Fix security and typo bugs in physchem_filters.py

[SergeiNikolenko]

Description

Fix two bugs in openadmet/toolkit/filtering/physchem_filters.py:

1. Unsafe dynamic code execution in DatamolFilter (line ~504): eval(f"dm.descriptors.{self.name}") allows arbitrary code execution through crafted descriptor names. Replaced with safe getattr(dm.descriptors, self.name) which is functionally identical but eliminates the injection risk.

2. AttributeError in ProximityFilter.calculate (line ~215): self.set_mols(smiles=smiles) calls a non-existent method. The correct method is self.get_mols() (defined in BaseFilter). This causes AttributeError when calculate() is called with mols=None.

Status

• Ready to go

Developers certificate of origin

• I certify that this contribution is covered by the License and the Developer Certificate of Origin at https://developercertificate.org/

[hmacdope]

Hi @SergeiNikolenko thanks for the contribution. Can I ask what brought you here and what you are hoping to achieve with the toolkit?

[codecov]

Codecov Report

❌ Patch coverage is 50.00000% with 1 line in your changes missing coverage. Please review.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[SergeiNikolenko]

Hi @hmacdope! Thank you for getting back to me. I really appreciate the work you’re doing — it’s genuinely exciting and very relevant to what we’re building.
I lead a team of cheminformaticians at my company, and we’re currently exploring plans to integrate OpenADMET as the ADMET prediction engine within our molecular generator pipeline. The idea is to use it as part of early-stage drug discovery workflows in applied medicinal chemistry projects.
I’d be very glad to contribute where possible and help improve the toolkit and models reps along the way.

[SergeiNikolenko]

At the moment, I’m going through the codebase to better understand the architecture and design decisions. I may submit some PRs if I find improvements or additions that seem useful.
If anything doesn’t align with your roadmap or expectations, please let me know — I’m happy to adjust.

[hmacdope]

No problem! Appreciate any and all bug fixes.

May I suggest that the core of our work on the modelling side is done over at openadmet-models here, this functionality works but has more rough edges: https://github.com/OpenADMET/openadmet-models. We also have a discord and I just made a channel for us to talk infra etc: https://discord.gg/eUjpFaUv6m