How to convert chemdraw file in CDX format either into Mol2 or SDF format?

Question

[muhammadhassam8]

How to convert chemdraw file in CDX format either into Mol2 or SDF format to further convert in 3D format?

[ATpoint]

Hi muhammadhassam8, I replaced the unspecific tags you initially used by chemdraw which is the (I think) only relevant one here. Using correct tags often attracts experts or even the developers of tools (given they are active here) so it is encouraged to put in some effort into setting them.

Answer 1

[Wolf Ihlenfeldt]

You can for example use the CACTVS toolkit (free for academic users, www.xemistry.com/academic documentation at www.xemistry.com/docs):

Minimal sample command line input with Python interface:

pycactvs>Molfile.Write('myfile.sdf',Molfile.Read('myfile.cdx'))

Sybyl Mol2 is a mandatory 3D format. You can write it in exactly the same fashion, but then you already implicitly invoke the built-in 3D atomic coordinate generation methods of the toolkit (like lookup in PubChem), which is probably not what you want if you have your own software for this.

[muhammadhassam8]

Via Python interface, can we convert let say 1000 sketches in CDX format into SDF or mol. format?

[Manoj]

@muhammadhassam8 have you tried openbabel ?

[Wolf Ihlenfeldt]

Yes, of course.

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Answer 2

[Manoj]

You can convert CDX format either into Mol2 or SDF format using chemdraw also.

Open .cdx file in chemdraw and click on File -> Save as -> File Name (Example.sdf or Example.Mol2) and save as type (Select file type of your choice)

Hope this help !!