Oh yes. It was said in the documentation that 3D Model Builder is having
issues, but I thought it should work for small molecules?
The SMILES for my assembled molecules (NewHeptane) = *CC[CH3]C[CH3]CC*
Thank you for your interest in this post.
On Mon, Oct 30, 2017 at 11:39 AM, John Mayfield <john.wilkinson...@gmail.com
> wrote:
> Oh right, yeah sorry I missed that.
>
> The 3D coordinate generation in the CDK is really bad, it kind of works
> but not really. Been meaning up to update, anyways this simple molecule
> should be okay... what does the SMILES look like for your assembled
> molecule?
>
> John
>
> On 30 October 2017 at 09:05, Vinothkumar Mohanakrishnan <
> kmvin...@gmail.com> wrote:
>
>> Dear John
>>
>> Thanks for your valuable insight.
>>
>> I messed up with the indices in my first post where I numbered atoms
>> sequentially for clarity purpose of the question, but I should have
>> mentioned about CDK indices and renumbering in the NewHeptane atom
>> container, which I am quite aware of, (thanks a lot for your clarity in
>> explaining it)
>>
>> To me, it seems that the real issue is with the model builder. (After
>> generating SMILES)
>>
>> 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 with CDK atom indices
>>
>> NewHeptane.add(Propane)
>>
>>
>> *NewHeptane.addBond(1, // second atom in heptane
>> 4, // first atom in propane*
>>
>> * IBond.Order.Single);*
>>
>>
>> *NewHeptane.addBond(2, // third atom in heptane (was sixth before we
>> deleted some)*
>> * 6, // third atom in propane*
>> * IBond.Order.Single);*
>>
>> //Generate smiles
>> SmilesGenerator sg = SmilesGenerator.absolute();
>> String smi = sg.create(NewHeptane);
>>
>> //Parse smiles
>> SmilesParser sp = new SmilesParser(SilentChemObjectB
>> uilder.getInstance());
>> IAtomContainer m = sp.parseSmiles(smi);
>>
>> // Build 3d model
>> ModelBuilder3D builder3d = ModelBuilder3D.getInstance(m.getBuilder());
>> IAtomContainer newHeptane = builder3d.generate3DCoordinates(m, false);
>>
>> Any insights in the right direction are highly appreciated. Thank you.
>>
>>
>>
>> On Sat, Oct 28, 2017 at 5:38 PM, John Mayfield <
>> john.wilkinson...@gmail.com> wrote:
>>
>>> 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(SilentChemObjectB
>>>> uilder.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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>>>>
>>>>
>>>
>>
>>
>> --
>> Regards
>> Vinothkumar Mohanakrishnan
>>
>>
>> ------------------------------------------------------------
>> ------------------
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>>
>>
>
--
Regards
Vinothkumar Mohanakrishnan
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