Re: [Cdk-user] 2nd Line of Double Bond Misplaced

[John May]

What does your code look like - John On 4 Sep 2024, at 21:03, Velusamy Velu <kool.v...@gmail.com> wrote:  Hi John: I appreciate your feedback. I'm using version 2.9 of CDK. Our requirement needs to construct the Porphyrin molecule programmatically as instance of the IAtomContainer and use the depictor. The >N-H decision is a matter of choice. When I replaced the >N-H as you have done (>NH) the result I received was still with the second lines of double bonds out. Thanks for the pointers you provided, I will review those documents. Velusamy K. Velu 614-323-9649     On Tue, Sep 3, 2024 at 2:33 AM John Mayfield <john.wilkinson...@gmail.com> wrote: It's true we do still push the hydrogens out like that (see below), it's a bit tricky to fix as is due the macrocycle processor. However since you had that it hints perhaps you have just found some old documentation on how to depict molecules are using the wrong classes (generators). There is lots of info here: https://github.com/cdk/cdk/wiki/Standard-Generator but start here: https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/depict/DepictionGenerator.html On Tue, 3 Sept 2024 at 07:27, John Mayfield <john.wilkinson...@gmail.com> wrote: You are probably using a very ancient version. Pasting the SMILES for Porphyrin on Wikipedia: C1=CC2=CC5=CC=C(C=C4C=CC(C=C3C=CC(=CC1=N2)N3)=N4)N5 in here: https://www.simolecule.com/cdkdepict/depict.html I get: On Tue, 3 Sept 2024 at 04:36, Velusamy Velu <vv...@peruselab.com> wrote: Hi I ran into an issue with the image of the porphyrin molecule.  The original image from Wikipedia is: I drew it as below: Then I let the CDK layout the image, which did a good job except for the placement of the second lines of double bonds, as shown below. I thought the explicit bond between H & N was the cause, so I replaced those N-H instances with NH, then tried again. This time it still put those second lines out, as below. Any idea how to fix this? Thanks Velusamy K. Velu (614) 323-9649       _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user

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