Parameter Documentation

RetSynth’s primary script is: rs.py (main script)

RetSynth Parameters

--targets: List of target molecules and the selected organisms

--output_path: Destination for output files

--output_xlsx_format: Convert output txt files to xlsx files (warning: do not do this if getting pathways for 100s of compounds)

--verbose: Control Level of output

--solver_time_limit: time limit for solver to solve shortest path (note: only function with PULP python solver package)

--timer_output: Generates output file calculating time it took to do various functions througout the software (default False)

--inchidb: Retrieve InChI's and use them as compound IDs in the database

--generate_database: Generates metabolic database

--database: Saved metabolic database (.db file)

--generate_database_constraints: Generates full stoichometric matrix for a metabolic database

--database_constraints: Saved stoichmetric matrix for a metabolic database (.constraints file)

--patric_models: Set whether to build database with patric data (using patric, patric.org), (NOTE: To use patric one must have a patric account, patric username and password are required!!)

--patric_username: Specify patric useername

--patric_pasword: Specify patric password

--patric_reaction_type: Define type of reactions that are being added to database (default: bio)

--patric_media: Type of media to build patric FBA models for (default is Complete) other options include Carbon-D-Glucose and LB

--patricfile: List of patric genomes user wants to add into RetSynth database (Default is list includes Escherichia coli DH1, Streptomyces venezuelae ATCC 10712 and Streptomyces venezuelae ATCC 10712 genomes) if user wants to use their own specific set of models file must be a csv file with header followed by the the list of patric genome IDs and Names (i.e genomeID,genomeName) (NOTE: Also patric file can be generated on patric website. To do this go to https://www.patricbrc.org and go to Organisms banner and then click on All Bacteria.  Then click on the Genomes tab and select the genomes you want to add to your database and then click the download select (csv) button

--patric_sbml_output: Output FBA models generated by patric as SBML files (will be stored in the output_path folder)

--patric_models_already_built: If user wants add patric FBA models to the RetSynth Database that were previously generated by RetSynth stored in the patric users /home/models/ folder then this option should be specified

--kbase: Set whether to build database with Kbase data, requires folder of fba models (SBML format) previously downloaded from kbase website https://kbase.us/

--kbase_dump_directory: Directory of metabolic networks used to construct metabolic database (xml files)

--kbase_reaction_type: Define type of reactions that are being added to database (options are bio (default) and chem)

--metacyc: Set to build database with metacyc data

--metacyc_addition: Add metacyc xml file to database can be downloaded from the metacyc website https://metacyc.org/ should be named (metabolic-reactions.xml)

--metacyc_reaction_type: Type of reactions being added to database from metacyc files bio (default) or chem

--kegg: Set to build database with Kegg data

--kegg_organism_type: Define type of organisms reactions to be added to the database bacteria (default) or archea

--kegg_number_of_organisms: Define number of organisms from kegg database to add

--kegg_number_of_organism_pathways: Define number of pathways from an organism to add

--kegg_reaction_type: type of reactions being added to database from atlas files bio (default) or chem

--atlas: Set whether to build database with ATLAS of biochemistry data lcsb-databases.epfl.ch/atlas/ (NOTE: user will have to submit a request through website to get files of ATLAS information)

--atlas_dump_directory: Directory of ATLAS files (.csv)

--atlas_reaction_type: Type of reactions being added to database from atlas files bio (default) or chem

--mine: Set whether to build database with Metabolic In Silico Network Expansion (MINE) database http://minedatabase.mcs.anl.gov/#/home data (NOTE: This option reads in msp files which can be found on the website in the Download section)

--mine_dump_directory: Directory of MINE files (.msp)

--mine_reaction_type: Type of reactions being added to database from mine files bio (default) or chem

--SPRESI: Set whether to build database with SPRESI information (NOTE: to integrate spresi database into RetSynth database the user must have purchased this database and have it stored in rdf file format)

--spresi_dump_directory: Directory of SPRESI files (.rdf)

--spresi_reaction_type: Type of reactions being added to database from spresi files chem (default) or bio

--user_rxns_2_database: Add user defined reactions  to the metabolic database (tab delimnated text file)

--user_rxns_2_database_type: Add user defined reactions  to the metabolic database (tab delimnated text file)

--flux_balance_analysis: Run flux balance analysis

--media_for_FBA: Define media for Flux Balance Analysis Complete media is the default, has to match --patric_media, or if using precompiled database the --patric_media option that was used to build the database

--knockouts: Simulates metabolism using FBA for each reaction knockout

--limit_reactions: Limit the number of reactions in a identified pathway

--limit_cycles: Limits the number of cycle checks

--evaluate_reactions: Defines which type of reactions (bio, chem, or all (default)) to be evaluated in identifying shortest paths

--start_compounds: List of compounds that the shortest path should start from (use in place of target organism)

--k_number_of_paths: Specifies the number of shortest paths wanted by the user

--multiple_solutions: Find all shortest paths (True (defualt) or False)

--cycles: Elimate cycles when finding shortest paths (True (default) or False)

--run_tanimoto_threshold: ells program to run tanimoto threshold analysis identify strucutrally similar compounds in database to targets

--tanimoto_threshold: Set the tanimoto threshold to identify related compounds

--processors: Number of processors to use when solving for shortest path (default 4)

--figures_graphviz: generates pathway figures using graphviz

--figures_chemdraw: generates chemdraw figures

‘’–show_chemical_rxn_info: In chemdraw figures show all chemical reaction information``

--images: Set whether to use chemical images or round nodes in graphviz output figures (default is True, meaining images will be used)