Ah okay,
thanks I built it from sources again and got it.
But I think I will change it to Maven.
Thank you very much!
Niko
> On 26. Apr 2017, at 15:35, John Mayfield <[email protected]> wrote:
>
> You should be able to add the library from maven... releases are on the
> central repo. You should be able to add releases from the UI (see
> screenshot). But I would read up on using Maven.
>
> Our Snapshot Repo is here:
> https://oss.sonatype.org/content/repositories/snapshots/
> <https://oss.sonatype.org/content/repositories/snapshots/>
>
> John
>
> On 26 April 2017 at 14:26, Nikolas Glaser <[email protected]
> <mailto:[email protected]>> wrote:
> Ah yeah you’re right, it is not -1 its +1 -> my fault -.-
> Okay thank you. So it is correct.
>
> I will try to get cdk 2.0-SNAPSHOT get working. I built it from source after
> description on github but when I insert the jar in IntelliJ as library the
> classes are not found. I will have a look on it.
>
>> On 26. Apr 2017, at 15:19, John Mayfield <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> Ha! hang on... the output is correct... index != number. Sorry jumped to the
>> more technical problems that can happen. getAtomNumber reports the atom
>> index 0 ≤ i < n (the atom numbers are 1 < i ≤ n).
>>
>> 39 connected to 38, 40, 41
>>
>> in the depiction is
>>
>> 40 connected to 39, 41, 42
>>
>> which is correct.
>>
>> I actually added a patch to help with this confusion (see
>> https://github.com/cdk/cdk/pull/306 <https://github.com/cdk/cdk/pull/306>).
>> In future it will be mol.indexOf(atom) which is much clearer.
>>
>> Anyways following on from my previous code you can print the "index" as
>> follows:
>>
>> SmilesParser smipar = new
>> SmilesParser(SilentChemObjectBuilder.getInstance());
>> SmilesGenerator smigen = new SmilesGenerator(SmiFlavor.Canonical |
>> SmiFlavor.CxAtomValue);
>> for (String smi : new String[]{"CCO", "C(C)O", "OCC"}) {
>> IAtomContainer mol = smipar.parseSmiles(smi);
>> for (int i = 0; i < mol.getAtomCount(); i++)
>> mol.getAtom(i).setProperty(CDKConstants.COMMENT, i);
>> System.out.println(smigen.create(mol));
>> }
>> OCC |$_AV:2;1;0$| -
>> https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=OCC%20%7C%24_AV%3A2%3B1%3B0%24%7C&w=80&h=50&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=atomvalue
>>
>> <https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=OCC%20%7C%24_AV%3A2%3B1%3B0%24%7C&w=80&h=50&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=atomvalue>
>> OCC |$_AV:2;0;1$| -
>> https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=OCC%20%7C%24_AV%3A2%3B0%3B1%24%7C&w=80&h=50&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=atomvalue
>>
>> <https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=OCC%20%7C%24_AV%3A2%3B0%3B1%24%7C&w=80&h=50&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=atomvalue>
>> OCC |$_AV:0;1;2$| -
>> https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=OCC%20%7C%24_AV%3A0%3B1%3B2%24%7C&w=80&h=50&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=atomvalue
>>
>> <https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=OCC%20%7C%24_AV%3A0%3B1%3B2%24%7C&w=80&h=50&abbr=on&suppressh=true&showtitle=false&zoom=1.3&annotate=atomvalue>
>>
>>
>>
>>
>> John
>>
>> On 26 April 2017 at 14:12, John Mayfield <[email protected]
>> <mailto:[email protected]>> wrote:
>> I forgot to say that I use idk 1.5.3 and the substance which is used in the
>> code is parsed from the same smiles as the one which is printed in the svg
>> file.
>>
>> Why? 1.5.3 is really old, use 2.0-SNAPSHOT if you can.
>>
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>
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