I/O Functions¶

Functions for loading and writing models in VCML, SBML, and Antimony formats.

VCML¶

load_vcml_file¶

handler: python options: show_source: false show_signature_annotations: true

load_vcml_str¶

handler: python options: show_source: false show_signature_annotations: true

load_vcml_url¶

Load a VCML model from a URL.

handler: python options: show_source: false show_signature_annotations: true

write_vcml_file¶

handler: python options: show_source: false show_signature_annotations: true

to_vcml_str¶

Convert a Biomodel object to a VCML string, after refreshing its content with a round trip to libvcell

handler: python options: show_source: false show_signature_annotations: true

SBML¶

load_sbml_file¶

handler: python options: show_source: false show_signature_annotations: true

load_sbml_str¶

handler: python options: show_source: false show_signature_annotations: true

load_sbml_url¶

Load a SBML model from a URL.

handler: python options: show_source: false show_signature_annotations: true

write_sbml_file¶

handler: python options: show_source: false show_signature_annotations: true

to_sbml_str¶

handler: python options: show_source: false show_signature_annotations: true

Antimony¶

load_antimony_file¶

handler: python options: show_source: false show_signature_annotations: true

load_antimony_str¶

handler: python options: show_source: false show_signature_annotations: true

write_antimony_file¶

handler: python options: show_source: false show_signature_annotations: true

to_antimony_str¶

handler: python options: show_source: false show_signature_annotations: true

Utilities¶

update_biomodel¶

Update the BioModel object with the latest changes.

Parameters:

Name	Type	Description	Default
`bio_model`	`Biomdel`	The Biomodel object to parse and update (e.g. regenerating math and geometry).	required

Returns:

Name	Type	Description
`BioModel`	`Biomodel`	The updated BioModel object.

handler: python options: show_source: false show_signature_annotations: true

field_data_refs¶

Extract field data references from the VCML model and return them as a list of tuples. Each tuple contains the following elements: - field_data_name: str - field_data_varname: str - field_data_type: VariableType - field_data_time: float

handler: python options: show_source: false show_signature_annotations: true

Workspace¶

set_workspace_dir¶

Set the workspace directory for VCell simulations.

handler: python options: show_source: false show_signature_annotations: true

get_workspace_dir¶

Get the current workspace directory for VCell simulations.

handler: python options: show_source: false show_signature_annotations: true