a.setName(atom.getLabel_atom_id());
public static void main(String[] args){ Chain c = new ChainImpl(); c.setId("X"); Group g = new AminoAcidImpl(); g.setResidueNumber(ResidueNumber.fromString("1A")); try { g.setPDBName("ALA"); } catch (Exception e){} Atom a = new AtomImpl(); a.setName("CA"); g.addAtom(a); c.addGroup(g); System.out.println(getPdbInfo(a)); }
/** * Use unit vectors NC and NCalpha Add them. Calc unit vector and * substract it from N. * C coordinates are from amino acid i-1 * N, CA atoms from amino acid i * * @link http://openbioinformatics.blogspot.com/ * 2009/08/how-to-calculate-h-atoms-for-nitrogens.html */ @SuppressWarnings("unused") private static Atom calc_H(Atom C, Atom N, Atom CA) throws StructureException { Atom nc = Calc.subtract(N,C); Atom nca = Calc.subtract(N,CA); Atom u_nc = Calc.unitVector(nc) ; Atom u_nca = Calc.unitVector(nca); Atom added = Calc.add(u_nc,u_nca); Atom U = Calc.unitVector(added); // according to Creighton distance N-H is 1.03 +/- 0.02A Atom H = Calc.add(N,U); H.setName("H"); // this atom does not have a pdbserial number ... return H; }
private static Atom calcSimple_H(Atom c, Atom o, Atom n) { Atom h = Calc.subtract(c,o); double dist = Calc.getDistance(o,c); //System.out.println(dist); double x = n.getX() + h.getX() / dist; double y = n.getY() + h.getY() / dist; double z = n.getZ() + h.getZ() / dist; h.setX(x); h.setY(y); h.setZ(z); h.setName("H"); return h; }
Group altGroup = null; atom.setPDBserial(serialNumber); atom.setName(atomName.trim()); atom.setElement(Element.valueOfIgnoreCase(element)); if(alternativeLocationId==MmtfStructure.UNAVAILABLE_CHAR_VALUE){
virtualCB.setName("CB");