ptm (version 0.2.2)

res.dpx: Residue Depth Analysis

Description

Computes the depth from the surface for each protein's residue.

Usage

res.dpx(pdb, aa = 'all')

Arguments

pdb

is either a PDB id, or the path to a pdb file.

aa

one letter code for the amino acid of interest, or 'all' for all the protein residues.

Value

A dataframe with the computed depths.

Details

This function computes the depth, defined as the distance in angstroms between the residue and the closest atom on the protein surface.

References

Pintar et al. 2003. Bioinformatics 19:313-314 (PMID: 12538266)

See Also

atom.dpx(), acc.dssp(), str.part()

Examples

# NOT RUN {
res.dpx('1cll')
# }