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Obchiral Tool


The obchiral program is a tool to print the chirality information for all molecules in a file.


Output format includes:

Molecule number

Id and atomic symbol of the chiral atom

Ordered list of id of the four substituents connected to the chiral atom [Atom4refs]

Chiral volume [Volume]

Ordered list of the arbitrary initial priority [Atom refs]

0 or 1 [Clockwise?]



The “$$$” is the separator between multiple molecular entries in a file.


The "clockwise" value (0/1) corresponds to the stereochemical parity available in the atom block of the SDFile. To specify the parity, the atoms surrounding the stereo center are numbered 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). The center is observed from a position such that the highest-numbered atom (4) is behind the plane formed by atoms 1, 2, and 3. If these three atoms are arranged clockwise in ascending numerical order the parity value is 1. Otherwise it is 0.


Obchiral command:

obchiral name.mol

If you want to save the obchiral results into a file results.txt you can enter the command:

obchiral name.mol > result.txt




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Webmaster: Vasco Bonifácio

last update: 01.06.2010