shortcut groups in images

When a structure that contains shortcut groups is made into a JPEG image, the shortcut groups are always expanded. Can we keep them contracted? 'Twould be more desirable to do so. For example:

Code:

<?xml version="1.0"?> <MDocument>   <MChemicalStruct>     <molecule>       <atomArray           atomID="a1 a2 a3 a4 a5 a6 a7"           elementType="C C C C C R R"           sgroupRef="0 0 0 0 0 sg1 sg2"           x2="-5.899413333333334 -4.565866666666667 -3.232133333333334 -1.8985866666666666 -0.5648533333333334 0.7686933333333335 -7.233146666666668"           y2="3.045093333333334 2.275093333333334 3.045093333333334 2.275093333333334 3.045093333333334 2.275093333333334 2.275093333333334"           />       <bondArray>         <bond atomRefs2="a1 a2" order="1" />         <bond atomRefs2="a2 a3" order="1" />         <bond atomRefs2="a3 a4" order="1" />         <bond atomRefs2="a4 a5" order="1" />         <bond atomRefs2="a5 a6" order="1" />         <bond atomRefs2="a7 a1" order="1" />       </bondArray>       <molecule id="sg1" role="SuperatomSgroup" title="CO2Et">         <atomArray             atomID="a8 a9 a10 a11 a12"             elementType="C C O C O"             attachmentPoint="1 0 0 0 0"             x2="0.7686933333333335 -0.5650400000000001 0.7686933333333335 -0.5652266666666669 2.102426666666667"             y2="2.275093333333334 -0.034906666666666676 0.7350933333333335 -1.574906666666667 3.045093333333334"             />         <bondArray>           <bond atomRefs2="a11 a9" order="1" />           <bond atomRefs2="a9 a10" order="1" />           <bond atomRefs2="a10 a8" order="1" />           <bond atomRefs2="a8 a12" order="2" />         </bondArray>       </molecule>       <molecule id="sg2" role="SuperatomSgroup" title="EtO2C">         <atomArray             atomID="a13 a14 a15 a16 a17"             elementType="C C O C O"             residueType="UNK UNK UNK UNK UNK"             residueId="r1 r1 r1 r1 r1"             residueAtomName="0 0 0 0 0"             attachmentPoint="1 0 0 0 0"             x2="-7.233146666666668 -8.566693333333333 -8.566880000000001 -9.900426666666668 -7.233146666666668"             y2="2.275093333333334 4.585093333333334 3.045093333333334 5.355093333333334 0.7350933333333335"             />         <bondArray>           <bond atomRefs2="a16 a14" order="1" />           <bond atomRefs2="a14 a15" order="1" />           <bond atomRefs2="a15 a13" order="1" />           <bond atomRefs2="a13 a17" order="2" />         </bondArray>       </molecule>     </molecule>   </MChemicalStruct> </MDocument>

becomes the JPEG attached.

Image export in Marvin does not expand s-groups.


When you save a molecule with Marvin, each s-groups' status (contracted or expanded displaying) is stored in the molstring. (Image export also preserves groups' status.)


Since the older versions of Marvin always expanded s-groups in the molecule before saving, you may have got a few mol files with expanded structures.


Your attached example also contains expanded s-groups.





There is not any image export option in current Marvin to display all s-groups in contracted format.


Until we solve this problem, I can suggest only one workaround for this problem.


Open in sketcher those mol files which contain expanded s-groups to contract them by selecting the "Edit/Groups/Contract" menu item. Then saves the edited molecules.

You can use Molecule.contractSgroups() to contract s-groups:


http://www.chemaxon.com/marvin/doc/api/chemaxon/struc/Molecule.html#contractSgroups()





You should contract groups before exporting the structure:

Code:

mol.contractSgroups();     byte[] data = mol.toBinFormat("jpeg");

Tamas wrote:

Image export in Marvin does not expand s-groups. When you save a molecule with Marvin, each s-groups' status (contracted or expanded displaying) is stored in the molstring. (Image export also preserves groups' status.) Since the older versions of Marvin always expanded s-groups in the molecule before saving, you may have got a few mol files with expanded structures. Your attached example also contains expanded s-groups. There is not any image export option in current Marvin to display all s-groups in contracted format. Until we solve this problem, I can suggest only one workaround for this problem. Open in sketcher those mol files which contain expanded s-groups to contract them by selecting the "Edit/Groups/Contract" menu item. Then saves the edited molecules.

Tamas,





I compared the code for the structure below with S-groups contracted and expanded, and the S-groups are definitely contracted in the example. However, when I create the image from Marvin under the File menu, the shortcut groups remain contracted. EPOCH must be using some image-creating method that ignores the S-groups, or maybe the S-groups are expanded before creation of the image. I will have our programmer look into it.





-- Bob