Confused about parity of atom and chirality
This is really a cheminformatics problem. It's a reflection of the chirality or atomic stereochemistry about the atom you mention.
There are multiple ways of specifying chiral information in 2D and 3D.
As mentioned by Dave SMILES uses a clockwise and counter-clockwise from left to right in the string.
In 2D, we usually use wedge and hash notation. The problem is that some users use wedges and hashes for graphical appearance and not for stereochemical information (e.g., pseudo-3D look). So file formats also add atom parity to indicate the actual stereochemistry of atoms.
The &quot;parity&quot; idea has to do with the relationship between the atoms as they are ordered in the file, vs. the stereochemistry around the central atom. As indicated in the other answer, these are enantiomers, even though they use the same &quot;@@&quot; SMILES stereochemical indicator:

$\ce{O[C$@@$](F)(Cl)Br}$
$\ce{O[C$@@$](F)(Br)Cl}$

Note that the atom ordering is different, so the &quot;parity&quot; will be different. For your example, $\ce{O[C$@@$](F)(Cl)Br}$ I get &quot;1&quot; for the MDL parity.
From the MDL specification (Appendix A: Stereo Notes):

Number the atoms surrounding the stereo center with 1, 2, 3, and 4 in order of increasing atom number (position in the atom block) (a hydrogen atom should be considered the highest numbered atom, in this case atom 4). View the center from a position such that the bond connecting the highest-numbered atom (4) projects behind the plane formed by atoms 1, 2, and 3.
Sighting towards atom number 4 through the plane (123), you see that the three remaining atoms can be arranged in either a clockwise or counterclockwise direction in ascending numerical order.


For more details, you might want to look at the Open Babel documentation, OpenSMILES or the MDL specification.