Changing MolAtoms programmatically

User 6ef33138f9

22-12-2005 20:34:24

Hello,

I have some code that changes a MolAtom from one atom to another (i.e. it changes the atomic number). I've noticed that calling setAtNo alone does not seem to be enough; in particular, the MolAtom seems to retain some information about its valency.

First let's look at the starting molecule, before changing any atoms. The following code will display something like "1 CH3--Pb (v1) 2". That's what I expect: the (v1) indicates the "unusual" valency of Pb in this (contrived) example.

Code:

   String smiles = "[CH3:1][Pb:2]";

   Molecule mol = MolImporter.importMol(smiles.toString());

   JFrame frame = new JFrame();

   MViewPane pane = new MViewPane();

   pane.setM(0, mol);

   frame.getContentPane().add(pane);

   frame.pack();

   frame.setVisible(true);

Now let's add a few lines to change Pb to Cl. Note that the "(v1)" is still displayed next to the Cl, even though it has one bond as usual.

Code:

   String smiles = "[CH3:1][Pb:2]";

   Molecule mol = MolImporter.importMol(smiles.toString());

   MolAtom atom = mol.getAtom(1);

   atom.setAtno(17);

   JFrame frame = new JFrame();

   MViewPane pane = new MViewPane();

   pane.setM(0, mol);

   frame.getContentPane().add(pane);

   frame.pack();

   frame.setVisible(true);

Is there something else I need to call to "reset" the MolAtom? I tried valenceCheck() and various other things to no avail.

Also, a related question: What are the exact rules for when "(v1)", "(v2)", etc. are displayed, versus some number of dots? For example, replacing [Pb:1] with [Tl:1] in the first example above will show the Tl atom with two dots (as placeholders for the missing hydrogens, I guess).

Thanks,

Chris

ChemAxon fb166edcbd

24-12-2005 14:09:02

cbingham wrote:

Is there something else I need to call to "reset" the MolAtom? I tried valenceCheck() and various other things to no avail.

You should call MolAtom.setValenceProp(-1) to unset the valence property:

Code:

String smiles = "[CH3:1][Pb:2]";

Molecule mol = MolImporter.importMol(smiles.toString());

MolAtom atom = mol.getAtom(1);

atom.setAtno(17);

// reset valence

atom.setValenceProp(-1);

JFrame frame = new JFrame();

MViewPane pane = new MViewPane();

pane.setM(0, mol);

frame.getContentPane().add(pane);

frame.pack();

frame.setVisible(true);

cbingham wrote:

Also, a related question: What are the exact rules for when "(v1)", "(v2)", etc. are displayed, versus some number of dots? For example, replacing [Pb:1] with [Tl:1] in the first example above will show the Tl atom with two dots (as placeholders for the missing hydrogens, I guess).

The dots denote a radical, which can be reset by MolAtom.setRadical(0):

Code:

String smiles = "[CH3:1][Tl:2]";

Molecule mol = MolImporter.importMol(smiles.toString());

   MolAtom atom = mol.getAtom(1);

   atom.setAtno(17);



// reset radical

atom.setRadical(0);

JFrame frame = new JFrame();

MViewPane pane = new MViewPane();

pane.setM(0, mol);

frame.getContentPane().add(pane);

frame.pack();

frame.setVisible(true);