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Last data update: 2014.03.03

R: Extract Data from a PDB-File

extractPDB

R Documentation

Extract Data from a PDB-File

Description

This function reads a PDB file and extracts data from it.

Usage

extractPDB(file.name, verbose = TRUE)

Arguments

`file.name`	name of the PDB file
`verbose`	logical, if TRUE prints the output from both functions `read.pdb()` and `atom.select()`.

Details

The input PDB file is read. All C_{α} atoms are extracted. For each C_{α} atom the x-, y- and z-coordinates as well as the amino acid type and the B factor are extracted. The sequence length is compared to the number of C_{α} atoms in the PDB. For each chain of the protein the length is computed.

Value

Returns a list with the following components:

`pdb`	list of class “pdb” as originally extracted by `read.pdb()` in the bio3d package
`seq`	sequence according to the “SEQRES” entries of the PDB file
`lseq`	length of the extracted sequence `seq`
`lca`	number of C_{α} atoms
`caseq`	sequence data for the C_{α} selection
`coords`	matrix of coordinates for each C_{α} atom, the rows are the C_{α}'s, the columns are x, y, z
`b`	B factor for each C_{α}
`chains`	integer vector with the lengths of the different chains in the protein sequence

Note

Alternate and insert records in the PDB file are ignored. When removing alternate records a message is printed. Please check the PDB file.

If the number of C_{α} atoms lca and the length of the extracted sequence seq differ, a message is printed. It is not advisable to use any other parts of the BioPhysConnectoR-package until you have found an appropriate solution to deal with this problem in the pdb-file.

This function includes source code of the bio3d package.

Author(s)

Franziska Hoffgaard

References

Grant, Rodrigues, ElSawy, McCammon, Caves, (2006) Bioinformatics 22, 2695–2696.

Examples

pdb<-extractPDB(system.file("1KZK.pdb", package = "BioPhysConnectoR"))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(BioPhysConnectoR)
Loading required package: snow
Loading required package: matrixcalc
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BioPhysConnectoR/extractPDB.Rd_%03d_medium.png", width=480, height=480)
> ### Name: extractPDB
> ### Title: Extract Data from a PDB-File
> ### Aliases: extractPDB
> ### Keywords: IO
> 
> ### ** Examples
> 
> pdb<-extractPDB(system.file("1KZK.pdb", package = "BioPhysConnectoR"))
  HEADER    VIRAL PROTEIN, HYDROLASE                06-FEB-02   1KZK               
   PDB has ALT records, taking A only, rm.alt=TRUE
      segid  chain  resno  resid  eleno  elety
Stest ""     ""     ""     ""     ""     "CA" 
Natom "3019" "3019" "3019" "3019" "3019" "198"
 *  Selected a total of: 198 intersecting atoms  *
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>