private Atom getAtom(String atomId, Group group) { Atom a = group.getAtom(atomId); // Check for deuteration if(a==null && atomId.startsWith("H")) { a = group.getAtom(atomId.replaceFirst("H", "D")); // Check it is actually deuterated if(a!=null){ if(!a.getElement().equals(Element.D)){ a=null; } } } return a; }
if ( e.equals(Element.R)) { eString = "X";
/** * 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(); }
if ( e.equals(Element.R)) { eString = "X";