biosimulators_utils.model_lang.smoldyn package#
Submodules#
biosimulators_utils.model_lang.smoldyn.simularium_converter module#
Using the Biosimulators side of Smoldyn to generate a modelout.txt Smoldyn file for a specified OMEX/COMBINE archive which then is used to generate a .simularium file for the given simulation. That .simularium file is then stored along with the log.yml and report.{FORMAT} relative to the simulation. Remember: each simulation, while not inherently published, has the potential for publication based purely on the simulation’s ability to provide a valid OMEX/COMBINE archive. There exists (or should exist) an additional layer of abstraction to then validate and verify the contents therein.
- class biosimulators_utils.model_lang.smoldyn.simularium_converter.BiosimulatorsDataConverter(archive: SmoldynCombineArchive)[source]#
Bases:
ABC- static generate_camera_data_object(position: ndarray, look_position: ndarray, up_vector: ndarray) CameraData[source]#
- static generate_display_data_object(name: str, radius: float, display_type=DISPLAY_TYPE.SPHERE, obj_color: str | None = None) DisplayData[source]#
- generate_display_data_object_dict(agent_names: List[Tuple[str, str, float, str]]) Dict[str, DisplayData][source]#
Generate a display object dict.
- Parameters:
agent_names – List[Tuple[str, str, float]] -> a list of tuples defining the Display Data configuration parameters.
such (The Tuple is expected to be as) – [(agent_name: str, display_name: str, radius: float, color: str)]
- Returns:
Dict[str, DisplayData]
- generate_input_file_data_object(model_output_file: str | None = None) InputFileData[source]#
Generates a new instance of simulariumio.data_model.InputFileData based on self.archive.model_output_filename (which itself is derived from the model file) if no model_output_file is passed.
- Parameters:
model_output_file (
str) – Optional: file on which to base the InputFileData instance.- Returns:
simulariumio input file data object based on self.archive.model_output_filename
- Return type:
(
InputFileData)
- abstract generate_output_data_object(file_data: InputFileData, display_data: Dict[str, DisplayData] | None = None, spatial_units='nm', temporal_units='ns')[source]#
Generate a data object to fit the simulariumio.TrajectoryData interface.
- abstract generate_simularium_file(simularium_filename: str, box_size: float, spatial_units='nm', temporal_units='ns', n_dim=3, display_data: Dict[str, DisplayData] | None = None) None[source]#
Create a data_object, optionally translate it, convert to simularium, and save.
- prepare_agent_data() AgentData[source]#
Create a new instance of an AgentData object following the specifications of the simulation within the relative combine archive.
- static prepare_simularium_fp(**simularium_config) str[source]#
Generate a simularium dir and joined path if not using the init object.
- Kwargs:
(obj):**simularium_config: keys are ‘simularium_dirpath’ and ‘simularium_fname’
- Returns:
str: complete simularium filepath
- Return type:
(obj)
- static save_simularium_file(data: SmoldynData | TrajectoryData, simularium_filename) None[source]#
Takes in either a SmoldynData or TrajectoryData instance and saves a simularium file based on it with the name of simularium_filename. If none is passed, the file will be saved in self.archive.rootpath
- Parameters:
data (
Union[SmoldynData, TrajectoryData]) – data object to save.simularium_filename (
str) – Optional: name by which to save the new simularium file. If None is passed, will default to self.archive.rootpath/self.archive.simularium_filename
- class biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynCombineArchive(rootpath: str, outputs_dirpath: str | None = None, model_output_filename: str | None = None, simularium_filename: str | None = None, name='my_combine_archive')[source]#
Bases:
object- get_manifest_filepath() List[str] | str[source]#
Read SmoldynCombineArchive manifest files. Return all filepaths containing the word ‘manifest’.
- Returns:
path if there is just one manifest file, otherwise List[str] of manifest filepaths.
- Return type:
str
- verify_smoldyn_in_manifest() bool[source]#
Pass the return value of self.get_manifest_filepath() into a new instance of CombineArchiveReader such that the string manifest object tuples are evaluated for the presence of smoldyn.
- Returns:
Whether there exists a smoldyn model in the archive based on the archive’s manifest.
- Return type:
bool
- class biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter(archive: SmoldynCombineArchive)[source]#
Bases:
BiosimulatorsDataConverter- generate_output_data_object(file_data: InputFileData, display_data: Dict[str, DisplayData] | None = None, meta_data: MetaData | None = None, spatial_units='nm', temporal_units='ns') SmoldynData[source]#
- Generate a new instance of SmoldynData. If passing meta_data, please create a new MetaData instance
using the self.generate_metadata_object interface of this same class.
- Parameters:
file_data – (
InputFileData): simulariumio.InputFileData instance based on model output.display_data – (
Dict[Dict[str, DisplayData]]): Optional: if passing this parameter, please use the self.generate_display_object_dict interface of this same class.meta_data – (
Metadata): new instance of Metadata object. If passing this parameter, please use the self.generate_metadata_object interface method of this same class.spatial_units – (
str): spatial units by which to measure this simularium output. Defaults to nm.temporal_units – (
str): time units to base this simularium instance on. Defaults to ns.
- Returns:
SmoldynData
- generate_simularium_file(box_size=1.0, spatial_units='nm', temporal_units='ns', n_dim=3, simularium_filename: str | None = None, display_data: Dict[str, DisplayData] | None = None) None[source]#
Create a data_object, optionally translate it, convert to simularium, and save.