This module contains parallel versions of analysis tasks in
InterRDF(g1, g2, nbins=75, range=0.0, 15.0, exclusion_block=None)¶
Intermolecular pair distribution function
The distance \(r\) at which the distribution function \(g(r)\) is determined; these are calculated as the centers of the bins that were used for histogramming.
The value of the pair distribution function \(g(r)\) at \(r\).
g1 (AtomGroup) – First AtomGroup
g2 (AtomGroup) – Second AtomGroup
nbins (int (optional)) – Number of bins in the histogram 
exclusion_block (tuple (optional)) – A tuple representing the tile to exclude from the distance array. [None]
rdf = InterRDF(ag1, ag2) rdf.run()
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 0.2.0.
Universe) – a
MDAnalysis.core.groups.Universe(the atomgroups must belong to this Universe)
atomgroups (tuple of
AtomGroup) – atomgroups that are iterated in parallel
The raw data from each process are stored as a list of lists, with each sublist containing the return values from
Calculate the cumulative distribution functions (CDF). Note that this is the actual count within a given radius, i.e., \(N(r)\).
cdf – a numpy array with the same structure as
- Return type
New in version 0.3.0.
Set the attributes of this class to be read only
Useful to avoid the class being modified when passing it around.
To be used as a context manager:
with analysis.readonly_attributes(): some_function(analysis)
run(start=None, stop=None, step=None, n_jobs=1, n_blocks=None)¶
Perform the calculation
start (int, optional) – start frame of analysis
stop (int, optional) – stop frame of analysis
step (int, optional) – number of frames to skip between each analysed frame
n_jobs (int, optional) – number of jobs to start, if -1 use number of logical cpu cores. This argument will be ignored when the distributed scheduler is used
n_blocks (int, optional) – number of blocks to divide trajectory into. If
Noneset equal to n_jobs or number of available workers in scheduler.