Locate framents by id in a fragmented molecule

Hi,

Not sure if i picked the right forum to post this question. If not please forward to the right place.

I strategically cut the molecule into multiple fragments and track the bond and atoms where i made the cut, i.e. indexing the cuts/fragments by atom. Now after the cuts i am trying to locate the particular fragment by the atom involved the cuts. i went through a couple of API functions and i could not find one that suit my needs. The most close one is molecule.convertToFrags(), but after that the original atom I used to make the cut cannot longer be used in the child  molecules (fragments) for searching purpose. I hope i described my question clearly, can you give me some advice as to how to go about this. I am using java API to do this.

Thanks

Dong 

OK, after reading the API doc look like following would do what i want:

SelectionMolecule[] mols=molecule.findFrags()

 for(SelectionMolecule mol:mols){

mol.indexOf(atom);

}

 

atom is my bookmark atom

Dong

Hi Dong,

yes, you are right, the fragment for which mol.indexOf(atom) >= 0 will contain the thought atom. Or you can use contains(atom) alternatively.

Regards,

Zsuzsa