/**
* Gets the van der Waals radius of the given atom following the values defined by Chothia (1976)
* J.Mol.Biol.105,1-14 NOTE: the vdw values defined by the paper assume no Hydrogens and thus
* "inflates" slightly the heavy atoms to account for Hydrogens. Thus this method cannot be used
* in a structure that contains Hydrogens!
*
* <p>If atom is neither part of a nucleotide nor of a standard aminoacid, the default vdw radius
* for the element is returned. If atom is of unknown type (element) the vdw radius of {@link
* #Element().N} is returned
*
* @param atom
* @return
*/
public static double getRadius(Atom atom) {
if (atom.getElement() == null) {
System.err.println(
"Warning: unrecognised atom "
+ atom.getName()
+ " with serial "
+ atom.getPDBserial()
+ ", assigning the default vdw radius (Nitrogen vdw radius).");
return Element.N.getVDWRadius();
}
Group res = atom.getGroup();
if (res == null) {
System.err.println(
"Warning: unknown parent residue for atom "
+ atom.getName()
+ " with serial "
+ atom.getPDBserial()
+ ", assigning its default vdw radius");
return atom.getElement().getVDWRadius();
}
String type = res.getType();
if (type.equals(GroupType.AMINOACID)) return getRadiusForAmino(((AminoAcid) res), atom);
if (type.equals(GroupType.NUCLEOTIDE)) return getRadiusForNucl((NucleotideImpl) res, atom);
return atom.getElement().getVDWRadius();
}
