Index

A

accession (marsi.io.db.Reference attribute) add_known_analogs() (marsi.cli.controllers.database.DatabaseController method) add_reference() (marsi.io.db.Reference class method) ale() (marsi.cli.controllers.modeling.OptimizationController method) ALEDesign (class in marsi.cobra.strain_design) (class in marsi.cobra.strain_design.design_methods) align_molecules() (in module marsi.chemistry.openbabel) analog (marsi.io.db.Metabolite attribute) annotate_metabolite() (in module marsi.cobra.utils)

annotate_model() (in module marsi.cobra.utils) AntiMetaboliteManipulationTarget (class in marsi.cobra.strain_design.target) api_version (marsi.bigg_api.DBVersion attribute) apply() (marsi.cobra.strain_design.target.AntiMetaboliteManipulationTarget method) (marsi.cobra.strain_design.target.MetaboliteKnockoutTarget method) apply_anti_metabolite() (in module marsi.cobra.flux_analysis.manipulation) arguments (marsi.cli.controllers.chemistry.ChemistryController.Meta attribute) (marsi.cli.controllers.database.DatabaseController.Meta attribute) (marsi.cli.controllers.modeling.OptimizationController.Meta attribute)

B

base_controller (marsi.cli.app.MarsiApp.Meta attribute) (marsi.cli.MarsiApp.Meta attribute) build_data() (marsi.cli.controllers.database.DatabaseController method)

build_database() (in module marsi.io.build_database) (marsi.cli.controllers.database.DatabaseController method) build_nearest_neighbors_model() (in module marsi.nearest_neighbors)

C

calc_solubility() (marsi.io.db.Metabolite method) ChemistryController (class in marsi.cli.controllers.chemistry) ChemistryController.Meta (class in marsi.cli.controllers.chemistry) cl_context (marsi.nearest_neighbors.model.NearestNeighbors attribute) ClFail (class in marsi.nearest_neighbors.model) CNearestNeighbors (class in marsi.nearest_neighbors.model_ext)

compete_metabolite() (in module marsi.cobra.flux_analysis.manipulation) convert() (marsi.cli.controllers.modeling.OptimizationController method) convert_design() (in module marsi.cobra.strain_design.post_processing) convert_strain_design_results() (in module marsi.cobra.strain_design.post_processing) convert_target() (in module marsi.cobra.strain_design.post_processing) convert_target_group() (in module marsi.cobra.strain_design.post_processing) convex_hull_volume() (in module marsi.chemistry)

D

data_frame (marsi.nearest_neighbors.model.DBNearestNeighbors attribute) (marsi.nearest_neighbors.model.NearestNeighbors attribute) Database (class in marsi.io.db) database (marsi.io.db.Reference attribute) database_version() (in module marsi.bigg_api) DatabaseController (class in marsi.cli.controllers.database) DatabaseController.Meta (class in marsi.cli.controllers.database) db_status() (marsi.cli.controllers.MarsiBaseController method) DBNearestNeighbors (class in marsi.nearest_neighbors.model) DBVersion (class in marsi.bigg_api) DEBUG (marsi.config.Level attribute) default() (marsi.cli.controllers.chemistry.ChemistryController method) (marsi.cli.controllers.MarsiBaseController method) (marsi.cli.controllers.database.DatabaseController method) (marsi.cli.controllers.modeling.OptimizationController method) description (marsi.cli.controllers.chemistry.ChemistryController.Meta attribute) (marsi.cli.controllers.database.DatabaseController.Meta attribute) (marsi.cli.controllers.modeling.OptimizationController.Meta attribute)

Distance (class in marsi.nearest_neighbors.model) distance_matrix() (marsi.nearest_neighbors.model.DistributedNearestNeighbors method) distances() (marsi.nearest_neighbors.model.DBNearestNeighbors method) (marsi.nearest_neighbors.model.DistributedNearestNeighbors method) (marsi.nearest_neighbors.model.NearestNeighbors method) distances_cl() (marsi.nearest_neighbors.model.NearestNeighbors method) distances_py() (marsi.nearest_neighbors.model_ext.CNearestNeighbors method) DistributedNearestNeighbors (class in marsi.nearest_neighbors.model) downgrade() (in module marsi.alembic.versions.c1b678211e9d_baseline) (in module marsi.alembic.versions.ef39a4ae2c8c_add_solubility) download() (marsi.cli.controllers.database.DatabaseController method) download_bigg() (marsi.cli.controllers.database.DatabaseController method) download_chebi() (marsi.cli.controllers.database.DatabaseController method) download_drug_bank() (marsi.cli.controllers.database.DatabaseController method) download_kegg() (marsi.cli.controllers.database.DatabaseController method) download_model() (in module marsi.bigg_api) download_pubchem() (marsi.cli.controllers.database.DatabaseController method) download_zinc() (marsi.cli.controllers.database.DatabaseController method) dump() (marsi.io.db.Metabolite method)

E

ERROR (marsi.config.Level attribute) essential_metabolites (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute)

essential_metabolites_reactions() (marsi.cobra.strain_design.design_methods.GenericMARSIDesignMethod method) exclude_reactions (marsi.cli.controllers.modeling.OptimizationController attribute)

F

feature() (marsi.nearest_neighbors.model.DistributedNearestNeighbors method) features (marsi.nearest_neighbors.model.DBNearestNeighbors attribute) (marsi.nearest_neighbors.model_ext.CNearestNeighbors attribute) features_lengths (marsi.nearest_neighbors.model_ext.CNearestNeighbors attribute) find_analogs() (marsi.cli.controllers.chemistry.ChemistryController method) find_anti_metabolite_knockouts() (in module marsi.cobra.strain_design.post_processing) find_anti_metabolite_modulation() (in module marsi.cobra.strain_design.post_processing) find_best_chebi_structure() (in module marsi.io.enrichment) find_chebi_id() (in module marsi.io.enrichment) find_inchi_for_bigg_metabolite() (in module marsi.cobra.utils) find_pubchem_id() (in module marsi.io.enrichment) fingerprint() (in module marsi.chemistry.openbabel) (in module marsi.chemistry.rdkit) (marsi.chemistry.molecule.Molecule method) (marsi.io.db.Metabolite method)

fingerprint_to_bits() (in module marsi.chemistry.openbabel) (in module marsi.chemistry.rdkit) fingerprints (marsi.io.db.Metabolite attribute) formula (marsi.io.db.Metabolite attribute) fp (marsi.nearest_neighbors.model.Distance attribute) (marsi.nearest_neighbors.model.KNN attribute) (marsi.nearest_neighbors.model.RNN attribute) frange() (in module marsi.utils) from_inchi() (marsi.chemistry.molecule.Molecule class method) from_mol() (marsi.chemistry.molecule.Molecule class method) from_molecule() (marsi.io.db.Metabolite class method) from_references() (marsi.io.db.Metabolite class method) from_sdf() (marsi.chemistry.molecule.Molecule class method)

G

GenericMARSIDesignMethod (class in marsi.cobra.strain_design.design_methods) get() (marsi.io.db.Metabolite class method) (marsi.io.db.Reference class method) get_metabolite() (in module marsi.bigg_api) get_model_gene() (in module marsi.bigg_api)

get_model_metabolite() (in module marsi.bigg_api) get_model_reaction() (in module marsi.bigg_api) get_model_target() (marsi.cobra.strain_design.target.AntiMetaboliteManipulationTarget method) get_reaction() (in module marsi.bigg_api) get_spectrophore_data() (in module marsi.chemistry.openbabel)

H

handlers (marsi.cli.app.MarsiApp.Meta attribute) (marsi.cli.MarsiApp.Meta attribute)

has_radical() (in module marsi.chemistry.openbabel) heuristic_method (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute)

I

id (marsi.io.db.Metabolite attribute) (marsi.io.db.Reference attribute) inchi (marsi.chemistry.molecule.Molecule attribute) (marsi.io.db.Metabolite attribute) inchi_key (marsi.chemistry.molecule.Molecule attribute) (marsi.io.db.Metabolite attribute) inchi_to_inchi_key() (in module marsi.chemistry.openbabel) (in module marsi.chemistry.rdkit)

inchi_to_molecule() (in module marsi.chemistry.openbabel) (in module marsi.chemistry.rdkit) index (marsi.nearest_neighbors.model.DBNearestNeighbors attribute) (marsi.nearest_neighbors.model.DistributedNearestNeighbors attribute), [1] (marsi.nearest_neighbors.model.NearestNeighbors attribute) INFO (marsi.config.Level attribute) inhibit_metabolite() (in module marsi.cobra.flux_analysis.manipulation) init() (marsi.cli.controllers.database.DatabaseController method) input_buffer() (marsi.nearest_neighbors.model.NearestNeighbors method)

K

k (marsi.nearest_neighbors.model.KNN attribute) k_nearest_neighbors() (marsi.nearest_neighbors.model.DistributedNearestNeighbors method) KNN (class in marsi.nearest_neighbors.model)

knn() (marsi.nearest_neighbors.model.DBNearestNeighbors method) (marsi.nearest_neighbors.model.NearestNeighbors method) knockout_metabolite() (in module marsi.cobra.flux_analysis.manipulation)

L

label (marsi.cli.app.MarsiApp.Meta attribute) (marsi.cli.MarsiApp.Meta attribute) (marsi.cli.controllers.MarsiBaseController.Meta attribute) (marsi.cli.controllers.chemistry.ChemistryController.Meta attribute) (marsi.cli.controllers.database.DatabaseController.Meta attribute) (marsi.cli.controllers.modeling.OptimizationController.Meta attribute) last_update (marsi.bigg_api.DBVersion attribute)

Level (class in marsi.config) list_metabolites() (in module marsi.bigg_api) list_model_genes() (in module marsi.bigg_api) list_model_metabolites() (in module marsi.bigg_api) list_model_reactions() (in module marsi.bigg_api) list_models() (in module marsi.bigg_api) list_reactions() (in module marsi.bigg_api) load_nearest_neighbors_model() (in module marsi.nearest_neighbors)

M

main() (in module marsi.cli.app) manipulation_type (marsi.cobra.strain_design.evolutionary.OptMet attribute) (marsi.cobra.strain_design.OptMet attribute) map_uniprot_from_pdb_ids() (in module marsi.io.enrichment) marsi (module) marsi.alembic (module) marsi.alembic.versions (module) marsi.alembic.versions.c1b678211e9d_baseline (module) marsi.alembic.versions.ef39a4ae2c8c_add_solubility (module) marsi.bigg_api (module) marsi.chemistry (module) marsi.chemistry.common (module) marsi.chemistry.common_ext (module) marsi.chemistry.molecule (module) marsi.chemistry.openbabel (module) marsi.chemistry.rdkit (module) marsi.cli (module) marsi.cli.app (module) marsi.cli.controllers (module) marsi.cli.controllers.chemistry (module) marsi.cli.controllers.database (module) marsi.cli.controllers.modeling (module) marsi.cobra (module) marsi.cobra.flux_analysis (module) marsi.cobra.flux_analysis.analysis (module) marsi.cobra.flux_analysis.manipulation (module) marsi.cobra.strain_design (module) marsi.cobra.strain_design.design_methods (module) marsi.cobra.strain_design.evolutionary (module) marsi.cobra.strain_design.metaheuristic (module) marsi.cobra.strain_design.post_processing (module) marsi.cobra.strain_design.target (module) marsi.cobra.utils (module) marsi.config (module) marsi.io (module) marsi.io.bigg (module) marsi.io.build_database (module) marsi.io.db (module) marsi.io.enrichment (module) marsi.io.parsers (module) marsi.io.plots (module) marsi.io.retriaval (module) marsi.nearest_neighbors (module)

marsi.nearest_neighbors.model (module) marsi.nearest_neighbors.model_ext (module) marsi.utils (module) MarsiApp (class in marsi.cli) (class in marsi.cli.app) MarsiApp.Meta (class in marsi.cli) (class in marsi.cli.app) MarsiBaseController (class in marsi.cli.controllers) MarsiBaseController.Meta (class in marsi.cli.controllers) max_memory_allocation_size() (marsi.nearest_neighbors.model.NearestNeighbors method) maximum_common_substructure() (in module marsi.chemistry.rdkit) mcs_similarity() (in module marsi.chemistry.rdkit) Metabolite (class in marsi.io.db) metabolite_knockout_fitness() (in module marsi.cobra.flux_analysis) (in module marsi.cobra.flux_analysis.analysis) metabolite_knockout_phenotype() (in module marsi.cobra.flux_analysis) (in module marsi.cobra.flux_analysis.analysis) MetaboliteKnockoutOptimization (class in marsi.cobra.strain_design.metaheuristic) MetaboliteKnockoutTarget (class in marsi.cobra.strain_design.target) metabolites (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute) (marsi.io.db.Database attribute) migrate() (marsi.cli.controllers.database.DatabaseController method) mode (marsi.nearest_neighbors.model.Distance attribute) (marsi.nearest_neighbors.model.KNN attribute) (marsi.nearest_neighbors.model.RNN attribute) model (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute) model_details() (in module marsi.bigg_api) mol_chebi_id() (in module marsi.chemistry.openbabel) mol_drugbank_id() (in module marsi.chemistry.openbabel) mol_pubchem_id() (in module marsi.chemistry.openbabel) mol_str_to_inchi() (in module marsi.chemistry.openbabel) mol_to_inchi() (in module marsi.chemistry.openbabel) (in module marsi.chemistry.rdkit) mol_to_inchi_key() (in module marsi.chemistry.openbabel) (in module marsi.chemistry.rdkit) mol_to_molecule() (in module marsi.chemistry.rdkit) mol_to_svg() (in module marsi.chemistry.openbabel) Molecule (class in marsi.chemistry.molecule) molecule() (marsi.io.db.Metabolite method) monte_carlo_volume() (in module marsi.chemistry) (in module marsi.chemistry.common) (in module marsi.chemistry.common_ext) (in module marsi.chemistry.rdkit) mutagenesis() (marsi.cli.controllers.modeling.OptimizationController method)

N

NearestNeighbors (class in marsi.nearest_neighbors.model) neighbors (marsi.nearest_neighbors.model.DBNearestNeighbors attribute) num_atoms (marsi.chemistry.molecule.Molecule attribute) (marsi.io.db.Metabolite attribute)

num_bonds (marsi.chemistry.molecule.Molecule attribute) (marsi.io.db.Metabolite attribute) num_rings (marsi.chemistry.molecule.Molecule attribute) (marsi.io.db.Metabolite attribute)

O

objective_function (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute) OptimizationController (class in marsi.cli.controllers.modeling) OptimizationController.Meta (class in marsi.cli.controllers.modeling) optimize_with_metabolites() (marsi.cobra.strain_design.ALEDesign method) (marsi.cobra.strain_design.RandomMutagenesisDesign method) (marsi.cobra.strain_design.design_methods.ALEDesign method) (marsi.cobra.strain_design.design_methods.GenericMARSIDesignMethod method) (marsi.cobra.strain_design.design_methods.RandomMutagenesisDesign method)

optimize_with_reaction() (marsi.cobra.strain_design.ALEDesign method) (marsi.cobra.strain_design.RandomMutagenesisDesign method) (marsi.cobra.strain_design.design_methods.ALEDesign method) (marsi.cobra.strain_design.design_methods.GenericMARSIDesignMethod method) (marsi.cobra.strain_design.design_methods.RandomMutagenesisDesign method) OptMet (class in marsi.cobra.strain_design) (class in marsi.cobra.strain_design.evolutionary) output_buffer() (marsi.nearest_neighbors.model.NearestNeighbors method)

P

parse_chebi_data() (in module marsi.io.parsers) parse_kegg_brite() (in module marsi.io.parsers) parse_pubchem() (in module marsi.io.parsers)

pickle_large() (in module marsi.utils) plot (marsi.cobra.strain_design.evolutionary.OptMet attribute) (marsi.cobra.strain_design.OptMet attribute) program (marsi.nearest_neighbors.model.NearestNeighbors attribute)

Q

queue() (marsi.nearest_neighbors.model.NearestNeighbors method)

R

radius (marsi.nearest_neighbors.model.RNN attribute) radius_nearest_neighbors() (marsi.nearest_neighbors.model.DistributedNearestNeighbors method) RandomMutagenesisDesign (class in marsi.cobra.strain_design) (class in marsi.cobra.strain_design.design_methods) Reference (class in marsi.io.db) references (marsi.io.db.Metabolite attribute) replace_design() (in module marsi.cobra.strain_design.post_processing) replace_strain_design_results() (in module marsi.cobra.strain_design.post_processing) restore() (marsi.io.db.Metabolite class method) retrieve_bigg_metabolites() (in module marsi.io.retriaval) retrieve_bigg_reactions() (in module marsi.io.retriaval) retrieve_chebi_names() (in module marsi.io.retriaval) retrieve_chebi_relation() (in module marsi.io.retriaval) retrieve_chebi_structures() (in module marsi.io.retriaval) retrieve_chebi_vertice() (in module marsi.io.retriaval)

retrieve_drugbank_open_structures() (in module marsi.io.retriaval) retrieve_drugbank_open_vocabulary() (in module marsi.io.retriaval) retrieve_kegg_brite() (in module marsi.io.retriaval) retrieve_kegg_mol_files() (in module marsi.io.retriaval) retrieve_pubchem_mol_files() (in module marsi.io.retriaval) retrieve_zinc_properties() (in module marsi.io.retriaval) retrieve_zinc_structures() (in module marsi.io.retriaval) rmsd() (in module marsi.chemistry.common) (in module marsi.chemistry.common_ext) RNN (class in marsi.nearest_neighbors.model) rnn() (marsi.nearest_neighbors.model.DBNearestNeighbors method) (marsi.nearest_neighbors.model.NearestNeighbors method) run() (marsi.cobra.strain_design.evolutionary.OptMet method) (marsi.cobra.strain_design.OptMet method) (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization method) run_kernel() (marsi.nearest_neighbors.model.NearestNeighbors method)

S

sdf (marsi.io.db.Metabolite attribute) sdf_to_molecule() (in module marsi.chemistry.rdkit) search() (in module marsi.bigg_api) seed (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute) sensitivity_analysis() (in module marsi.cobra.flux_analysis) (in module marsi.cobra.flux_analysis.analysis) simulation_kwargs (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute) simulation_method (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute), [1] smiles_to_molecule() (in module marsi.chemistry.openbabel) solubility() (in module marsi.chemistry.openbabel)

stacked_on (marsi.cli.controllers.chemistry.ChemistryController.Meta attribute) (marsi.cli.controllers.database.DatabaseController.Meta attribute) (marsi.cli.controllers.modeling.OptimizationController.Meta attribute) stacked_type (marsi.cli.controllers.chemistry.ChemistryController.Meta attribute) (marsi.cli.controllers.database.DatabaseController.Meta attribute) (marsi.cli.controllers.modeling.OptimizationController.Meta attribute) start_positions (marsi.nearest_neighbors.model_ext.CNearestNeighbors attribute) status() (marsi.cli.controllers.database.DatabaseController method) structural_similarity() (in module marsi.chemistry.rdkit) summary_plot() (in module marsi.io.plots) synonyms (marsi.io.db.Metabolite attribute)

T

tanimoto_coefficient() (in module marsi.chemistry) (in module marsi.chemistry.common) (in module marsi.chemistry.common_ext) tanimoto_distance() (in module marsi.chemistry) (in module marsi.chemistry.common) (in module marsi.chemistry.common_ext)

termination (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute) test_target_substitutions() (in module marsi.cobra.strain_design.post_processing) to_dict() (marsi.io.db.Metabolite method) (marsi.io.db.Reference method) to_gnomic() (marsi.cobra.strain_design.target.AntiMetaboliteManipulationTarget method) (marsi.cobra.strain_design.target.MetaboliteKnockoutTarget method)

U

unpickle_large() (in module marsi.utils) upgrade() (in module marsi.alembic.versions.c1b678211e9d_baseline) (in module marsi.alembic.versions.ef39a4ae2c8c_add_solubility) upload_chebi_entries() (in module marsi.io.build_database)

upload_drugbank_entries() (in module marsi.io.build_database) upload_kegg_entries() (in module marsi.io.build_database) upload_pubchem_entries() (in module marsi.io.build_database) upload_zinc_entries() (in module marsi.io.build_database)

V

validate_inchi_key() (marsi.io.db.Metabolite method) venn_plot() (in module marsi.io.plots)

version (marsi.bigg_api.DBVersion attribute) volume (marsi.io.db.Metabolite attribute)

W

WARNING (marsi.config.Level attribute)

write_excel_file() (in module marsi.io) wt_reference (marsi.cobra.strain_design.metaheuristic.MetaboliteKnockoutOptimization attribute)