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   JOIN

JOIN

JOIN a b c d e f maxdist

The JOIN command must be followed by six integers and one floating point number. The command takes two C-H bonds, and turns them into a C-C bond, if the carbon atoms are separated by less than maxdist Angstrom (default value 4.0). The command assumes that the two C-H bonds are in the same molecule, so they cannot be made closer by translation and rotation.

a, b and d, e are the atom numbers of the two C-H bonds, a and d are the carbons, b and e the hydrogens. The hydrogens will be deleted by the procedure.

c and f are the numbers of the atoms attached to carbons a and d respectively. The program will rotate around c-a and f-d to optimise the new C-C bond. If one or both of these bonds is to be fixed, then 0 should be used in place of an atom number for c and f.

If b or e is zero, then the new bond will be made, but few checks will be completed, so chiral centres may be inverted, and odd structures may result.


Acca and Acca documentation: © 1996,1997 J M Goodman, Cambridge.
Acca documentation may not be copied without the written permission of the author.



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department of chemistry University of Cambridge