Constructing an Molecule object containing a superatom

Hi,





I want to construct a molecule using the class Molecule. The location of the atoms and the arbitrary atomsymbols are given as Point2D and String object respectively. If that molecule contains a superatom x represented by a string e.g. PO3 (it might also be given as a string in SMILES format), I have to specify the structure of this superatom. How can I reconstruct the structure of a superatom from a string representation?





Many thanks for help!


lt

The problem is solved.





Best regards,


lt

Hello,





I have the same problem. I want to generate a molecule that contains some superatoms. How can I specify the superatom group, the crossing bond and its label for the contracted state? Let say I have to construct one simple molecule like that one in the image. What methods can I use for this purpose?





Thanks a lots,


Jean

Here is an example to create a molecule with a superatom.

Code:

// import a molecule             String smiles = "[H]OOCCC";             Molecule m = MolImporter.importMol(smiles.getBytes());             m.clean(2,null);             // define an sgroup             SuperatomSgroup sgroup = new SuperatomSgroup(m,true);             sgroup.setSubscript("COOH");             // add atoms to sgroup             for(int i=0;i<m.getAtomCount()-2;i++) {                 MolAtom a = m.getAtom(i);                 m.setSgroupParent(a, sgroup, true);             }