vanddraabe (version 1.1.1)

aaStandardizeNames: Standardize Amino Acid Names

Description

Standardize the various three-letter amino acid residue names.

Usage

aaStandardizeNames(residue.names)

Arguments

residue.names

A vector of strings containing the three-letter residue names (strings)

Value

vector of standardized amino acid residue names

Details

The various three-letter amino acid residue names used to indicate protonation state or uncommon sidechain bonding (ligatation) are converted to the standard amino acid residue name.

See Also

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

Examples

# NOT RUN {
  residue.names <- c("HIS", "HID", "HIE", "HIP", "HSD", "HSE", "HSP",
                     "CYS", "CYM", "CYX", "ASP", "ASH", "GLU", "GLH",
                     "LYS", "LYN")
  aaStandardizeNames(residue.names)
  # [1] "HIS" "HIS" "HIS" "HIS" "HIS" "HIS" "HIS" "CYS" "CYS" "CYS"
  #     "ASP" "ASP" "GLU" "GLU" "LYS" "LYS"

# }