Here we use distances.distance_array to quantify the distances between each atom of a target set to each atom in a reference set, and show how we can extend that to calculating the distances between the centers-of-mass of residues. Last executed: Feb 06, 2020 with MDAnalysis 0.20.2-dev0. Last updated: January 2020. Minimum version of MDAnalysis: 0.19.0, MDAnalysis.analysis.distances.between (group, A, B, distance) [source] ¶ Return sub group of group that is within distance of both A and B. This function is not aware of periodic boundary conditions. Can be used to find bridging waters or molecules in an interface. Similar to “group and (AROUND A distance and AROUND B distance )”.
All distances within a selection¶ Here we calculate the distance of every atom to every other atom in a selection, and show how we can extend this to residues. Last executed: Feb 06, 2020 with MDAnalysis 1.0.0. Last updated: January 2020. Minimum version of MDAnalysis : 0.19.0. Packages required: MDAnalysis (, ) MDAnalysisTests, Chem. 32 (2011), 2319–2327, doi:10.1002/jcc.21787 # # Distance analysis — :mod:` MDAnalysis .analysis. distances ` ===== This module provides functions to rapidly compute distances between atoms or groups of atoms.:func:`dist` and :func:`between` can take atom groups that do not even have to be from the same :class:`~ MDAnalysis .core.universe …
The boolean attribute ` MDAnalysis .lib. distances .USED_OPENMP` can be checked to see if OpenMP was used in the compilation of MDAnalysis . Selection of acceleration (backend)—–All functions take the optional keyword `backend`, which determines the type of acceleration. Currently, the following …
MDAnalysis.lib.distances.distance_array(reference, configuration, box=None, result=None, backend=’serial’) [source] ¶ Calculate all possible distances between a reference set and another configuration. If there are n positions in reference and m positions in configuration, a distance array of shape (n, m) will be computed.
Atom-wise distances between matching AtomGroups¶ Here we compare the distances between alpha-carbons of the enzyme adenylate kinase in its open and closed conformations. distances .dist can be used to calculate distances between atom groups with the same number of atoms within them. Last executed: Feb 06, 2020 with MDAnalysis 0.20.2-dev0, Chem. 32 (2011), 2319–2327, doi:10.1002/jcc.21787 # # Distance analysis — :mod:` MDAnalysis .analysis. distances ` ===== This module provides functions to rapidly compute distances between atoms or groups of atoms.:func:`dist` and :func:`between` can take atom groups that do not even have to be from the same :class:`~ MDAnalysis .core.universe …
Distances and contacts. The MDAnalysis.analysis.distances module provides functions to rapidly compute distances. These largely take in coordinate arrays. Atom-wise distances between matching AtomGroups. All distances between two selections. All distances within a selection. Residues can be determined to be in contact if atoms from the two residues …
MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.. MDAnalysis allows one to read particle-based trajectories (including individual coordinate frames such as biomolecules in the …
