Wei-Tse Hsu

A problem with slicing in subsampling

6

Hi `alchemlyb` developers, Thank you all for the development of this package. I was using `alchemlyb` to analyze some output files from the simulation performed by GROMACS. When using the...

A problem of file parsing for simulations with multiple coupled states

3

Hi `alchemlyb` developers, I was running a Hamiltonian replica exchange simulation of 140 states, with the first 4 states being the coupled states (\lambda_{coul}, \lambda_{vdw}, \lambda_{restr}) = (0, 0, 0)...

In the current implementation of the RC loss function, we use scikit-learn to perform kernel density estimation (along with k-fold cross-validation for the optimization of the bandwidth), which returns a...

Hi, This PR adds support to optionally output ligand-only SDF files when running `boltz predict`, which is enabled by the flag `--ligand_sdf`. Separate SDF files will be generated if there...

Issue of failed featurizer from version 0.4.1

2

Hi, I was using Boltz-1 version 0.4.1 for some inference tasks, among which some failed with a series of errors like below and it took a long time to fail:...

`compute_3d_conformer` takes a long time to run - Would it be reasonable to bypass it?

3

Thanks to the team for making this amazing tool publicly available! As I tested Boltz-1, I noticed that for some cases, the step of "processing input data" could take an...

Pairwise sequence identity matrix is not symmetric

4

As instructed by the user manual and this [blogpost](https://www.blopig.com/blog/2023/05/pairwise-sequence-identity-and-tanimoto-similarity-in-pdbbind/), I used the following script to compute pairwise sequence identity for a dataset (called bindingnet here): ``` fake_pref() { QDB="$1" TDB="$2"...