Index

_

__compute_similarity() (microberx.MetabolitePredictor.RunPredictionRule method) (microberx.RunPredictionRule method) __documentation_web__ (in module microberx) __get_mol_substructure() (microberx.MetabolitePredictor.RunPredictionRule method) (microberx.RunPredictionRule method) __get_product_atom_indexes() (microberx.MetabolitePredictor.RunPredictionRule method) (microberx.RunPredictionRule method) __get_substructure_neighbors() (microberx.MetabolitePredictor.RunPredictionRule method) (microberx.RunPredictionRule method) __github_issues_web__ (in module microberx)

__github_web__ (in module microberx) __init__() (microberx.Reaction method) (microberx.RuleGenerator.Reaction method) __mapped_reaction_raw (microberx.Reaction attribute) (microberx.RuleGenerator.Reaction attribute) __mapped_reaction_sanitized (microberx.Reaction attribute) (microberx.RuleGenerator.Reaction attribute) __trim_mol() (microberx.MetabolitePredictor.RunPredictionRule method) (microberx.RunPredictionRule method) __version__ (in module microberx)

B

biosystem (microberx.MetabolitePredictor attribute) (microberx.MetabolitePredictor.MetabolitePredictor attribute)

C

classify_molecules() (in module microberx) (in module microberx.MetaboliteAnalyzer) compute_isotopic_mass() (in module microberx) (in module microberx.MetaboliteAnalyzer)

compute_molecular_descriptors() (in module microberx) (in module microberx.MetaboliteAnalyzer) cut_off (microberx.MetabolitePredictor attribute) (microberx.MetabolitePredictor.MetabolitePredictor attribute)

D

decompose_reaction() (in module microberx) (in module microberx.RuleGenerator)

display_molecules() (in module microberx) (in module microberx.MetaboliteVisualizer)

F

fetch_batch_sequences() (in module microberx) (in module microberx.OmicsIntegrator)

G

generate_rules() (in module microberx) (in module microberx.RuleGenerator) generate_single_reactant_reactions() (in module microberx) (in module microberx.RuleGenerator) get_config() (in module microberx._version) get_interpro() (in module microberx) (in module microberx.OmicsIntegrator)

get_keywords() (in module microberx._version) get_versions() (in module microberx) (in module microberx._version) git_get_keywords() (in module microberx._version) git_pieces_from_vcs() (in module microberx._version) git_versions_from_keywords() (in module microberx._version)

H

HANDLERS (in module microberx._version)

L

load_evidences() (in module microberx) (in module microberx.DataFiles) load_microbes_data() (in module microberx) (in module microberx.DataFiles)

load_microbes_reactions() (in module microberx) (in module microberx.DataFiles) load_reaction_rules() (in module microberx) (in module microberx.DataFiles) LONG_VERSION_PY (in module microberx._version)

M

MappedReaction (microberx.Reaction attribute), [1] (microberx.RuleGenerator.Reaction attribute), [1] MetabolitePredictor (class in microberx) (class in microberx.MetabolitePredictor) microberx module microberx._version module microberx.DataFiles module microberx.MetaboliteAnalyzer module microberx.MetabolitePredictor module

microberx.MetaboliteVisualizer module microberx.OmicsIntegrator module microberx.RuleGenerator module module microberx microberx._version microberx.DataFiles microberx.MetaboliteAnalyzer microberx.MetabolitePredictor microberx.MetaboliteVisualizer microberx.OmicsIntegrator microberx.RuleGenerator

N

NotThisMethod

P

parentdir_prefix (microberx._version.VersioneerConfig attribute) pep440_split_post() (in module microberx._version) plot_aligment_chart() (in module microberx) (in module microberx.OmicsIntegrator) plot_boiled_egg() (in module microberx) (in module microberx.MetaboliteVisualizer) plot_confidence_scores() (in module microberx) (in module microberx.MetaboliteVisualizer) plot_interpro_results() (in module microberx) (in module microberx.OmicsIntegrator) plot_isotopic_masses() (in module microberx) (in module microberx.MetaboliteVisualizer) plot_metabolic_accesibility() (in module microberx) (in module microberx.MetaboliteVisualizer)

plot_molecular_descriptors() (in module microberx) (in module microberx.MetaboliteVisualizer) plot_relationships() (in module microberx) (in module microberx.MetaboliteVisualizer) plot_similarity_matrix() (in module microberx) (in module microberx.OmicsIntegrator) plot_species_sunburst() (in module microberx) (in module microberx.OmicsIntegrator) plus_or_dot() (in module microberx._version) predict() (microberx.MetabolitePredictor.RunPredictionRule method), [1] (microberx.RunPredictionRule method), [1] predicted_metabolites (microberx.MetabolitePredictor attribute), [1] (microberx.MetabolitePredictor.MetabolitePredictor attribute), [1]

Q

query (microberx.MetabolitePredictor attribute), [1] (microberx.MetabolitePredictor.MetabolitePredictor attribute), [1] (microberx.MetabolitePredictor.RunPredictionRule attribute), [1] (microberx.RunPredictionRule attribute), [1]

query_atoms_num (microberx.MetabolitePredictor attribute), [1] (microberx.MetabolitePredictor.MetabolitePredictor attribute), [1] query_name (microberx.MetabolitePredictor attribute), [1] (microberx.MetabolitePredictor.MetabolitePredictor attribute), [1]

R

reacting_atoms (microberx.MetabolitePredictor attribute), [1] (microberx.MetabolitePredictor.MetabolitePredictor attribute), [1] reacting_atoms_in_unique_metabolites (microberx.MetabolitePredictor attribute), [1] (microberx.MetabolitePredictor.MetabolitePredictor attribute), [1] Reaction (class in microberx) (class in microberx.RuleGenerator) reaction (microberx.MetabolitePredictor.RunPredictionRule attribute), [1] (microberx.RunPredictionRule attribute), [1] real_product (microberx.MetabolitePredictor.RunPredictionRule attribute), [1] (microberx.RunPredictionRule attribute), [1] real_substrate (microberx.MetabolitePredictor.RunPredictionRule attribute), [1] (microberx.RunPredictionRule attribute), [1] register_vcs_handler() (in module microberx._version) render() (in module microberx._version) render_git_describe() (in module microberx._version) render_git_describe_long() (in module microberx._version) render_pep440() (in module microberx._version)

render_pep440_branch() (in module microberx._version) render_pep440_old() (in module microberx._version) render_pep440_post() (in module microberx._version) render_pep440_post_branch() (in module microberx._version) render_pep440_pre() (in module microberx._version) reverse_reaction() (in module microberx) (in module microberx.RuleGenerator) ReversedReaction (microberx.Reaction attribute) (microberx.RuleGenerator.Reaction attribute) rule_smarts (microberx.MetabolitePredictor.RunPredictionRule attribute), [1] (microberx.RunPredictionRule attribute), [1] run_command() (in module microberx._version) run_multi_sequence_aligment() (in module microberx) (in module microberx.OmicsIntegrator) run_prediction() (microberx.MetabolitePredictor method), [1] (microberx.MetabolitePredictor.MetabolitePredictor method), [1] RunPredictionRule (class in microberx) (class in microberx.MetabolitePredictor)

S

sanitize_reaction() (in module microberx), [1] (in module microberx.RuleGenerator) SanitizedReaction (microberx.Reaction attribute), [1] (microberx.RuleGenerator.Reaction attribute), [1]

search_pubchem() (in module microberx) (in module microberx.MetaboliteAnalyzer) set_reaction_ids() (in module microberx) (in module microberx.RuleGenerator) style (microberx._version.VersioneerConfig attribute)

T

tag_prefix (microberx._version.VersioneerConfig attribute)

U

unique_products (microberx.MetabolitePredictor.RunPredictionRule attribute) (microberx.RunPredictionRule attribute)

V

VCS (microberx._version.VersioneerConfig attribute) verbose (microberx._version.VersioneerConfig attribute)

VersioneerConfig (class in microberx._version) versionfile_source (microberx._version.VersioneerConfig attribute) versions_from_parentdir() (in module microberx._version)