├── .gitignore ├── GPRuler_requirements.txt ├── LICENSE ├── README.md ├── Tutorial_GPRuler_fromOrganismName.ipynb ├── Tutorial_GPRuler_fromSBML.ipynb ├── furtherAnalyses ├── MetaNetX_compounds.py ├── gprulerVsBenchmarkEvaluation.py ├── hmrCore_comparisonMetaNetX_FuzzyWuzzy.csv ├── recon3D_comparisonMetaNetX_FuzzyWuzzy.csv ├── yeast7_comparisonMetaNetX_FuzzyWuzzy.csv └── yeast8_comparisonMetaNetX_FuzzyWuzzy.csv ├── pipeline ├── GPRULER.py ├── GPRULERLib.py ├── README.md ├── RESTmoduleModified.py ├── fromOrganismName2ReactionsList.py ├── fromReactions2Genes.py ├── fromReactions2Genes_fromOrgName.py ├── fromReactions2Genes_wFilteredData.py ├── fromReactions2Genes_wFilteredData_fromOrgName.py ├── genericLib.py ├── genesLib.py ├── genesLocationFilter.py ├── genesLocationFilter_fromOrgName.py ├── metaboliteIdentification.py ├── metabolitesIdentification_FuzzyWuzzy.py ├── metabolitesIdentification_FuzzyWuzzy_part2.py ├── metabolitesIdentification_joiningData.py ├── metabolitesLib.py ├── prepareGPRulerInput.py ├── reactionsIdentification.py ├── reactionsIdentification_TCDB.py └── reactionsLib.py ├── rawData ├── HMRcore_20200328_wReconNames.xml ├── README.md ├── chebiId_inchi_20201216.tsv.bz2 ├── chebi_chemical_data_20201216.tsv ├── chebi_compounds_20201216.tsv.bz2 ├── chebi_compounds_20201216153117.csv.bz2 ├── chebi_compounds_20201216153117_exploded.csv.bz2 ├── chebi_database_accession_20201216.tsv.bz2 ├── chebi_names_20201216.tsv.bz2 ├── chebi_relation_20201216.tsv.bz2 ├── chebi_uniprot_20201216.tsv.bz2 ├── dfJoin_metacyc_kegg_rhea_20201218164915.csv ├── kegg_compounds_20201216150802.csv ├── kegg_glycans_20201216150802.csv ├── metacyc_compounds_20201216152513.csv ├── metacyc_genes_20201216152513.csv ├── metacyc_proteins_20201216152513.csv ├── tcdb_tc2Uniprot.csv ├── tcdb_tc2substrates.csv ├── toymodel.xml ├── yeast8.xml └── yeast_7.6_cobra.xml └── tutorial └── outputs ├── HMRcore_GenesData.csv ├── HMRcore_GenesRelationships.csv ├── HMRcore_Kegg2UniprotGenes.csv ├── HMRcore_Rxns2Genes.csv ├── HMRcore_gprRules.csv ├── Scerevisiae_GeneId2Rxns.csv ├── Scerevisiae_Kegg2UniprotGenes.csv ├── Scerevisiae_RxnId2ECs.csv ├── Scerevisiae_RxnId2Equation.csv ├── Scerevisiae_Rxns2Genes.csv ├── Scerevisiae_genes2Compartments.csv ├── hmrCore_genes2Compartments.csv ├── hmrCore_genes2Compartments_wFilter.csv ├── hmrCore_mappingChebi_100.tsv ├── hmrCore_mappingChebi_91_99_checked.tsv ├── hmrCore_mappingChebi_allResults.tsv ├── hmrCore_mappingChebi_empty.tsv ├── hmrCore_mappingFuzzy.tsv ├── hmrCore_mappingFuzzyAndClassic.tsv ├── hmrCore_mappingKeggC_100.tsv ├── hmrCore_mappingKeggC_91_99_checked.tsv ├── hmrCore_mappingKeggC_allResults.tsv ├── hmrCore_mappingKeggC_empty.tsv ├── hmrCore_mappingKeggG_100.tsv ├── hmrCore_mappingKeggG_91_99_checked.tsv ├── hmrCore_mappingKeggG_allResults.tsv ├── hmrCore_mappingKeggG_empty.tsv ├── hmrCore_mappingMetaCyc_100.tsv ├── hmrCore_mappingMetaCyc_91_99_checked.tsv ├── hmrCore_mappingMetaCyc_allResults.tsv ├── 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