amir-tagh

KeyError: 'PiStacking'

4

Hello, I am using the following steps to get the interactions between an RNA and a ligand and in getting the pi-stacking interactions I am getting an error message. Can...

energy decomposition of individual terms

2

Hello, I am using Autodock GPU to study RNA-ligand interactions and I was wondering if there is anyway to get the individual contribution of energy terms in the output file....

java.lang.module.FindException: Module javafx.controls not found

3

Hello, I am trying to launch the RNArtist in Ubuntu 18 and I am getting the following error message: (openjdk 11.0.14 2022-01-18) I googled the problem but could't find a...

Hello, I have some small molecules which interact with a rather high binding affinity toward my protein. I was wondering if I could use MolDQN to optimize these compounds and...

Hello, I am trying to move step by step with this analysis using the currently downloaded Zinc data base (6_p0.smi.gz) (/http://zinc12.docking.org/subsets/all-purchasable) but I am stuck in the beginning with the...

how to use MAP similarity search for databases other than Chembl

4

Hello, Thanks for sharing your great work. I was wondering if it is possible to use a custom build library for similarity search. In running the fingerprint from terminal how...

marker size and shape in bioinfokit.visuz.cluster.pcaplot

1

Hello, I am using cluster.pcaplot to plot 2D and 3D plots for a set of data. Is there any option for marker size and marker shape that I can use?...

TypeError: forward() missing 2 required positional arguments: 'y_orders' and 'beta'

2

I am using the train_translator.py for lead optimization and I am getting the following error. does anybody know how I can fix this? Thanks, Traceback (most recent call last): File...

TypeError: can't convert cuda:0 device type tensor to numpy. Use Tensor.cpu() to copy the tensor to host memory first

2

Hello, I am using the finetune_generator.py and I am getting the following error. does anybody know how to solve this. Thanks, Loading from checkpoint ckpt/inforna-pretrained/model.ckpt.5000 After pruning 257 -> 257...

IndexError: tuple index out of range

12

Hello, I am following the the example for "Molecule generation pretraining procedure". first step "python get_vocab.py --ncpu 16 < data/chembl/all.txt > vocab.txt" is done with no error, but I am...