>
> If getAtomNumber works like an array indexOf and does reference equality.
It does...
*The getAtomNumber works like an array indexOf and does reference equality.*
sorry in a rush was going to say if i understand correctly..
On 7 April 2017 at 20:25, John Mayfield <john.wilkinson...@gmail.com> wrote:
> HI Niko,
>
> If getAtomNumber works like an array indexOf and does reference equality.
> I'm a bit confused by your description but I think what your trying to do
> is find a hydroxy in CHEMBL501674? In general you need to find a
> substructure, https://en.wikipedia.org/wiki/Subgraph_isomorphism_problem.
> Easiest way to do this is with a SMARTS pattern match
> <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>.
>
> String smi =
> "CO[C@@H]1[C@H](O)[C@@H](C)O[C@@H](OC[C@@H]2[C@@H](C)OC(=O)\\C=C\\[C@H](C)[C@H](CC[C@@H](C)C(=O)\\C=C\\[C@H]3O[C@@H]23)O[C@@H]4O[C@H](C)C[C@H](O)[C@H]4O)[C@@H]1OC";
> SmilesParser smipar = new
> SmilesParser(SilentChemObjectBuilder.getInstance());
> IAtomContainer target = smipar.parseSmiles(smi);
>
> Pattern ptrn = SmartsPattern.create("*[OH]");
> for (int[] mapping : ptrn.matchAll(target)) {
> IAtom a = target.getAtom(mapping[1]); // 0=*, 1=[OH]
> System.out.println(target.getAtomNumber(a));
> }
>
>
> 4
> 40
> 42
>
>
> There are indexes so add one to get the num in the depiction, 5, 41, 43: CDK
> Depict
> <https://cdkdepict-openchem.rhcloud.com/depict/bow/png?smi=CO[C@@H]1[C@H](O)[C@@H](C)O[C@@H](OC[C@@H]2[C@@H](C)OC(=O)%5C%5CC=C%5C%5C[C@H](C)[C@H](CC[C@@H](C)C(=O)%5C%5CC=C%5C%5C[C@H]3O[C@@H]23)O[C@@H]4O[C@H](C)C[C@H](O)[C@H]4O)[C@@H]1OC&abbr=on&suppressh=true&showtitle=false&sma=*%5BOH%5D&zoom=1.3&annotate=number>
>
> [image: Inline images 1]
>
>
> On 7 April 2017 at 17:28, Nikolas Glaser <glase...@gmail.com> wrote:
>
>> Hey guys,
>> I have a general question to the working of the method getAtomNumber().
>> What are the criteria an atom is chosen in the IAtomContainer?
>>
>> For example I have following test code:
>> Created a AtomContainer from following smiles: [Z]O // in
>> this case the [Z] is a placeholder for the link position of the fragment in
>> the main substance
>> So I take the Atom at index position 1 in the Fragment. When I print the
>> Symbol it is the O.
>>
>> Now I want to get the Index in the complete substance and it is sure that
>> O is in the substance present. I get the index -1 so I think the method
>> cannot find the Atom.
>> The complete substance I use for my test is CHEMBL501674.
>> If I do getAtom(0) on the substance it returns an O Atom.
>>
>> So the general Question is, is it impossible to get the Atomposition in
>> this way in the original substance with a fragment created from a smiles
>> string?
>> Or how does the method correctly work, on the documentation I was not
>> able to find a detailed information and I had not the time to watch in the
>> code, also I thought if it is the wrong way you can tell it me much more
>> faster.
>>
>> I want to realise the idea of John to get the starting position of the
>> fragment in the specific molecule on this way.
>>
>> Thanks for your help again.
>>
>> Cheers
>> Niko
>>
>>
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>
>
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