DetermineChainsOfInterest: Determine Chains Of Interest

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

Description

Determine the chains identification

Usage

DetermineChainsOfInterest(chains.to.explore)

Arguments

chains.to.explore

NOTE: "first" is alphabetically first. Thus if the order within the original PDB file is L and then H, this function will return H because it is alphebetically first.

Details

Standardizes user provided chain(s) of interest. This function simply standardizes the user provided chains of interest. Acceptable values are: - first: alphabetically the first chain - all: all chains within a structure file - user defined: a single letter or a set of letters; e.g.; "A" or c("H", "L")

NOTE: This is a non-public function and is NOT available for general use. Please contact the author if you believe this function should be available for general use.

Value

string indicating which chain designation (e.g., "first" chain, "all" chains, or "user" defined) to include in the conserved water analysis

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other utilities: ConservationSet, 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: 
  DetermineChainsOfInterest("first")
  # [1] "first"
  DetermineChainsOfInterest("ALL")
  # [1] "all"
  DetermineChainsOfInterest("D")
  # [1] "user"
  DetermineChainsOfInterest(c("H", "L"))
  # [1] "user"
  DetermineChainsOfInterest("vanddraabe")
  # The provided chain ID VANDDRAABE is not valid and the first chain will
  # be used; likely chain A.
  # [1] "first"
  
## End(Not run)

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