4.7.3. Radial Distribution Functions — MDAnalysis.analysis.rdf
¶
Tools for calculating pair distribution functions (“radial distribution functions” or “RDF”).
-
class
MDAnalysis.analysis.rdf.
InterRDF
(g1, g2, nbins=75, range=(0.0, 15.0), exclusion_block=None, **kwargs)[source]¶ Intermolecular pair distribution function
InterRDF(g1, g2, nbins=75, range=(0.0, 15.0))
Parameters: - g1 (AtomGroup) – First AtomGroup
- g2 (AtomGroup) – Second AtomGroup
- nbins (int (optional)) – Number of bins in the histogram [75]
- range (tuple or list (optional)) – The size of the RDF [0.0, 15.0]
- exclusion_block (tuple (optional)) – A tuple representing the tile to exclude from the distance array. [None]
- start (int (optional)) – The frame to start at (default is first)
- stop (int (optional)) – The frame to end at (default is last)
- step (int (optional)) – The step size through the trajectory in frames (default is every frame)
- verbose (bool (optional)) – Show detailed progress of the calculation if set to
True
; the default isFalse
.
Example
First create the
InterRDF
object, by supplying two AtomGroups then use therun()
methodrdf = InterRDF(ag1, ag2) rdf.run()
Results are available through the
bins
andrdf
attributes:plt.plot(rdf.bins, rdf.rdf)
The exclusion_block keyword allows the masking of pairs from within the same molecule. For example, if there are 7 of each atom in each molecule, the exclusion mask (7, 7) can be used.
New in version 0.13.0.