Can't run the code without more context but I think I know what's
happening.
Firstly atom indices start at 0, so to remove atom numbers 3, 4, 5 (as in
picture) you remove 2, 3, 4. Secondly, when you delete atoms the indices
are renumbered/repacked. So the new indices will always be 0, 1, 2
(previously index 5 - atom number 6).
[image: Inline images 1]
Now this wouldn't actually cause the error because you're adding pentane...
but 5 atoms from pentane + the 3 from the fragmented hexane means the
maximum index as 7 but you've requested atom 10...
NewHeptane.addBond(6,10, IBond.Order.Single)
There are a couple of ways to do this for example tagging atoms, map
indices, or use the atom object to create the bonds (most efficient).
NewHeptane.add(Propane)
> //adding bonds
> NewHeptane.addBond(1, // second atom in heptane
> 4, // was second atom in propane...
> 3+1
> IBond.Order.Single);
> NewHeptane.addBond(2, // third atom in heptane (was sixth before we
> deleted some)
> 6, // was forth atom in propane 3+3
IBond.Order.Single)
Using the addBond() API you can get the index in the new molecule as
follows... which makes it easier
NewHeptane.add(Propane)
> //adding bonds
> NewHeptane.addBond(1, // second atom in heptane
>
> NewHeptane.indexOf(Propane.getAtom(1)), // second atom in propane ->
> find index in the combined mol
> IBond.Order.Single);
> NewHeptane.addBond(2, // third atom in heptane (was sixth before we
> deleted some)
> NewHeptane.indexOf(Propane.getAtom(3)),
> // forth atom in propane -> find index in the combined mol
IBond.Order.Single)
>
Hope that helps,
John
On 25 October 2017 at 12:53, Vinothkumar Mohanakrishnan <kmvin...@gmail.com>
wrote:
> Dear All
>
> I am using CDK to create a tool (Java GUI) for editing molecules. To start
> with I am considering linear alkanes. I will describe my problem briefly.
>
> I have an IAtomcontainer with *Heptane(H) *molecule loaded into it (all
> atoms and bonds are connected)
>
> I* removed atoms 3,4,5* from the container and the bonds connecting them.
> So now I have two fragments of ethane(*atom1 - atom2 connected *similarly*
> atom6-atom7 connected*) in the atom container.
>
> I have another IAtomcontainer with *Propane(P)* (say with *atom numbers
> 8, 9, 10*) loaded into it (again all atoms and bonds are connected )
>
> I added the propane Iatomcontainer to the heptane Iatomcontaner. Then I
> added a bond between (atom2(H) -atom8(P)) and (atom6(H)-atom10(P)) and
> created a new molecule called NewHeptane.
>
> When I tried creating a 3d model of the NewHeptane using model3dbuilder I
> get an exception
>
> *org.openscience.cdk.exception.NoSuchAtomTypeException: Atom is unkown:
> Symbol:C does not MATCH AtomType. HoseCode:C-5;CC(C,C/C,/)*
>
> By the way, I checked with
> AtomContainerManipulator.perceiveatomsandconfigure()
> and all atoms in the NewHeptane Iatomcontainer has C.Sp3 hybridized.
>
>
> *Below is the code*
>
> //add propane to heptane
> NewHeptane.add(Propane)
>
> //adding bonds
> NewHeptane.addBond(2,8,IBond.Order.Single)
> NewHeptane.addBond(6,10, IBond.Order.Single)
>
> //Generate smiles
> SmilesGenerator sg = SmilesGenerator.absolute();
> String smi = sg.create(NewHeptane);
>
> //Parse smiles
> SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
> IAtomContainer m = sp.parseSmiles(smi);
>
> // Build 3d model
> ModelBuilder3D builder3d = ModelBuilder3D.getInstance(m.getBuilder());
> IAtomContainer newHeptane = builder3d.generate3DCoordinates(m, false);
>
>
> Any suggestion in the right direction is highly appreciated. Thank you.
>
> --
> Regards
> Vinothkumar Mohanakrishnan
>
>
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