DiffSBDD

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Scaffold Hopping

1

Hello! Thank you for sharing the code. Could you please share an example how you do scaffold hopping (or scaffold elaboration/ fragment merging/ fragment growing). I tried using the inpaint_ligand...

sirine90

Is it possible to get the scripts and settings for the evolutionary algorithm presented in the paper?

TommyBiomodellingAU

i have been trying to download the correct packages for running DiffSBDD, but I get a "Segmentation Fault (core dumped)" after I tried to fix the following error: "ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6:...

TommyBiomodellingAU

Hi all, When I ran generate_ligands.py with parameters "--sanitize --relax --num_nodes_lig 50 --n_samples 20" in moad_fullatom_cond model. It took 5368MB CUDA memory!!! Is it OK for only sampling 20 molecules...

CADDfarmer

Hi there, I am working on reproducing the results reported in the paper on the crossdocked dataset, and was able to successfully do so when running `test.py` with the `crossdocked_fullatom_cond`...

amitkadan

hi, Arn, thanks for your update on the repo. but when I try to run generate_ligands.py, I get the following error: ```bash File "d:\Cheminfo_Workshop\4_Fragment_Scaffold_Evolution\DiffSBDD-main\utils.py", line 69, in write_xyz_file with open(filename,...

MachineGUN001

I downloaded DiffSBDD program around April and used it. I downloaded the latest ckpt file and used generate_ligands.py, but the program did not run because the dynamics was (maybe) updated....

msako82

Data preprocessing with coarse graining does not seem to work

1

Following the readme instructions I have downloaded the crossdocked, unzipped it and am trying to run the preprocessing script on it with and without the flag `--ca_only`. Running ``` python...

stratisMarkou

Error occurs at Line 146 of get_edges()

5

When I use your full_atom.ckpt to sample for the protein pockets in the test set of CrossDocked dataset, the following error occured. ``` File "DiffSBDD/equivariant_diffusion/dynamics.py", line 146, in get_edges edges...

mathfirst

Openbabel error

2

Hi Arne, Every time I run generate_ligands.py script, I get babel error: *** Open Babel Error in TetStereoToWedgeHash Failed to set stereochemistry as unable to find an available bond. Though...

githubrudramani