RemoveOoR.o: Remove Occupancy Out of Range Atoms

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

Description

Removes atoms with occupancy values out of accepted range.

Usage

RemoveOoR.o(atoms.chains.oi)

Arguments

atoms.chains.oi

The data.frame containing the PDB file information; aka the PDB structure

Details

Accepted occupancy values range from 0 to 1 with values for modeled atoms being 0.0 or 0.01 and highly conserved or represented atoms throughout the lattice having values greater than 0.9 and commonly possessing values of 1.0. This function identifies occupancy values less than 0 and greater than 1 and removes them from the structure.

Value

data.frame of the PDB structure without the offending atoms

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other "Clean Protein Structure": CleanProteinStructures, RemoveHydrogenAtoms, RemoveModeledAtoms, RemoveOoR.b, RetainWatersWithinX

Examples

  
  nrow(PDB.4dfr$atom)
  PDB.4dfr.OoR.o <- RemoveOoR.o(PDB.4dfr$atom)
  nrow(PDB.4dfr.OoR.o)
  

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