Tom's rewrite

[Tomodovodoo]

Implemented the plan from our meeting in september:
context manager is lifecycle-only
service logic is abstracted behind adapters
exhaustive all-name/all-service search with grouping is supported
best-structure selection now uses deterministic RDKit stereo/chirality scoring (no SMILES-length heuristic)
strict OPSIN isomer validation is available
cross-service evidence/correlation output is explicit
default usage remains backward-compatible.

API changes:

• search_strategy added (default first_hit)
• resolution_mode added (default legacy)
• include_evidence added for crosschecked search
• include_evidence=True returns ResolutionResult
• exhaustive searches all names/services
• strict_isomer enforces OPSIN stereo match
• legacy and consensus currently share the same path
• Existing calls still work unchanged

Added features:

• Lifecycle-only context manager
• Service adapter ABC + registry
• Per-identifier adapter resolution (resolve_one)
• Exhaustive candidate dedupe/grouping
• Deterministic consensus ranking
• RDKit stereo/chirality-based scoring
• Explicit tie-break ordering
• Evidence model (CandidateEvidence)
• Correlation fields (service/identifier/synonym)
• New scoring/search/adapter tests
• New scoring documentation

[Tomodovodoo]

From my notes back then:

More maintainable.

Usually to clean up stuff, context managers. Not meant for logic

molecule resolver contextmanager should be rewritten

Abstract Base Class

Algorithm for best structure;
Implement isomer specific, if name == except for isomer.
OPSIN already does this.

Optional; Detailed/isomer by running through Opsin. If isomeric; OPSIN check.

5 names -> search 5 names on all service, for first found name, return.
Might be value in searching all names, getting all results, grouping, parse.

Correlations between databases.

[Tomodovodoo]

Figured I might as well :P

[simonmb]

Hi Tom, I will have to take some time to review this. :) It's a lot of changes. Thanks! I will try to get back to you in 1-2 weeks.

[Tomodovodoo]

Great, that's perfect. If there's anything missing, wanted, or necessary to change, just let me know or send me an email. Don't have a lot of free time anymore (I work as an AI-engineer at the moment, with some other projects going on), but enough to work on this when I want to in my free time.