PyMOL plugin, in-memory structure input, and the 2.2.0 release

[bobbypaton]

The visual side of wSterimol, brought over to DBSTEP as a PyMOL plugin, plus the version bump so 2.2.0 ships together with the legacy-gap features from #58.

PyMOL plugin (dbstep/pymol_plugin.py)

Install dbstep into PyMOL's Python, then import dbstep.pymol_plugin (or run .../pymol_plugin.py; python -m dbstep.pymol_plugin prints the path). Commands take PyMOL selections and draw on the open object:

• dbstep_sterimol atom1, atom2 [, atom3, radii, measure, selection, name]: L axis and Bmin/Bmax circles plus direction cylinders, in the object's own frame.
• dbstep_vbur atom1 [, radius, radii, selection, decompose=1]: translucent sphere; residue contributions written to B-factors and coloured white to red. selection="polymer and not resi 45" gives the exclude-self, no-water pocket measurement (atoms named as atom1 outside the selection become zero-radius ghosts).
• dbstep_cone metal [, ligand, radii=cpk]: translucent cone of the Tolman angle, centroid pseudoatom and distance object, Sterimol axes of the ligand.
• dbstep_vdw object [, radii, scale]: the Add_VDW equivalent, using radii.for_atoms so CPK atom typing is shared with the CLI.
• dbstep_ensemble files, atom1, atom2 [, radii, temperature, window, vbur]: Boltzmann weighting over QM outputs or a multi-structure file; conformers loaded with populations as titles, minor conformers faded by transparency. Formats PyMOL cannot read (e.g. .out.gz) are loaded from the measured coordinates.
• dbstep_conformers folder, dbstep_style.

Package changes that make this possible

• parse_data.Structure + from_coords(atoms, coords, name, metadata, **kwargs): in-memory input through the normal parser path; metadata arrays enable --decompose (tested equal to the PDB residue route).
• run.aligned_coords, run.sterimol_vectors() and calculator.rigid_transform (Kabsch) recover the rigid map from DBSTEP's aligned frame back to the input coordinates, so drawings land on the loaded structure instead of a transformed copy.
• dbstep.radii, dbstep.cone and dbstep.ensemble are now exported from the package namespace.

Testing

• tests/test_pymol_plugin.py runs the plugin against headless open-source PyMOL (pymol-open-source from PyPI, new optional extra pymol, wheels for 3.9 to 3.13; the extra carries a python_version < '3.14' marker and the tests skip when PyMOL is absent). CI installs the extra. Checks: Sterimol values and the drawn L axis against the CLI, %V_bur and contributions equal to --residue A:3 --decompose, the selection route equal to --exclude-self --nowater --nohet, the legacy 173.97° cone angle, CPK radii on the vdW copy, ensemble loading and titles, error handling.
• tests/test_from_coords.py covers the in-memory route and the transform.
• Full suite: 420 passed, 2 skipped; ruff clean.

Release

__version__ and meta.yaml bumped to 2.2.0; CHANGELOG has the 2.2.0 section covering #57, #58 and this PR. After merging, publish a GitHub Release with tag 2.2.0 and the release workflow uploads to PyPI.

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📒 Files selected for processing (14)

• .github/workflows/ci.yml
• CHANGELOG.md
• CLAUDE.md
• README.md
• dbstep/Dbstep.py
• dbstep/__init__.py
• dbstep/calculator.py
• dbstep/parse_data.py
• dbstep/pymol_plugin.py
• dbstep/radii.py
• meta.yaml
• pyproject.toml
• tests/test_from_coords.py
• tests/test_pymol_plugin.py

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