visualization

Renderer = Literal['html', 'notebook', 'streamlit', 'raw'] module-attribute

Which molstar renderer to use for visualization.

load_fitted_models(*, fitted_models_csv, report_csv, runs_csv)

Load fitted models from CSV files generated by the PowerFit CLI commands.

Parameters:

Name	Type	Description	Default
fitted_models_csv	Path	CSV file containing fitted models. Can be generated with protein-detective powerfit fit-models command.	required
report_csv	Path	CSV file containing PowerFit report. Can be generated with protein-detective powerfit report command.	required
runs_csv	Path	CSV file containing PowerFit runs. Can be generated with protein-detective powerfit list-runs command.	required

Returns:

Type

Description

DataFrame

DataFrame containing fitted models with additional information from the report and runs. The returned columns are: powerfit_run_id: ID of the PowerFit run structure: Name of the structure file rank: Rank of the solution cc: Cross-correlation coefficient of the solution fishz: FishZ score of the solution relz: Relative Z-score of the solution translation: Translation vector of the solution as a list of floats rotation: Rotation matrix of the solution as a list of floats fitted_model_file: Path to the fitted model file unfitted_model_file: Path to the unfitted model file density_map: Path to the density map used for fitting run_dir: Path to the PowerFit run directory options: Stringified PowerFit options for the run uniprot_accessions: List of UniProt accessions for the template structure structure_id: Structure ID of the template structure (UniProt or PDB) is_alphafold: Boolean indicating if the template structure is from AlphaFoldDB

show_fitted_models_and_density(fitted_models, renderer='notebook')

Visualizes fitted models and their associated density map with molstar.

Parameters:

Name	Type	Description	Default
fitted_models	DataFrame	The fitted models returned by load_fitted_models. Expected columns: powerfit_run_id, structure, rank, cc, fishz, relz, translation, rotation, fitted_model_file, unfitted_model_file, density_map, run_dir, options, uniprot_accessions, structure_id, is_alphafold.	required
renderer	Renderer	Renderer to use for visualization.	'notebook'

show_structure_and_density(structure, density, renderer='notebook')

Visualizes a structure and its associated density map with molstar.

Parameters:

Name	Type	Description	Default
structure	Path | str	Path to the structure file (PDB format).	required
density	Path	Path to the density map file (e.g., CCP4 format).	required
renderer	Renderer	Renderer to use for visualization.	'notebook'