AlloViz.Protein.calculate

Protein.calculate(pkgs='all', cores=1, **kwargs)

Calculate rwa edge weights of allosteric networks.

Send the computation of the raw edge weights for the selected network construction methods.

Parameters:

pkgsstr or list, default: “all”

Package(s)/Network construction method(s) for which to send raw edge weight computation. “all” sends the computation for all available methods within AlloViz (check AlloViz.AlloViz.utils.pkgsl).

coresint, default: 1

Number of cores to use for parallelization with a multiprocess Pool. Default value only uses 1 core with a custom AlloViz.utils.dummypool that performs computations synchronously.

Other Parameters:

taskcpusint, optional

Optional kwarg to specify the amount of cores that parallelizable network construction methods can use (i.e., AlloViz’s method, getcontacts, dynetan, PyInteraph, MDEntropy and gRINN).

strideint, optional

Optional kwarg to specify the striding to be done on the trajectory(ies) for computationally-expensive network construction methods: i.e., dynetan and AlloViz’s own method. Default is no striding.

namdstr, optional

Optional kwarg pointing to the namd2 executable location; if the namd command is accessible through the CLI it is automatically retrieved with the distutils package.

chisint, optional

Optional kwarg to specify the number of side-chain chi dihedral angles (up to 5) to combine when sending the calculation of a child of the Combined_Dihs Wrappers’ base class that includes chi dihedrals in its calculation.

MDEntropy_methodstr, optional, {“knn”, “grassberger”, “chaowangjost”}

Optional kwarg to specify the method to calculate the entropy of the variables for Mutual Information estimation when using one of the MDEntropy network construction methods (default: “grassberger”).

See also

AlloViz.Wrappers.Base.Base

Base class to launch and store calculation results.

AlloViz.Protein.filter

Class method to filter the network raw edge weights with different criteria.

AlloViz.Protein.analyze

Class method to analyze the calculated raw edge weights with graph theory-based methods.

AlloViz.Protein.view

Class method to visualize the network on the protein structure.

Notes

Calculation results are stored as new instance attributes with the same name as the selected packages/network construction methods. If the object is created providing more than one trajectory file, the average and standard error of the weights between the replicas are also calculated.

Examples

If we have a 6-core computer and want to use 2 cores to compute the values for each of the three trajectories of the protein (e.g., GPCRmd stores three replicas of each structure):

>>> opioidGPCR = AlloViz.Protein(GPCR=169)
>>> opioidGPCR.calculate("dynetan", cores=6, taskcpus=2)
>>> print(opioidGPCR.dynetan.raw.shape)
(41041, 5)