If the atomic coordinates are zero then the molecule's spatial dimension is zero. The parity information is stored in the atom flag of the stereocenter.
The parity information of a single atom can be modified using the setParity(int i, int p)method of MoleculeGraphclass. For setting parities of all atoms in the molecule, the setParity (int[] p) method of MoleculeGraphclass can be used. It is important to mention that, this method is faster than setting parities with setParity(int i, int p)one by one.
Examples: Setting parity of one atom
// setting the first atom parity to ODD
boolean success = molecule.setParity(1, StereoConstants.PARITY_ODD);
System.out.println("Setting parity to atom 1 was "+ ((!success) ? "not" : "") + " successful"); Setting parity for all atoms
int ODD = StereoConstants.PARITY_ODD;
int EVEN = StereoConstants.PARITY_EVEN;
// we have a molecule with 7 atoms
int[] parities = new int[]{0, ODD, 0, 0, EVEN, 0, 0};
// setting parities
boolean success = molecule.setParity(parities);
System.out.println("Setting parities for the whole molecule was "+
((!success) ? "not" : "")+ " successful"); The parity information of a 0 dimensional molecule is stored in the atom flags . It can be retrieved with the getFlags() function of the MolAtom class or with the getParity(int i) method of the MoleculeGraph class.
Examples: Using getFlags() method
MolAtom a = molecule.getAtom(1);
int f = a.getFlags();
// mask flags
int p = f & StereoConstants.PARITY_MASK;Using getParity() method
int p = molecule.getParity(1);