Structure.to_volume#

Structure.to_volume(shape=None, sampling_rate=None, origin=None, chain=None, weight_type='atomic_weight', weight_type_args={})[source]#

Maps class instance to a volume.

Parameters:

shapetuple of ints, optional

Output array shape in (z,y,x) form.

sampling_ratetuple of float, optional

Sampling rate of the output array in units of Structure.atom_coordinate

origintuple of floats, optional

Origin of the coordinate system in (z,y,x) form.

chainstr, optional

Chains to be included. Either single or comma separated string of chains. Defaults to None which returns all chains.

weight_typestr, optional

Weight given to individual atoms. Supported weights are:

atomic_weight	Using element weight point mass
atomic_number	Using atomic number point mass
gaussian	Using element weighted Gaussian mass
van_der_waals_radius	Using binary van der waal spheres
scattering_factors	Using experimental scattering factors
lowpass_scattering_factors	Lowpass filtered scattering_factors

weight_type_argsdict, optional

Additional arguments used for individual weight_types. gaussian accepts resolution, scattering accepts method.

Returns:

Tuple[NDArray, NDArray, NDArray]: Volume, origin and sampling_rate.

Examples

>>> from importlib_resources import files
>>> from tme import Structure
>>> fname = str(files("tests.data").joinpath("Structures/5khe.cif"))
>>> structure = Structure.from_file(filename=fname)
>>> vol, origin, sampling = structure.to_volume()
>>> vol.shape, origin, sampling
((59, 35, 53), array([-30.71,  12.42, -27.15]), array([1., 1., 1.]))
>>> vol, origin, sampling = structure.to_volume(sampling_rate=(2.2,1,3))
((27, 35, 18), array([-30.71,  12.42, -27.15]), array([2.2, 1. , 3. ]))

sampling_rate and origin can be set to ensure correct alignment with corresponding density maps such as the ones at EMDB. Analogous to Structure.subset_by_chain() only parts of the structure can be mapped onto grids using a variety of weighting schemes

>>> structure.to_volume(weight_type="van_der_waals_radius")
>>> structure.to_volume(
>>>     weight_type="lowpass_scattering_factors",
>>>     method_args={"source" : "dt1969", "downsampling_factor" : 1.35},
>>> )