Density.match_structure_to_density#

classmethod Density.match_structure_to_density(target, template, cutoff_target=0, scoring_method='NormalizedCrossCorrelation', optimization_method='basinhopping', maxiter=500)[source]#

Aligns a tme.structure.Structure template to Density target and returns an aligned tme.structure.Structure instance.

If voxel sizes of target and template dont match coordinates are scaled to the numerically smaller voxel size. Prealignment is done by center’s of mass. Finally tme.matching_optimization.optimize_match is used to determine translation and rotation to match a template to target.

Parameters:

targetDensity: The target map for template matching.
templateStructure: The template that should be aligned to the target.
cutoff_targetfloat, optional: The cutoff value for the target map, by default 0.
cutoff_templatefloat, optional: The cutoff value for the template map, by default 0.
scoring_methodstr, optional: The scoring method to use for template matching. See tme.matching_optimization.create_score_object for available methods, by default “NormalizedCrossCorrelation”.
optimization_methodstr, optional: Optimizer that is used. See tme.matching_optimization.optimize_match().
maxiterint, optional: Maximum number of iterations for the optimizer. See tme.matching_optimization.optimize_match().

Returns:

Structure: Tuple containing template aligned to target as tme.structure.Structure object, translation and rotation matrix used for the transformation.

Notes

Translation and rotation are in xyz format, different from match_densities(), which is zyx.