ConservationSet: Conservation Set

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

Description

Assign the percent conservation to a "set#" for plotting.

Usage

ConservationSet(pct.conserved)

Arguments

pct.conserved

A vector from containing the ConservedWaters() function containing the percent conservation (pct.conserved)

Details

Several of the plots color-code conserved water clusters based on percent conservation (see ClusterSummaryPlots() for color-coding) and is controlled by a conserve.set column. This function assigns less than 50% conservation to set0, 50 to 69% set1, 70 to 79% set2, 80 to 89% set3, 90 to 99% set4, and eqaul to 100% set5,

NOTE: This is a non-public function.

Value

vector indicating the conservation set

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other utilities: DetermineChainsOfInterest, ExtractFileTimeStamp, ExtractPDBids, FileTimeStamp, HasXWaters, 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: 
  pct.conserved <- c(100, 95, 90, 85, 80, 75, 70, 65, 60, 55, 50,
                      45, 40, 35, 30, 25, 20, 15, 10, 10)
  ConservationSet(pct.conserved)
  # [1] "set5" "set4" "set4" "set3" "set3" "set2" "set2" "set1" "set1" "set1"
  # "set1" "set0" "set0" "set0" "set0" "set0" "set0" "set0" "set0" "set0"
  
## End(Not run)

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