StandardizeCysteineNames: Standardize Cysteine Names

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

Description

Standardize the two three-letter cysteine residue names to CYS.

Usage

StandardizeCysteineNames(residue.names)

Arguments

residue.names

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

Details

The two three-letter cysteine residue names used to indicate the different cystine states (CYM: deprotonated cysteine and CYX: no proton, neutral charge, part of a disulfide bridge) are converted to the standard "CYS" (protonated) residue name. This function is part of the aaStandardizeNames().

NOTE: This is a non-public function.

Value

vector of three-letter residue names with standardized cysteine 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, StandardizeGlutamicAcidNames, StandardizeHistidineNames, StandardizeLysineNames, TimeSpan, UniqueAtomHashes, aaStandardizeNames, 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")
  StandardizeCysteineNames(residue.names)
  # [1] "HIS" "HID" "HIE" "HIP" "HSD" "HSE" "HSP" "CYS" "CYS" "CYS"
  #     "ASP" "ASH" "GLU" "GLH" "LYS" "LYN"
  
## End(Not run)

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