Straight bond and squiggly bond

Hi,





Marvin or MSketch applets allow users to specify a bond for a chiral center in Up or Down orientation. They also allow users to make it as Up/Down, the squiggly bond (see my attachment). However straight bond also means that the band can be Up or Down. So I try to learn the difference between the squiggly bond and the straight bond. Or any special purpose for the squiggly bond.





Thanks.





Ben Li

Hi,


The difference between the squiggly bond and the straight bond is the following:


An atom with squiggly bond (query) matches a target atom for which the chirality is specified (for example with UP or DOWN bonds), however it doesn't match an atom for which no chirality info is specified.





An atom with straight bonds (query) matches a target atom irrespectively of the chirality info.





See http://www.jchem.com/doc/user/Query.html#stereobond for details. (Though it seems we should give more details about this issue)





All the best


Andras

volfi wrote:

The difference between the squiggly bond and the straight bond is the following: An atom with squiggly bond (query) matches a target atom for which the chirality is specified (for example with UP or DOWN bonds), however it doesn't match an atom for which no chirality info is specified. An atom with straight bonds (query) matches a target atom irrespectively of the chirality info.

We needed to change JChem's match pattern so that squiggly bonds would match only squiggly bonds, whereas straight bonds would match any bonds. We implemented the following algorithm:

Code:

Call the author's structure, A. Call the number of squiggly bonds in A, s. Call the student's response, R. n = 0 If R matches A then match = yes else match = no While match = yes and n < s    n = n + 1    Convert A to A1 by changing squiggly bond number n to an up bond.    Convert A to A2 by changing squiggly bond number n to a down bond.    If R matches A1 or R matches A2 then match = no Wend

Alternatively:

Code:

Call the author's structure, A. Call the number of bonds of all types in A, b. Call the student's response, R. n = 0 If R matches A then match = yes else match = no While match = yes and n < b    n = n + 1    If bond n is squiggly then       Convert A to A1 by changing bond n to an up bond.       Convert A to A2 by changing bond n to a down bond.       If R matches A1 or R matches A2 then match = no    EndIf Wend

-- Bob