Jannis Born

**Is your feature request related to a problem? Please describe.** Currently the artifact-based property predictors (like `gt4sd.properties.molecules.core.Tox21`) are not usable as functions via `gt4sd.properties.molecules.tox_21`, unlike all the non-artifact-based properties). Moving...

Relax sklearn version dependency caused by TDC

1

**Is your feature request related to a problem? Please describe.** Some of our property computations rely on TDC and thus an old and specific sklearn version **Describe the solution you'd...

Regression Transformer - facilitate scaffold decoration

2

Currently, the RT supports only plain inference with user provided masked inputs like: ```txt 0.123|[C][MASK][C][O] ``` which is prohibitive, especially since we use SELFIES. Til now, scaffold decoration was impossible...

All PaccMann based models, e.g. proteomic and omics based generator should be retrained using the pypi-distribution of pytoda. This will enable all paccmann-related repos in `vcs_requirements.txt` to be pip installable...

Convert SMILES to FASTA

1

**Configuration:** - RDKit Version: `2019.09.1` - Operating system: Mac OS - Python version (if relevant): Python 3.7.4 - Are you using conda? Yes - If you are using conda, which...

Handling case where all molecules are invalid in property optimization

1

Currently (with the current code on `master`), if one runs the property optimization and the model produces only one *unique* molecule, we get this error: ```sh torchdrug/torchdrug/tasks/generation.py", line 147, in...

- Expanding controllability of the tolerances by setting one tolerance value per property. So tolerance can be provided as `float` or now also as `Dict[str, float]`. Missing keys are imputed...

**Is your feature request related to a problem? Please describe.** Multiproperty RTs can become almost impossible to sample from, at least if a low tolerance value for the property deviation...

**Is your feature request related to a problem? Please describe.** Intregrate TorchProtein: https://torchprotein.ai/get_started

**Is your feature request related to a problem? Please describe.** Expand Regression Transformer trainer to support multi-entity discriminations, i.e., support the `multientity_cg` collator from the RT repo **Describe the solution...