AlloViz.AlloViz.Classes.Delta#

class AlloViz.AlloViz.Classes.Delta(refstate, state2, pymol_aln='super')[source]#

Bases: object

AlloViz class for calculating a delta-network.

Used to calculate the delta-network between two Protein objects, using all the available combinations of packages/network construction methods, filterings, and elements-metrics that they have in common. A structural alignment of the structures is performed with PyMOL with the selected method to find the corresponding residues between the two structures for subtraction of edge weights.

Parameters:

refstateAlloViz.Protein: Object of the AlloViz.Protein class to use as reference (values of the other AlloViz.Protein object will be subtracted from this one’s values).
state2AlloViz.Protein: Object of the AlloViz.Protein class to compare with the reference one to build the delta-network (this one’s values will be subtracted from the reference one’s values).
pymol_aln{“super”, “align”, “cealign”}, default: “super”: PyMOL’s method to apply for the structural alignment of the two structures, used to retrieve the corresponding residues between the two for subtraction of edge weights. It is performed by AlloViz.Delta._make_struct_aln().

See also

AlloViz.Protein: AlloViz main class for calculation of protein allosteric communication networks.

Notes

For PyMOL’s structural alignment, align starts from a sequence alignment and is optimal to align structures with identical sequences, but is deeply affected by sequence differences. super performs a sequence-independent dynamic programming structural alignment and it works well for structures with low sequence identity. cealign uses the Combinatorial Extension (CE) algorithm and it is preferred for structures with little to no sequence similarity (twilight zone). The methods are described in PyMOL’s documentation.

Examples

>>> activeB2AR = AlloViz.Protein(GPCR=117, name="Active B2AR")
>>> inactiveB2AR = AlloViz.Protein(GPCR=160, name="Inactive B2AR")
>>> for protein in [activeB2AR, inactiveB2AR]:
>>>     protein.calculate("pytraj_CA")
>>>     protein.analyze(metrics="btw")
>>> delta = AlloViz.Delta(activeB2AR, inactiveB2AR)
>>> print(delta.pytraj_CA.Whole.edges.df.shape)
(40690, 5)

Attributes:

refstate
state2

Methods

view(pkg, metric[, filtering, element, num, ...])

Visualize the analyzed delta-networks on the protein structure.