UniqueAtomHashes: Create Unique Atom Hashes

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

Description

Constructs unique atom hashes from the provided

Usage

UniqueAtomHashes(atoms.oi, cols.oi, separator = "_")

Arguments

atoms.oi	A data.frame containing the common PDB information in columns
cols.oi	A vector of column names to be used in the construction of the unique atom hashes
separator	A single character string to separate the atom specific identifiers. Acceptable separators include: _ (default), -, +, ., :, |, " " (space), and "" (no separator).

Details

Using atom specific identifiers from a PDB-like formatted data.frame, unique atom hashes are constructed. The identifiers are separated by a user-defined separator, the default separator is an underscores ("_"), and the constructed hashes are returned as a vector.

Select a separator to allow easy splitting of the the unique atom hashes using the base::strsplit() function to access the individual components.

NOTE: This is a non-public function.

Value

a vector of strings containing the unique atom hashes

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, aaStandardizeNames, getAtomTypeCounts, getResTypeCounts, res2xyz, resAtomType2AtomClass, write.basic.pdb, write.conservedWaters.pdb

Examples

  ## Not run: 
  atoms.oi <- thrombin.1hai$atom[1:10, ]
  cols.oi <- c("elety", "resid", "chain", "resno")
  UniqueAtomHashes(atoms.oi, cols.oi, separator = "_")
  # [1] "N_THR_L_1"   "CA_THR_L_1"  "C_THR_L_1"   "O_THR_L_1"   "CB_THR_L_1"
  #     "OG1_THR_L_1" "CG2_THR_L_1" "N_PHE_L_1"   "CA_PHE_L_1"  "C_PHE_L_1"

  UniqueAtomHashes(atoms.oi, cols.oi, separator = "!")
  # The provided separator "!" is not acceptable. The default separator "_" is being used.
  #  [1] "N_THR_L_1"   "CA_THR_L_1"  "C_THR_L_1"   "O_THR_L_1"   "CB_THR_L_1"
  #      "OG1_THR_L_1" "CG2_THR_L_1" "N_PHE_L_1"   "CA_PHE_L_1"  "C_PHE_L_1"
  
## End(Not run)

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