RetainChainsOfInterest: Retain Chains Of Interest

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

Description

Retain chains of interest based on user input parameters

Usage

RetainChainsOfInterest(atoms.oi, chains.explore, chains.oi)

Arguments

atoms.oi	data.frame containing the PDB of the protein
chains.explore	String of chains to explore
chains.oi	String from the DetermineChainsOfInterest() function indicating if "first", "all", or a "user" defined set of chains should be used. NOTE: "first" is alphabetically first. Thus if the order within the original PDB file is L and then H, this function will return H because it is alphebetically first.

Details

Using the user provided chains of interest, indicate the PDB chains to retain.

NOTE: This is a non-public function and is NOT available for general use. Please contact the author if you believe this function should be available for general use.

Value

data.frame of the protein atoms retained based on the indicated chains of interest

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

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

Examples

  ## Not run: 
  RetainChainsOfInterest(PDB.4dfr$atom, "B", "user")
  RetainChainsOfInterest(PDB.1hai$atom, c("H", "L"), "user")
  RetainChainsOfInterest(PDB.4dfr$atom, "A", "first")
  
## End(Not run)

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