Question

I want to try convolutional neural networks for drugs classification. I use PyTorch for 3D CNN implementation. Is there a way to obtain 3D tensors from SMILES or SDF/PDB structures?

Answer 1

Yes, it is possible to obtain 3D tensors from SMILES or SDF/PDB structures in PyTorch.

Step-by-step explanation:

Yes, it is possible to obtain 3D tensors from SMILES or SDF/PDB structures for use in 3D CNN implementation using PyTorch.

In order to convert SMILES or SDF/PDB structures into 3D tensors, you can use molecular modeling software libraries such as RDKit or Open Babel.

These libraries provide functions that allow you to read the SMILES or SDF/PDB structures, calculate molecular features, and generate 3D coordinates for each molecule. These coordinates can then be used to represent the molecules as 3D tensors for input into the 3D CNN.