ChemAxon Forum Archive » Drawing & visualization: Marvin/Sketch /View /Space

unexpected PARITY_EITHER returned

User f05f6b8c05

09-06-2011 13:28:23

[ .. sorry .. I meant to post this to the jchem area .. I have relisted it there .. not sure if I should delete this posting? ..]


 


Hi,


The following code returns a PARITY_EITHER value (value of 3) for the chiral center in the below mol structure.  Why does it not return a non ambiguous value?


We are using jchem 5.4.1.1, java 1.5.0_17, SunOS 5.10.


Thanks for an guidance.


Best,


Andrew


 


MolImporter mi = new MolImporter(new File(mol_file), "mol");


Molecule mol = null;


while ((mol = mi.read()) !=null) {


 


for (int i=0; i<mol.getAtomCount(); ++i) {


                int chirality = mol.getChirality(i);


                System.out.println("\t"+i+"\t"+chirality);


}


}


Mol-file data:


SOMENAME

  Mrv0541 06081108462D


 10  9  0  0  1  0            999 V2000

    4.9246   -0.0412    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

    4.1136   -0.1753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    3.7253    0.5463    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

    3.7493   -0.9176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    2.5637   -1.7114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    2.9245   -0.9726    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

    3.0276   -2.3954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

    4.2064   -1.5980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    5.0347   -1.5397    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

    4.2442   -0.8832    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0

  2  1  2  0  0  0  0

  4  2  1  0  0  0  0

  5  6  1  0  0  0  0

  4  6  1  1  0  0  0

  7  5  2  0  0  0  0

  8  4  1  0  0  0  0

  9  8  1  0  0  0  0

  4 10  1  6  0  0  0

  3  2  1  0  0  0  0

M  END

ChemAxon e274e1bada

09-06-2011 13:42:54

I have moved this topic to the appropriate forum. The Marvin experts will respond soon.


Edvard

User f05f6b8c05

09-06-2011 14:24:49

Thanks .. sorry for it landing in the wrong forum

ChemAxon 25dcd765a3

14-06-2011 13:22:05

We follow the


Graphical representation of stereochemical configuration


Pure Appl. Chem., Vol. 78, No. 10, pp. 1897–1970, 2006.
doi:10.1351/pac200678101897
© 2006 IUPAC


 


According to ST 1.1.10 page 1916:


Two plain bonds, one solid wedged bond, and one hashed wedged bond, with the two plain bonds separated
by other than 180° and not depicted as adjacent.



These depictions are formally ambiguous and cannot be interpreted with certainty. They should
never be used. Historically, they have been used in several situations that can sometimes be interpreted
without certainty, but alternate acceptable representations are possible in all of those cases.

User f05f6b8c05

15-06-2011 13:32:11

Thanks so much for the clarification .. very helpful!


Best,


Andrew