simulariumio.nerdss package¶
Submodules¶
simulariumio.nerdss.nerdss_converter module¶
- class simulariumio.nerdss.nerdss_converter.NerdssConverter(input_data: NerdssData)[source]¶
Bases:
TrajectoryConverter- Parameters:
- input_dataNerdssData
An object containing info for reading NERDSS simulation trajectory outputs and plot data
simulariumio.nerdss.nerdss_data module¶
- class simulariumio.nerdss.nerdss_data.NerdssData(path_to_pdb_files: str, meta_data: MetaData | None = None, display_data: Dict[str, DisplayData] | None = None, time_units: UnitData | None = None, spatial_units: UnitData | None = None, plots: List[Dict[str, Any]] | None = None, time_step: UnitData | None = None)[source]¶
Bases:
object- Parameters:
- path_to_pdb_filesstr
A path to the folder of PDB files for the trajectory. For this converter, it is expected that the frame numbers are the names of the file (plus the file extention). At this time, the frame numbers must be at consistent intervals
- meta_dataMetaData
An object containing metadata for the trajectory including box size, scale factor, and camera defaults
- display_data: Dict[str, DisplayData] (optional)
The particle type name from NERDSS data mapped to display names and rendering info for that type, Default: for names, use NERDSS name,
for radius, use 1.0, for rendering, use default representations and colors
- time_units: UnitData (optional)
multiplier and unit name for time values Default: 1.0 second
- spatial_units: UnitData (optional)
multiplier and unit name for spatial values (including positions, radii, and box size) Default: 1.0 meter
- plotsList[Dict[str, Any]] (optional)
An object containing plot data already in Simularium format
- time_stepUnitData (optional)
Time step between each frame, where the frame numbers are represented as the names of the .pdb files in path_to_pdb_files Default: 1.0 second
- display_data: Dict[str, DisplayData]¶
- path_to_pdb_files: str¶
- plots: List[Dict[str, Any]]¶