Parity

In case of tetrahedral parity the ligands around the stereocenter are numbered with 1, 2, 3, and 4 in the order of increasing atom index (position in the atom block). Hydrogen atom (if any) is considered to be the highest indexed atom (atom 4 regardless of its position in the atom block). The center is viewed from a position such that the bond connecting the highest-numbered atom (atom 4) projects behind the plane formed by atoms 1, 2, and 3. Viewing through the plane (1 2 3) towards atom number 4, the three remaining atoms can be arranged in either a clockwise or counterclockwise direction in ascending numerical order. If the atoms arranged in clockwise direction then the parity value is ODD otherwise, if they are arranged in counterclockwise direction then EVEN parity value is assigned. This is the parity definition also used by MDL.

An atom belongs to the tetrahedral parity class if:

• Implicit and explicit hydrogen count is less than two.
• The number of ligands plus the implicit hydrogen count equals four. Exceptions:
  • Sulfur atom can have a lone electron pair to allow chiral sulfoxides.
  • Nitrogen has parity if it's a bridgehead atom or is in a 3 membered ring and the if the graph invariant is different for all three ligands.
• The stereocenter has only single bond connections, double bond can exist only to terminal oxygen atom to support chiral sulfoxides, phosphates.
• Graph invariants of the ligands are different. Exception: ring atom have parity even if two graph invariants of the ring ligands equal and an other stereocenter is located in the ring.

The possible values for the tetrahedral parity class:

Note, it is not possible to change parity value from 0 to PARITY_EITHER and vice versa without changing atoms in the molecule.

Square-planar, trigonal-bipyramidal, and octahedral parity classes are not yet supported.

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.

Code example: 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"); 

Code example: 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.

Code example using getFlags method:

MolAtom a = molecule.getAtom(1); 
int f = a.getFlags(); 
// mask flags 
int p = f & StereoConstants.PARITY_MASK; 

Code example using getParity method:

int p = molecule.getParity(1); 

Parity information in 2 or 3 Dimensions

If the molecule is not 0 dimensional, then the parity information of the stereocenter is calculated from the spatial arrangement of the ligands. In case of 3 dimensions only the atomic coordinates are used. In case of 2 dimensions beside the atomic coordinates the out of plane information stored in the bond flags – known as wedges – are used.

Setting parity information in 2 Dimensions (API)

The parity information in 2 dimensions can be modified by setting wedge to the chiral center. PARITY_EITHER can be achieved for a chiral center with wiggly bond or equally, with removing all wedge from the center. There are two methods to define parity in 2 dimensions: a single atom can be modified using the setParity(int i, int p) method, while parities of all atoms in the molecule can be modified by the setParity(int[] p) method of MoleculeGraph class.

Setting parity information in 3 Dimensions (API)

The only possibility to change parity information of a 3 dimensional molecule is to change the atomic coordinates. However, it is not recommended to translate one atom as it may lead to unexpected bond length or collision of atoms. To overcome this problem one can convert the 3 dimensional molecule to 0 dimensional, change the parity information and finally clean the result to 3 dimensions. Please note that all parity values should be set to 0, CIS or TRANS, it is not possible to set PARITY_EITHER in case of 3D molecules.

Code example:

molecule.setDim(0); 
molecule.setParity(1, StereoConstants.PARITY_EVEN); 
Cleaner.clean(molecule, 3, null); 

Getting parity information in 2 or 3 Dimensions (API)

In case of 2 dimensions the parity information is calculated from the coordinates and from the wedges connected to the stereocenter. In case of 3 dimensions only the coordinates are used, any wedge information is neglected. To calculate the parity of an atom in 2 or 3 dimensions the getParity(int i) method of the MoleculeGraph class can be used.

Code example using getParity method:

int p = molecule.getParity(1);