Parity information in 0 Dimension

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.

Setting parity information in 0 Dimension (API)

The parity information of a single atom can be modified using the setParity(int i, int p) method of MoleculeGraph class. For setting parities of all atoms in the molecule, the setParity (int[] p) method of MoleculeGraph class 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.


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");

Getting parity information in 0 Dimension (API)

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.


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);