calcAtomHydrationEstimate: Estimated Atomic Hydration Fraction

In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

Description

Calculates the estimated atomic hydration fraction for an atom with unknown surface exposure.

Usage

calcAtomHydrationEstimate(df.AtomHydroTEMP, AT.hydratFract)

Arguments

df.AtomHydroTEMP	The newly calculated (determined) atomic hydrophilicity values
AT.hydratFract	The AtomTypeClasses.hydratFract variable calculated with the HydrophilicityEvaluation() function; the mean hydration fraction for the AtomTypes

Details

This function is called within HydrophilicityEvaluation() to calculate the estimated hydration of an atom with unknown surface exposure.

(num surface exposures)/(num atom occurrences) * atom class hydration fraction

NOTE: This is a non-public function.

Value

This function returns the hydration estimate values in a string to the variable AT.hydratFract.estimates and are included in the HydrophilicityTable results of HydrophilicityEvaluation().

Author(s)

Emilio Xavier Esposito [e-mail]

References

Leslie A Kuhn, Craig A Swanson, Michael E Pique, John A Tainer, and Elizabeth D Getzof. Atomic and Residue Hydrophilicity in the Context of Folded Protein Structures. PROTEINS: Structure, Function, and Genetics, 1995, 23 (4), pp 536-547. DOI: 10.1002/prot.340230408 PMID: 8749849

See Also

Other "Hydrophilicity Evaluation" "Bound Water Environment": HydrophilicityEvaluation, calcAtomClassHydrophilicity, getProtAtomsNearWater, getResidueData

Examples

 ## Not run: 
  calcAtomHydrationEstimate(df.AtomHydroTEMP, AT.hydratFract)
 
## End(Not run)

vanddraabe documentation built on June 8, 2019, 1:03 a.m.