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I would like to know how the train.lmdb and valid.lmdb files in the docking_v2/protein_ligand_binding_pose_prediction_v2 directory were processed from the MOAD dataset. I have checked the code and fou…
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Hi,
i have a PDB file with 20 models. I can see different conformations movements.
I can load the PDB file and see an animation with theses different frames.
Is there a way to have a slider bar to …
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As a force field developer and quantum chemistry user, I often find myself working with collections of structures (conformations) and associated energies. This could be useful for torsion drives in 1…
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I am highly interested in the prediction of protein conformations within this project. I recently attempted the prediction of adenosine kinase and obtained a pdb file along with two npz format files. …
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When a CID such as `//A/1-100` is passed to `molecules_container_T::delete_using_cid` the result contains alternative conformations for residues that should have been deleted.
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Such as: AUM6 401
Thank you for your help.
Best Regards
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Just an FYI, maybe doesn't need to be an issue. Most examples missing this key appear to be in the ion pairs set.
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Reported by Rintarou Suzuki in this thread: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg06543.html
```
In [4]: m = Chem.AddHs(Chem.MolFromSmiles('C1[C@H]2[C@@H]3O[C@@H]3[C@@H]…
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Hi, when I tried to follow your work, I encountered a problem called mode collapse. This means that the generator could only generate several similar conformations, but lacked the ability to generate …
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Hi Shengchao,
Thank you very much for your great work!
In your paper, you mentioned that "Yet, after confirming with the authors, certain mismatches exist between the 2D topologies and 3D confo…