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]> 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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