Maria Castellanos

Cinnabar analysis is outdated in the tutorial demo

1

I was going through the tutorial [**_Using alchemiscale to evaluate a relative binding free energy network_**](https://docs.alchemiscale.org/en/latest/tutorials/demo/Alchemiscale%20Demo.html#), and noticed that the Advanced example was assuming an older version of cinnabar. I'm...

The current saving format of asapdiscovery-simulation needs to be more general

4

I want to implement a minimization and re-docking step for the `ligand-transfer-docking` pipeline, but the current `outpath` format wouldn't allow for me to do a second docking step. Specifically, right...

`asapdiscovery-data` should be the base subdirectory with no dependancies from other subpackages, but currently some of the tests introduce unwanted dependencies. These tests need to be mode to the corresponding...

Remove spectrum.fitness

1

Drop the `fitness` module from `asap-spectrum`, and all dependencies in `asap-workflows`.

## Description Adding a few fixes and improvements to the structure alignment pipeline (moved PR from original package) ## Todos Notable points that this PR has either accomplished or will...

Small improvements to spectrum

1

## Description Adding visualization of sequence identity scores to html sequence alignments & optionally calculate approximated binding pocket similarity score on sequence alignment workflow. Fix #94 ## Todos Notable points...

Change codebase to pydantic2 models, instead of pydantic2.v1

1

We are currently using pydantic2.v1 in our code, but ML is failing because is MTENN implemented with (fully) pydantic2 models. Moving all our models to pydantic *should* fix the ML...

Add sequence and binding site similarity to spectrum alignment view

The following changes to spectrum are pending and need to be implemented in the next release. Copied @ijpulidos comments from #55: - Combining some functionalities with existing implementations in other...

New errors in asap-alchemy

1

macos is failing ``` def test_plan_from_names(tyk2_ligands, tyk2_small_custom_network): """Make sure we can plan a network using the names of the ligands.""" edges = extract_custom_ligand_network(tyk2_small_custom_network) planner = NetworkPlanner(network_planning_method=CustomNetworkPlanner(edges=edges)) network = planner.generate_network(ligands=tyk2_ligands).to_ligand_network() #...