Support direct CIF/mmCIF template inputs for inference

[taivu1998]

Summary

Adds inference support for directly supplied local CIF/mmCIF template files, addressing issue #263.

Users can now set proteinChain.templatesPath to a .cif or .mmcif file and optionally provide proteinChain.templateChainId when the file contains multiple protein chains. The direct structure is parsed, chain-selected, aligned to the query sequence, and converted into the existing template feature contract used by searched .a3m/.hhr templates and embedded JSON templates.

Root Cause

The inference template dispatcher only accepted embedded template JSON plus search-derived .a3m and .hhr files. A user-supplied CIF/mmCIF structure path fell through to Unsupported template format, and preprocessing could silently replace missing explicit template paths with automatic template-search output instead of honoring the user's intended custom template.

Changes

• Added direct CIF/mmCIF parsing and featurization through TemplateHitFeaturizer.parse_cif_template.
• Extended simplified CIF parsing to retain all protein-like chains and support optional chain filtering.
• Added shared template path/suffix helpers so direct CIF/mmCIF and embedded JSON templates do not require a local PDB mmCIF mirror.
• Wired inference template dispatch for .cif and .mmcif paths with clear errors for ambiguous or missing chains.
• Made preprocessing fail loudly when an explicit templatesPath is missing instead of silently replacing it.
• Updated CLI/docs for .cif, .mmcif, .json, .a3m, .hhr, and templateChainId.
• Added focused tests for direct CIF parsing, chain selection, alignment, preprocessing behavior, and mmCIF-dir gating.

Validation

• uvx ruff check protenix/data/template/template_parser.py protenix/data/template/template_utils.py protenix/data/template/template_featurizer.py protenix/data/template/template_path.py protenix/data/inference/infer_dataloader.py runner/template_search.py runner/batch_inference.py tests/test_custom_cif_templates.py
• python3.11 -m py_compile protenix/data/template/template_parser.py protenix/data/template/template_utils.py protenix/data/template/template_featurizer.py protenix/data/template/template_path.py protenix/data/inference/infer_dataloader.py runner/template_search.py runner/batch_inference.py tests/test_custom_cif_templates.py
• git diff --check
• uvx --python 3.11 --with pytest --with numpy --with rdkit --with biopython --with biotite --with requests --with typing-extensions pytest tests/test_custom_cif_templates.py -q (9 passed)
• uvx --python 3.11 --with pytest --with numpy --with rdkit --with biopython --with biotite --with requests --with typing-extensions pytest tests/test_custom_cif_templates.py tests/test_json_template_parser.py tests/test_fetch_remote_cif.py -q (19 passed)