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deeprank.features.rst

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Features

This module contains all the tools to compute feature values for molecular structure. Each submodule must be subclass deeprank.features.FeatureClass to inherit the export function. At the moment a few features have already been implemented. These are:
  • AtomicFeatures:Coulomb, van der Waals interactions and atomic charges
  • BSA : Burried Surface area
  • FullPSSM : Complete PSSM data
  • PSSM_IC : Information content of the PSSM
  • ResidueDensity : The residue density for polar/apolar/charged pairs

As you can see in the source each python file contained a __compute_feature__ function. This is the function called in deeprank.generate.

Here are detailed the class in charge of feature calculations.

Atomic Feature

deeprank.features.AtomicFeature

deeprank.features.AtomicFeature.__compute_feature__

Buried Surface Area

deeprank.features.BSA

deeprank.features.BSA.__compute_feature__

FullPSSM

deeprank.features.FullPSSM

deeprank.features.FullPSSM.__compute_feature__

PSSM Information Content

deeprank.features.PSSM_IC

deeprank.features.PSSM_IC.__compute_feature__

Contact Residue Density

deeprank.features.ResidueDensity

deeprank.features.ResidueDensity.__compute_feature__

Generic Feature Class

deeprank.features.FeatureClass