vanddraabe (version 1.1.1)

HasXWaters: Has "X" Waters

Description

Determines if PDB structure has water molecules.

Usage

HasXWaters(atoms.oi.resid, min.num.h2o = 20)

Arguments

atoms.oi.resid

vector of character strings containing the standardized three-letter amino acid residue names

min.num.h2o

numeric value indicating the minimum number of water molecules required to return a TRUE logical value

Value

logical indicating if the PDB structure has the minimum user defined number of waters

numeric value indicating the number of water oxygen atoms within the PDB structure

Details

Determine if the PDB structure has at least the user defined number of water oxygen atoms. The number of water oxygen atoms is returned along with a logical value indicating if the structure satisfies the user defined minimum.

Waters are identified using the three water three-letter residue names: HOH, WAT, and DOD.

See Also

Other utilities: ConservationSet, DetermineChainsOfInterest, ExtractFileTimeStamp, ExtractPDBids, FileTimeStamp, Nearby, ProtHetWatIndices, RescaleValues, RetainChainsOfInterest, ReturnPDBfullPath, StandardizeAsparticAcidNames, StandardizeCysteineNames, StandardizeGlutamicAcidNames, StandardizeHistidineNames, StandardizeLysineNames, TimeSpan, UniqueAtomHashes, aaStandardizeNames, getAtomTypeCounts, getResTypeCounts, res2xyz, resAtomType2AtomClass, write.basic.pdb, write.conservedWaters.pdb

Examples

# NOT RUN {
  resids <- c("ALA", "HOH", "WAT", "ALA", "HOH", "DOD", "ALA", "HOH")
  HasXWaters(resids, min.num.h2o = 4)
  # $has.h2o.tf
  # [1] TRUE
  #
  # $num.water
  # [1] 5

# }