Marvin - Isentris Incompatibility /not expanded groups

User 05d9866f9b

05-02-2013 14:34:11

We've used the function ....getMol('mol') to get the MoleculeString. This molfile is transfered to an Symx Database  and is rendered within a Isentris control.


The problem is that this doesn't work as soon as we've use draw abbreviations like NO2- please see the example.


If the user draws the molecule in ISIS, it works fine (see attached molfile).
If he draws it in Marvin, it'll fail.


Is there a setting/parameter for .getmol that creates an "Isentris compatible" molstring?
Is there a setting like "only expanded groups" - couldn't find so far.


Thanks for your help


 

ChemAxon 2c555f5717

05-02-2013 17:29:10

Dear Edith!


   What exact getMol(String) function do you use? The getMol() of MSketchPane? Or the getMol(String) of Molecule?


   However it might help you: could you try tu use chemaxon.formats.toFormat(Molecule, String) function instead? getMol(String) in Molecule is deprecated and not updated anymore. MSketchPane uses this function, what we should change soon. Anyway toFormat(Molecule, String) should give you a corresponding result.


   I hope I could help you.


Regadrs:
Balázs

ChemAxon d26931946c

06-02-2013 15:02:44

Dear Edith,


We have never written out that property and so far it did not caused any problem. 


We've implemented our Mol export according to the CTFile Formats document, which can be found on www.accelrys.com. Our oldest version of this file comes from 2001, and it has the following comment on this "G" block:


Group Abbreviation [CPSS]
G aaappp
x...
aaa: Atom number
ppp: Atom number
x: Abbreviation label.


Abbreviation is required for compatibility with CPSS. CPSS allowed abbreviations with only one
attachment. The attachment is denoted by two atom numbers, aaa and ppp. All of the atoms on the aaa side of the bond formed by aaa-ppp are abbreviated. The coordinates of the abbreviation are the coordinates of aaa. The text of the abbreviation is on the following line (x...). In current versions of ISIS, abbreviations can have any number of attachments and are written out using the Sgroup appendixes.
However, any ISIS abbreviations that do have one attachment are also written out in the CPSS-style, again for compatibility with CPSS, but this behavior might not be supported in future versions.

This block was not required for any of the MDL products since 2001, it was there only for backward compatibility reasons. We are not exporting it because we don't support MDL programs before ISIS 2.5, released in 2002.


There is only an import option to expand S-groups. This workaround may work:


- call getMol("mol") to get the molecule string


- call setMol(s, "mol:Xsg") to expand S-groups and set the expanded molecule to the applet


- call getMol("mol") again to get the mol file string without S-groups.


Regards,


Peter