if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius(); if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius(); return Element.C.getVDWRadius(); return atom.getElement().getVDWRadius();
/** * Gets the radius for given nucleotide atom * @param atom * @return */ private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) { if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius(); if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius(); if (atom.getElement()==Element.C) return NUC_CARBON_VDW; if (atom.getElement()==Element.N) return NUC_NITROGEN_VDW; if (atom.getElement()==Element.P) return PHOSPHOROUS_VDW; if (atom.getElement()==Element.O) return OXIGEN_VDW; logger.info("Unexpected atom "+atom.getName()+" for nucleotide "+nuc.getPDBName()+", assigning its standard vdw radius"); return atom.getElement().getVDWRadius(); }
logger.warn("Unrecognised atom "+atom.getName()+" with serial "+atom.getPDBserial()+ ", assigning the default vdw radius (Nitrogen vdw radius)."); return Element.N.getVDWRadius(); logger.warn("Unknown parent residue for atom "+atom.getName()+" with serial "+ atom.getPDBserial()+", assigning its default vdw radius"); return atom.getElement().getVDWRadius(); return atom.getElement().getVDWRadius();