aaStandardizeNames: Standardize Amino Acid Names

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

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)

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.

Value

vector of standardized amino acid residue names

Author(s)

Emilio Xavier Esposito [e-mail]

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

  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"

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