RetainWatersWithinX: Retain Waters Within X Angstroms of Protein

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

Description

Retains water oxygen atoms within a user defined distance

Usage

RetainWatersWithinX(atoms.dist, prot.het.h2o.idc, cutoff.prot.h2o.dist)

Arguments

atoms.dist	Atomic distances calculated with the stats::dist() function
prot.het.h2o.idc	List of protein, HET-atom, and water atom indices
cutoff.prot.h2o.dist	User defined maximum numerical distance, in Angstroms, between the protein and water oxygen atoms to be retained.

Details

Retain water oxygen atoms within a user defined distance. This function is a coarse grain method of removing waters beyond a predefined distance to reduce the computational load associated with the stats::dist() function for a collection of protein structure.

Value

numerical vector of water oxygen atom indicies to retain

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other "Clean Protein Structure": CleanProteinStructures, RemoveHydrogenAtoms, RemoveModeledAtoms, RemoveOoR.b, RemoveOoR.o

Examples

  
  ##--- determine the protein, hetatom, and  water indices
  prot.het.h2o.idc <- ProtHetWatIndices(data=PDB.1hah.aoi.clean)

  ##--- calculate the distances
  atoms.dist <- as.matrix(dist(PDB.1hah.aoi.clean[, c("x","y","z")],
                               method="euclidean",
                               diag=TRUE, upper=TRUE))
  diag(atoms.dist) <- NA

  water.idc.within.6 <- RetainWatersWithinX(atoms.dist,
                                            prot.het.h2o.idc,
                                            cutoff.prot.h2o.dist=6.0)
  # - 204 of the 204 water oxygen atoms are within 6 Angstroms of the protein
  

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