This module provides functions to rapidly compute distances between atoms or groups of atoms.
dist() and between() can take atom groups that do not even have to be from the same Universe.
Calculate all distances between a reference set and another configuration.
d = distance_array(ref,conf[,box[,result=d]])
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This method is slower than it could be because internally we need to make copies of the ref and conf arrays.
Calculate all distances d_ij between atoms i and j within a configuration ref.
d = self_distance_array(ref[,box[,result=d]])
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Note
This method is slower than it could be because internally we need to make copies of the coordinate arrays.
Calculates a matrix of contacts between a list of coordinates.
There is a fast, high-memory-usage version for small systems (returntype = ‘numpy’), and a slower, low-memory-usage version for larger systems (returntype = ‘sparse’).
If box dimensions are passed (box = [Lx, Ly, Lz]), then periodic boundary conditions are applied. Only orthorhombic boxes are currently supported.
Change progress_meter_freq to alter frequency of progress meter updates. Or switch suppress_progmet to True to suppress it completely.
Return distance between atoms in two atom groups.
The distance is calculated atom-wise. The residue ids are also returned because a typical use case is to look at CA distances before and after an alignment. Using the offset keyword one can also add a constant offset to the resids which facilitates comparison with PDB numbering.
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Returns: | NumPy array([resids_A, resids_B, distances]) |