[Cdk-user] [ cdk-Support Requests-738493 ] getting structure from RTools.Getoverlaps

[SourceForge.net <no...@so...>]

Support Requests item #738493, was opened at 2003-05-15 22:58
Message generated for change (Settings changed) made by egonw
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=220024&aid=738493&group_id=20024

Category: None
Group: None
>Status: Closed
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: getting structure from RTools.Getoverlaps

Initial Comment:
I am trying to use the CDK RTools feature :

getOverlaps
public static java.util.List getOverlaps
(AtomContainer g1,
                                         AtomContainer g2)
Returns all the maximal common substructure 
between 2 atom containers 
Parameters: 
g1 - first molecule 
g2 - second molecule 
Returns: 
the list of all the maximal common substructure 
found projected of g1 (list of AtomContainer )


My problem is that I can get out the list of 
AtomContainers, but I cannot cast them to 
Molecules in order to get the SMILES:

    int listsize = myList.size();
    if (myList.get(0) instanceof AtomContainer)
    {
      AtomContainer ac = (AtomContainer)myList.get
(0);
      if (ac instanceof Molecule)    //fails
      {
        SmilesGenerator sg = new SmilesGenerator
(); //
        Molecule m2 = (Molecule)ac;
        String myString = sg.createSMILES(m2);
      }
    }

Any ideas?

Many thanks.

Steve Jones.
ste...@gs...

----------------------------------------------------------------------

Comment By: Steve Jones (wag602389)
Date: 2003-08-05 13:40

Message:
Logged In: YES 
user_id=779860

Egon,

That worked fine.

Thanks.

Steve.

----------------------------------------------------------------------

Comment By: Egon Willighagen (egonw)
Date: 2003-05-21 09:11

Message:
Logged In: YES 
user_id=25678

AtomContainer's are easily converted to Molecules by doing:
Molecule mol = new Molecule((AtomContainer)ac); Note that
this constructor does not check wether the molecule is fully
connected.

The code could be:

int listsize = myList.size();
if (myList.get(0) instanceof AtomContainer) {
  AtomContainer ac = (AtomContainer)myList.get(0);
  Molecule mol = new Molecule(ac);
  SmilesGenerator sg = new SmilesGenerator();
  String myString = sg.createSMILES(mol);
} 

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=220024&aid=738493&group_id=20024