This module provides functions to rapidly compute distances between atoms or groups of atoms.
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, then periodic boundary conditions are applied.
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]) |