vanddraabe (version 1.1.1)

calcNumHydrogenBonds: Calculate Number of Hydrogen Bonds

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

Value

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

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.

See Also

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

Examples

# NOT RUN {
  
# }
# 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
  
# }
# NOT RUN {
# }