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ChenDdon / AGBTcode

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How to get the 3D structures of SMILES #5

Open xllgit opened 2 years ago

xllgit commented 2 years ago

In this repo, it needs the 3D structures of SMILES(the mol2 file) to Generate Algebraic Graph-based Fingerprints(AG-FPs). It is easy to get some properties of a SMILES(eg: from TDC) but it is hard to get the 3D structures of the SMILES. I tried to get the mol2 file of the SMILES using openbabel, but the coordinate results of the mol2 file all set to zero. Also, as far as I understand, the result of direct conversion from SMILES to mol2 file is not entirely credible. So how to get the 3D structures of SMILES, can you give some methods

ChenDdon commented 2 years ago

To convert the SMILES to 3d file by using openbabel or RDkit is not accurate. For this work, I use the data from previous work, I didn’t generate the 3D files myself. But I know that the software named Schrödinger can be used to generate reliable 3D coordinates from SMILES.

From: xllgit Sent: Friday, March 4, 2022 2:23 PM To: ChenDdon/AGBTcode Cc: Subscribed Subject: [ChenDdon/AGBTcode] How to get the 3D structures of SMILES (Issue #5)

In this repo, it needs the 3D structures of SMILES(the mol2 file) to Generate Algebraic Graph-based Fingerprints(AG-FPs). It is easy to get some properties of a SMILES(eg: from TDC) but it is hard to get the 3D structures of the SMILES. I tried to get the mol2 file of the SMILES using openbabel, but the coordinate results of the mol2 file all set to zero. Also, as far as I understand, the result of direct conversion from SMILES to mol2 file is not entirely credible. So how to get the 3D structures of SMILES, can you give some methods — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.Message ID: @.***>