api for setting chiral information in the Marvin Atom

JChem version 3.1





How can an external parser which reads the cis/trans and chirality information from the input file set the relevant options in the MarvinMolecule (i.e chirality information to be set for MolAtom and cis/trans for MolBond) , so that the marvin viewer shows the stereo options when it is displaying the molecule.





I need the method which sets the stereo information for MolAtom and cis/trans information for MolBond.





Thanks.


Regards,


Pranathi

Hi!





The chirality information can be set in 0D or 2D by the setChirality(...)


http://www.chemaxon.com/marvin/doc/api/chemaxon/struc/MoleculeGraph.html#setChirality(int,%20int)


function.


However, no such function exists for setting cis/trans information in 2D.


But you can solve the whole problem in 0D and than clean the molecule to 2 or 3D.


So the solution is the following:

Suppose you have a 0D molecule (or you can create one with Molecule setDim(0)).


You can set a bond stereo (cis/trans) information using the MolBond setStereo2Flags(..)


http://www.chemaxon.com/marvin/doc/api/chemaxon/struc/MolBond.html#setStereo2Flags(chemaxon.struc.CNode,%20chemaxon.struc.CNode,%20int)


function.


And also you can set the chirality of the chiral center with the previously mentioned setChirality(...) function.

I hope this helps


Andras