calcNumHydrogenBonds: Calculate Number of Hydrogen Bonds

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

Description

Calculate the number of hydrogen bonds.

Usage

calcNumHydrogenBonds(distances, nearby.atoms.idc, names.atoms, set.oi.idc)

Arguments

distances	between water atom of interest and the protein atoms, water oxygen atoms, or HETATMs
nearby.atoms.idc	numeric vector of atom indices near water of interest
names.atoms	names of atoms; e.g.; c("CB", "CA", "N", "O", "CZ")
set.oi.idc	numeric vector of indices for protein atoms, water oxygen atoms, or HETATMs

Details

The summation, mean, and standard deviation of the hydrophilicity fraction for the protein atoms within the user specified distance for the BoundWaterEnvironment() function are calculated and returned.

Value

Number of possible hydrogen bonds between the water of interest and the protein atoms within 3.5 Angstroms of the water.

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other "Bound Water Environment": BoundWaterEnvironment.interact, BoundWaterEnvironment.quality, BoundWaterEnvironment, Mobility, NormalizedBvalue, calcBvalue, calcNearbyHydrationFraction

Examples

  ## Not run: 
  distances <- PDB.1hai.h2o.prot.dists[3, ]
  nearby.atoms.idc <- Nearby(distances, set.idc = prot.idc, radius = 3.6)
  names.atoms <- PDB.1hai.aoi.clean$elety[prot.idc]
  calcNumHydrogenBonds(distances, nearby.atoms.idc, names.atoms,
    set.oi.idc = prot.idc)
  # [1] 4
  
## End(Not run)

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