ptm (version 0.2.2)

atom.dpx: Atom Depth Analysis

Description

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

Usage

atom.dpx(pdb)

Arguments

pdb

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

Value

A dataframe with the computed depths.

Details

This function computes the depth, defined as the distance in angstroms between the target atom and the closest atom on the protein surface. When the protein is composed of several subunits, the calculations are made for both, the atom being part of the complex, and the atom being only part of the polypeptide chain to which it belongs.

References

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

See Also

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

Examples

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