Module meteor.sfcalc

computing structure factors from models

Functions

def gemmi_structure_to_calculated_map(structure: gemmi.Structure, *, high_resolution_limit: float) ‑> Map

Expand source code

def gemmi_structure_to_calculated_map(
    structure: gemmi.Structure, *, high_resolution_limit: float
) -> Map:
    density_map = gemmi.DensityCalculatorX()
    density_map.d_min = high_resolution_limit
    density_map.grid.setup_from(structure)
    for i, _ in enumerate(structure):
        density_map.put_model_density_on_grid(structure[i])

    ccp4_map = gemmi.Ccp4Map()
    ccp4_map.grid = density_map.grid
    ccp4_map.update_ccp4_header()

    return Map.from_ccp4_map(ccp4_map, high_resolution_limit=high_resolution_limit)

def structure_file_to_calculated_map(cif_or_pdb_file: pathlib.Path, *, high_resolution_limit: float) ‑> Map

Expand source code

def structure_file_to_calculated_map(cif_or_pdb_file: Path, *, high_resolution_limit: float) -> Map:
    if not cif_or_pdb_file.exists():
        msg = f"could not find file: {cif_or_pdb_file}"
        raise OSError(msg)
    structure = gemmi.read_structure(str(cif_or_pdb_file))
    return gemmi_structure_to_calculated_map(structure, high_resolution_limit=high_resolution_limit)