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Is there an easy way to plot a 2D chemical structure?

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Julian Schmid 2017-9-26

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评论： Julian Schmid 2017-10-5

polyoxinA.zip

Is there a way to plot a chemical structure in 2D from input files like a .mol file or .xyz? The Matlab Bioinformatics toolbox provides a 3D molecule viewer, but there is no support for 2D chemical structures.

Example (image from Wikipedia.org):

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Arthur Goldsipe 2017-9-26

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Are you asking how to convert a 3D structure to 2D representation? Are you asking how to display a 2D structure that you have in a file? Or are you for a combination: Take a 3D structure in a MOL/XYZ file, convert that to 2D, and then display the 2D structure.

Julian Schmid 2017-9-27

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I am asking for a way to convert a .mol file (which contains 3D structure information, of course) into 2D and display the 2D structure.

KSSV 2017-9-27

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Why don't you attach that .xyz file or mol file.so that you can get help.

Julian Schmid 2017-9-27

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polyoxinA.zip

Attached, please find an example file (.mol file of Polyoxin A).

KSSV 2017-9-27

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With the given file...on using molviewer('polyoxinA.mol') the display is 2D only.

Julian Schmid 2017-9-27

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编辑：Julian Schmid 2017-9-27

Sorry couldn't test the file with my setup here. Seems that the file only contains 2D structure information. However, I am still looking for a way to present the structure in a way close to the example image above. Cound't find an option in Jmol for that... In addition, it would be awesome to plot this structure in a programmatically created GUI (axes).

Julian Schmid 2017-10-2

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编辑：Julian Schmid 2017-10-5

Looks like there is no way to so this in matlab only. Does anyone know a library in a language which can interact with matlab and can be used for the mentioned Problem?

Julian Schmid 2017-10-5

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I found a c++ library called "GraphMol" (GraphMol) which allows to convert a file to a svg graphic. Unfortunately, I am not familiar with c++ and Matlab does not provide svg support :(... Is there a workaround?

KSSV 2017-10-5

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If you are familiar with MATLAB..you can attempt to write your code to plot the stuff you want.

Julian Schmid 2017-10-5

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Yes, I could do that, but is it worth to spend hours of time for a feature which is nice to have but not absolutly necessary? I gonna look into c++ then, I think it is better to invest my time there, rather than writing something new, which, in my opinion, should aleady be implemented in (a commercial) scientific programming tool like Matlab. Anyway, thanks!

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