_f_gene ( sid: str, prefix: str = 'G_' ) → str ¶ The string with prefix clipped if it existed. _clip ( sid: str, prefix: str ) → str ¶Ĭlip a prefix from the beginning of a string if it exists. The first match between the underscores, converted to character. NumberStr ( Match) – Match object, identified by pattern_from_sbml Returns _number_to_chr ( numberStr: Match ) → str ¶Ĭonvert an ascii number to a character. NonASCII ( Match) – Match object, identified by pattern_from_sbml Returns _escape_non_alphanum ( nonASCII: Match ) → str ¶Ĭonverts a non alphanumeric character to a string representation of pattern_from_sbml :Pattern ¶ cobra.io.sbml. pattern_to_sbml :Pattern ¶ cobra.io.sbml. SBO_EXCHANGE_REACTION = SBO:0000627 ¶ cobra.io.sbml. SBO_DEFAULT_FLUX_BOUND = SBO:0000626 ¶ cobra.io.sbml. SBO_FBA_FRAMEWORK = SBO:0000624 ¶ cobra.io.sbml. BOUND_PLUS_INF = plus_inf ¶ cobra.io.sbml. BOUND_MINUS_INF = minus_inf ¶ cobra.io.sbml. ZERO_BOUND_ID = cobra_0_bound ¶ cobra.io.sbml. UPPER_BOUND_ID = cobra_default_ub ¶ cobra.io.sbml. LOWER_BOUND_ID = cobra_default_lb ¶ cobra.io.sbml. Return string representation of SBMLError.Įxception cobra.io.sbml. _error_string(error: libsbml.SBMLError, k: Optional = None) Validate SBML model and returns the model along with a list of errors. Validate_sbml_model(filename: Union, check_model: bool = True, internal_consistency: bool = True, check_units_consistency: bool = False, check_modeling_practice: bool = False, **kwargs) → Tuple, dict] Set SBase annotations based on cobra annotations. _sbase_annotations(sbase: libsbml.SBase, annotation: dict) → None Parse provider and term from given identifiers annotation uri. _parse_annotation_info(uri: str) → Union] Parse cobra annotations from a given SBase object. _parse_annotations(sbase: libsbml.SBase) → dict _sbase_notes_dict(sbase: libsbml.SBase, notes: dict) → None _check(value: Union, message: str) → NoneĬheck the libsbml return value and logs error messages. _check_required(sbase: libsbml.Base, value: str, attribute: str) → str _create_parameter(model: libsbml.Model, pid: str, value: float, sbo: Optional = None, constant: Optional = True, units: Optional = None, flux_udef: Optional = None) → None _create_bound(model: libsbml.Model, reaction: Reaction, bound_type: str, f_replace: dict, units: Optional = None, flux_udef: Optional = None) → strĬreate bound in model for given reaction. _model_to_sbml(cobra_model: Model, f_replace: Optional = None, units: bool = True) → libsbml.SBMLDocument Write_sbml_model(cobra_model: Model, filename: Union, f_replace: dict = F_REPLACE, **kwargs) → None _sbml_to_model(doc: libsbml.SBMLDocument, number: Type = float, f_replace: dict = F_REPLACE, set_missing_bounds: bool = False, **kwargs) → Model _get_doc_from_filename(filename: Union) → ‘libsbml.SBMLDocument’ Read_sbml_model(filename: Union, number: Type = float, f_replace: dict = F_REPLACE, **kwargs) → Model _escape_non_alphanum(nonASCII: Match) → strĬonvert non alphanumeric to string representation of ascii number.Ĭlip a prefix from the beginning of a string if it exists.
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