2
// This is a comment for the enzyme macro - you can use this macro like a programing language
// For more infos, please see https://stark-jena.de | enzyme
// Copyright (c) 2011-201 by Heiko Stark

load.metacycle "reactions.dat"
load.metacycle.compound "compounds.dat"
load.metacycle.enzyme "enzrxns.dat" // fill up enzyme names
load.metacycle.gene "genes.dat" // fill up gene names
load.metacycle.pathway "pathways.dat" // fill up pathway names

print "How many organisms? : " organism.size // only if you use more than one organism
print "How many metabolites? : " metabolite.size
print "How many reactions? : " reaction.size
print "How many enzymes? : " reaction.enzyme.size // only if you load additional enzymes (load.metacycle.enzyme)
print "How many reaction genes? : " reaction.gene.size // only if you load additional genes (load.metacycle.gene)
print "How many genes? : " regulator.gene.size // only if you load additional genes (load.metacycle.gene)
print "How many pathways? : " reaction.pathway.size // only if you load additional pathways (load.metacycle.pathway)

load.ontology "gene_ontology_ext.obo"
load.kegg "mmu.list"

annotation.clear 
database.save "database.fast" // full database

//!enzyme2
// This is a comment for the enzyme macro - you can use this macro like a programing language
// For more infos, please see https://stark-jena.de | enzyme
// Copyright (c) 2011-2015 by Heiko Stark

// Show statistics
metabolite.clearname := true // false S###S | true metabolite
metabolite.withlocation := true // false metabolite | true metabolite[?]

ifexists "database.fast"
then
	load.database "database.fast"
end
else
	print "No database found!"
	stop
end

print "How many organisms? : " organism.size // only if you use more than one organism
print "How many metabolites? : " metabolite.size
print "How many reactions? : " reaction.size

io.dir.hardchange "Complete"
pathway.complete
print "Reactions: " pathway.size

pathway.save "pathway.list" index
pathway.save "pathway.eclist" ec
pathway.save "pathway.namelist" name
pathway.savepathways "pathways.name" sortname
pathway.savepathways "pathways.count" sortcount
pathway.savepathways "pathways.index" sortindex
pathway.savepathways "pathways.group" group
pathway.saveignore "pathwayignore.eclist" ec
pathway.savemetaused "pathwaymetaused.list" index
pathway.savemetaused "pathwaymetaused.namelist" name
pathway.savemetacount "pathwaymetacount.list" index
pathway.savemetacount "pathwaymetacount.namelist" name

metabolite.clearname := false
pathway.savemetatool "pathway.dat" index auto
metabolite.clearname := true

pathway.savemetatool "pathway.ecdat" ec auto
pathway.savegml "pathway.gml" 18

metabolite.clearname := false
reaction.save "reaction.idlist" index
metabolite.clearname := true

reaction.save "reaction.eclist" ec
reaction.save "reaction.list" index
// metabolite.sort // after sorting the metabolite the reaction is empty
metabolite.save "metabolite.list" index