vanddraabe (version 1.1.1)

RetainChainsOfInterest: Retain Chains Of Interest

Description

Retain chains of interest based on user input parameters

Usage

RetainChainsOfInterest(atoms.oi, chains.explore, chains.oi)

Arguments

atoms.oi

data.frame containing the PDB of the protein

chains.explore

String of chains to explore

chains.oi

String from the DetermineChainsOfInterest() function indicating if "first", "all", or a "user" defined set of chains should be used. 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.

Value

data.frame of the protein atoms retained based on the indicated chains of interest

Details

Using the user provided chains of interest, indicate the PDB chains to retain.

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.

See Also

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

Examples

# NOT RUN {
  
# }
# NOT RUN {
  RetainChainsOfInterest(PDB.4dfr$atom, "B", "user")
  RetainChainsOfInterest(PDB.1hai$atom, c("H", "L"), "user")
  RetainChainsOfInterest(PDB.4dfr$atom, "A", "first")
  
# }
# NOT RUN {
# }