getRCSBdata: Clean RCSB Dataset

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

Description

Clean the protein dataset based on quality values.

Usage

getRCSBdata(prefix = "./alignTesting", resolution = 3, rFree = 0.26,
  rObserved = 0.2, filename = "ProteinSystem")

Arguments

prefix	Directory of aligned structures; string.
resolution	Structures with a resolution value greater than this value are removed from analysis; default: 3.0
rFree	Structures with a rFree values greater than this value are removed from analysis; default: 0.26
rObserved	Structures with a rObserved values greater than this value are removed from analysis; default: 0.20
filename	The filename prefix for the returned results. Default is "ProteinSystem"

Details

The provided protein models determined by X-ray crystallography and downloaded from the RCSB include structure quality measures. The resolution, rObservation, and rFree are the three commonly used and referenced evaluation measures.

The B-value normalization exclusion value is user defined within the main ConservedWaters() function but has a default value of 1.0.

Value

This function returns:

• PDB.info: RCSB provided information for all protein structures

• PDB.info.passed: RCSB provided information for all protein structures passing the user defined parameters

• PDB.info.rejected: RCSB provided information for all protein structures failing the user defined parameters

• call: parameters provided by the user

• Excel workbook: containing the PDB.info, PDB.info.passed, and PDB.info.rejected data as individual tabs

Author(s)

Emilio Xavier Esposito [e-mail]

Examples

  ## Not run: 
  proteins.info <- getRCSBdata(prefix="./thrombin_fitlsq_1.0ang/",
                               resolution=3.0, rFree=NULL, rObserved= 0.20,
                               filename="ProteinSystem")
  
## End(Not run)

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