orientation

[Vladimir Krystof]

Hello,
I have just installed LICSS, but immediately found a limitation for my work. Analogous compounds in a series are displayed in a random orientation (left/right, upside/down) and this complicates the comparison of structures. Is there any way how to unify displaying of molecules, or how to fix the position (certain atom or part of the molecule?). Or is it an intrinsic feature of smiles themselves?
Thanks.
Vladimir

[Kevin Lawson]

Hi Vladimir

No, I am sorry, SMILES strings cannot contain any orientation information so, to solve this issue, LICSS would need to record something about user-preferred orientation and control the JChemPaint structure renderer to render in the desired way (which I am not sure is possible with the default rendering code). I will have a look at whether there might be some way of recording preferred orientation for a future release.

Best wishes

Kevin

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[Kevin Lawson]

Hi Vladimir

No, I am sorry, SMILES strings cannot contain any orientation information so, to solve this issue, LICSS would need to record something about user-preferred orientation and control the JChemPaint structure renderer to render in the desired way (which I am not sure is possible with the default rendering code). I will have a look at whether there might be some way of recording preferred orientation for a future release.

Best wishes

Kevin

On Mon, May 30, 2016 at 10:15 AM, Vladimir Krystof <vladimir...@gmail.com> wrote:

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[John May]

You can fix positions of atoms/bonds in the latest version of CDK - https://github.com/cdk/cdk/blob/master/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java#L306. In general though molecule with the same scaffold are now likely to depict in the same orientation.

Random Selection of benzodiazepines from SMILES: 

https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=Clc1cc2c(N(C(=O)CN=C2c2ccc(Cl)cc2)C)cc1.Clc1cc2c(N(CCN)C(=O)CN=C2c2c(F)cccc2)cc1.Clc1cc2c(N(CCN3CCN(CC3)C)C(=O)CN=C2c2c(F)cccc2)cc1.Clc1cc2c(N(C(=O)C(O)N=C2c2c(F)cccc2)C)cc1.Clc1cc2c(N(CCCN(CC)CC)C(=O)CN=C2c2ccccc2)cc1.Clc1cc2C(=N[C@@H](Cc3ccc(O)cc3)C(=O)Nc2cc1)c1ccccc1.Clc1cc2c(N(CCN3CCOCC3)C(=O)CN=C2c2ccccc2)cc1.Clc1cc2c(N(C(=O)C(O)N=C2c2c(Cl)cccc2)C)cc1&abbr=off&suppressh=true&showtitle=false&zoom=1.3&annotate=none