ProtHetWatIndices: Protein, HET, and Water Atom Indices

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

Description

Indices for the protein, HET-atom, and water atoms

Usage

ProtHetWatIndices(data)

Arguments

data	The atom data.frame of the PDB read into the R session using the function bio3d::read.pdb().

Details

Returns individual numerical vectors for the protein, HET-atom, and water atoms from the atom base::data.frame() of a PDB.

NOTE: This is a non-public function.

Value

Individual vectors for the indices of the protein, HET-atom, and water atoms for a PDB file.

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

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

Examples

  ## Not run: 
  ProtHetWatIndices(thrombin.1hai$atom[c(1:10, 2341:2350, 2385:2394), ])
  # $prot.idc
  # [1]  1  2  3  4  5  6  7  8  9 10
  #
  # $het.idc
  # [1] 11 12 13 14 15 16 17 18 19 20
  #
  # $h2o.idc
  # [1] 21 22 23 24 25 26 27 28 29 30
  
## End(Not run)

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