Amit Roy

Getting error while running pip install .

3

Hi, I installed all the dependencies via conda in an environment called jtvae. Then, after cloning the repository, I ran: ``` (jtvae) hgraph2graph$ pip install . ``` But I got...

Error when running generate_ligands.py

3

When I run > (sbdd-env) user@machine:~/projects/repos/DiffSBDD$ python generate_ligands.py ./checkpoints/full_atom.ckpt --pdbfile ./data/targets/test_1.pdb --outdir ./outputs/test_1/ --resi_list A:115 A:121 A:123 I get the following error: > OSError: /home/user/miniconda3/envs/sbdd-env/lib/python3.10/site-packages/torch_scatter/_version_cuda.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs This error...

Is the prepareComplex.py code in the "Protein and ligand preparation" section correct?

5

Firstly, thank you very much for attempting to simplify the workflow for those who are not computational biologists. This is the specific excerpt that the title is referring to: `...

A question about how SMILES is being parsed

2

Assume I have constructed a molecule from the following SMILES: ```julia using Graphs, MolecularGraph sml = "CC(=O)OC1=CC=CC=C1C(=O)O"; mol = smilestomol(sml); ``` We see in `Pluto` that `mol` has one ring....

Unable to assemble a molecule using the SMILESMolGraph ctor

5

I would like to assemble a simple SMILESMolGraph O=C=O molecule by hand, as it were, in the following manner: ```julia import Graphs, MolecularGraph mol = let edge_list = [Graphs.Edge(1, 2),...