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* Enhance get_protoss.py with API v2 integration, including job polling and improved error handling for uploads and submissions. * Fix ligand sdf concatenation with correct separation * Update documentation to clarify changes in Protoss clash log handling under ProteinsPlus API v2 * Add live regression test for custom PDB Protoss uploads using ProteinsPlus API v2 * Apply suggestions from code review Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
* support mmCIF handling * Skip oversized mmCIF conversions in batch runs Raise OversizedStructureError for classic PDB size limits and continue the qp run with a warning instead of aborting the batch. Co-authored-by: Cursor <cursoragent@cursor.com> * Allow original mmCIF residue names in center matching Load the mmCIF remap sidecar when building CenterResidue so fuzzy and strict center specs can use pre-remap CCD codes (e.g. A1E3R) as well as mapped 3-letter names. Co-authored-by: Cursor <cursoragent@cursor.com> * Add in-repo mini mmCIF fixture for CI-stable tests Replace the external 21ZQ.cif dependency with qp/tests/data/mini_mmcif.cif so conversion and RCSB fallback coverage always runs in CI. Co-authored-by: Cursor <cursoragent@cursor.com> * Add live 21ZQ mmCIF fetch and A1E3R cluster integration test Exercise RCSB mmCIF-only download, 5-letter center matching via remap, and coordination-sphere extraction around A1E3R/A302. Co-authored-by: Cursor <cursoragent@cursor.com> * Compare CIF/PDB atom counts in 21ZQ integration test Avoid hard-coded atom totals that break when RCSB revises an entry; assert conversion preserves the parsed mmCIF atom count instead. Co-authored-by: Cursor <cursoragent@cursor.com> --------- Co-authored-by: Cursor <cursoragent@cursor.com>
* Restore CI by migrating to setup-micromamba The deprecated provision-with-micromamba action failed env setup before pytest could run. Refresh the workflow matrix and test env, and update parse_input coverage for the current API. Co-authored-by: Cursor <cursoragent@cursor.com> * Align cluster tests with CenterResidue and current outputs Fix ACE/NME capping calls, restore combine_pdbs HETATM filtering, and refresh sample goldens so pytest can pass once CI environment setup works. Co-authored-by: Cursor <cursoragent@cursor.com> * Default combine_pdbs to keep HETATM records Turn HETATM filtering off by default and refresh combined-PDB goldens plus charge/adjust tests so CI can finish green after env setup. Co-authored-by: Cursor <cursoragent@cursor.com> * Narrow PR CI to Ubuntu Python 3.12 Keep macOS and other Python versions available only via workflow_dispatch. Co-authored-by: Cursor <cursoragent@cursor.com> --------- Co-authored-by: Cursor <cursoragent@cursor.com>
* Expand docs for missing features and add exact: center syntax. Align user guides with the current CLI and cluster outputs, add runnable basics examples, and let single-residue strict centers use an exact: prefix without ambiguous FE_A199 parsing. Co-authored-by: Cursor <cursoragent@cursor.com> * Update config.yaml to enable implicit solvent usage by default with charge embedding options clarified. --------- Co-authored-by: Cursor <cursoragent@cursor.com>
…re and save in a *_backbone.txt file
…create *_backbone.txt file. Also included example
* Add coordination-step integration test cases with modeller/Protoss fixtures Co-authored-by: Cursor <cursoragent@cursor.com> * Translate coordination case readmes to English Co-authored-by: Cursor <cursoragent@cursor.com> * Enable Modeller in CI using MODELLER_LICENSE_KEY secret Co-authored-by: Cursor <cursoragent@cursor.com> * Fix path-sensitive Modeller alignment tests; disable non-portable build_model Co-authored-by: Cursor <cursoragent@cursor.com> --------- Co-authored-by: Cursor <cursoragent@cursor.com>
…on.py (#19) * Add coordination-step integration test cases with modeller/Protoss fixtures Co-authored-by: Cursor <cursoragent@cursor.com> * Enable Modeller in CI using MODELLER_LICENSE_KEY secret Co-authored-by: Cursor <cursoragent@cursor.com> * Fix path-sensitive Modeller alignment tests; disable non-portable build_model Co-authored-by: Cursor <cursoragent@cursor.com> * Stop tracking versioningit _version.py and soft-skip flaky Protoss CI tests Editable installs rewrote the tracked qp/_version.py every time. Live Protoss uploads that hit ProteinsPlus outages failed CI after long retries; skip those tests instead and fail fast in CI. Co-authored-by: Cursor <cursoragent@cursor.com> * Enhance charge computation for sugar and add new test cases * Stop skipping Protoss ValueError and refresh 2chb charge golden. Keep real Protoss job failures as test failures, and update 2chb charges for the N-terminus valence fix. Co-authored-by: Cursor <cursoragent@cursor.com> --------- Co-authored-by: Cursor <cursoragent@cursor.com>
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Description
This will include a function where the used can obtain the indices of the backbone atoms in the cluster. I have also included an example of what this will look like in examples/
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