extractPDB: 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().

Value

Returns a list with the following components:
pdblist of class pdb as originally extracted by read.pdb() in the bio3d package
seqsequence according to the SEQRES entries of the PDB file
lseqlength of the extracted sequence seq
lcanumber of $C_{\alpha}$ atoms
caseqsequence data for the $C_{\alpha}$ selection
coordsmatrix of coordinates for each $C_{\alpha}$ atom, the rows are the $C_{\alpha}$'s, the columns are x, y, z
bB factor for each $C_{\alpha}$
chainsinteger vector with the lengths of the different chains in the protein sequence

Details

The input PDB file is read. All $C_{\alpha}$ atoms are extracted. For each $C_{\alpha}$ 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 $C_{\alpha}$ atoms in the PDB. For each chain of the protein the length is computed.

References

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

Examples

Run this code

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

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