starling.structure.coordinates

Functions

compare_distance_matrices	Function to compare the original distance matrix with the computed distance matrix.
compute_pairwise_distances	Function to compute the pairwise distances in 3D space.
create_ca_topology_from_coords	Creates a CA backbone topology from a protein sequence and 3D coordinates.
create_incremental_coordinates	TO DO: Add docstring
distance_matrix_to_3d_structure_gd	Function to reconstruct a 3D structure from a distance matrix using gradient descent.
distance_matrix_to_3d_structure_mds	Generate 3D coordinates from a distance matrix using multidimensional scaling (MDS).
distance_matrix_to_3d_structure_torch_mds	SMACOF implementation using PyTorch with support for batched processing.
generate_3d_coordinates_from_distances	Function to generate 3D coordinates from distance maps.
get_tensor_dtype	Function which returns a tensor dtype based on the device passed.
loss_function	Function to compute the loss between the original distance matrix and the computed distance matrix.
save_trajectory	Saves the MDTraj trajectory to a specified file.