mmagithub

Updated docker image for YANK

11

Hello, I am wondering if there is an updated docker/singularity image for YANK. I tried to use the old one: https://hub.docker.com/r/choderalab/yank and tried building my own but in vain. There...

Hi, I am calculating the binding affinity of a small molecule sandwiched between two proteins. In the absence of the small molecule, these two proteins do not bind under physiological...

tautomer.TautomerEnumerator() function

6

Hi, I am trying to enumerate tautomers using the tautomer.TautomerEnumerator() function. I am wondering if the returned list is sorted by scores so that the best-scoring tautomer in the list...

Support for Parallel CPU execution (distributed parallelization)

1

Hi, Just wondering if aitextgen finetuning supports multi-threading/multi-CPU (parallel/distributed) training. I understand the execution is much faster on GPUs, but in case that GPU is not available, can we get...

Loading a tf_gpt2 model from local folder

1

Hi, It may be a trivial question, I am wondering how can we load a tf_gpt2 model from local folder. I tried: ai = aitextgen(tf_gpt2="124M") But it ignores the 124M...

Hi, I am wondering if FPSim2 supports substructure search by SMARTS patterns ? Thanks

Ignore bad molecules

1

### Issue summary Hi, I am wondering if there is a mechanism/command in Gnina to overcome bad molecules. I am trying to use Gnina (default CNN ensemble) to rescore poses...

stripH=off option still removes hydrogens

3

### Issue summary Hi, I am wondering what is the proper way of preventing Hydrogen removals from input sdf files in the outputs. It seems that the 'stripH=off' option still...

DeltaDeltaG

3

Hi, I am wondering if there is a Gnina branch supports the DeltaDeltaG method, as was announced in the recent CACHE challenge release. Thanks, Marawan

Inference from a multiclass classification model

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Hi, I am wondering how can i use the ''predict_from_model" function to make predictions on unknown molecules from a pre-trained tar.gz model, for a multi-class model (6 classes classification model)...