molstar-cli 0.0.1__py3-none-any.whl

molstar_cli-0.0.1.dist-info/METADATA

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+Metadata-Version: 2.5
+Name: molstar-cli
+Version: 0.0.1
+Summary: Open local structure and map files (mmCIF, PDB, EMDB maps, ...) in the Mol* viewer from the command line
+Project-URL: Homepage, https://github.com/aozalevsky/molstar_cli
+Project-URL: Issues, https://github.com/aozalevsky/molstar_cli/issues
+Project-URL: Mol*, https://molstar.org
+Author: Arthur Zalevsky
+License-Expression: MIT
+License-File: LICENSE
+License-File: molstar_cli/static/molstar/LICENSE.molstar
+Keywords: cryo-em,emdb,mmcif,mol*,molecular visualization,molstar,pdb,viewer
+Classifier: Environment :: Console
+Classifier: Environment :: Web Environment
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+
+# molstar-cli
+
+Open local structure and map files in the [Mol*](https://molstar.org) viewer from the terminal.
+
+```console
+$ pip install molstar-cli
+$ molstar 5me2.cif emd_3488.map.gz
+Mol* viewer: http://127.0.0.1:34037/MtXDcbb3cYRnGhsxczKvZw/
+Press Ctrl-C to stop.
+```
+
+All files open together in one Mol* scene in your default browser — e.g. a model fitted
+into its cryo-EM map. The Mol* viewer is bundled, so it works offline; there are no
+dependencies beyond Python ≥ 3.10.
+
+## Usage
+
+```
+molstar FILE [FILE ...] [-p PORT] [--no-browser]
+```
+
+```console
+$ molstar *.cif                      # several structures, one scene
+$ molstar model.cif emd_1234.map.gz  # model + EMDB map
+$ molstar PDBDEV_00000001.cif        # integrative (IHM) models, incl. coarse-grained beads
+```
+
+The command keeps serving while you look at the structures; stop it with Ctrl-C.
+Reloading the browser tab re-reads the files from disk.
+
+| Option | |
+|---|---|
+| `-p`, `--port PORT` | listen on a fixed port instead of a random free one |
+| `--no-browser` | only print the URL |
+| `-V`, `--version` | print the molstar-cli and bundled Mol* versions |
+
+### Supported formats
+
+Anything Mol*'s *Open Files* dialog accepts, detected by file extension, optionally
+wrapped in `.gz` or `.zip`:
+
+- **Structures:** mmCIF / PDBx (`.cif`, `.mmcif`, `.mcif`) including IHM integrative
+  models, BinaryCIF (`.bcif`), PDB (`.pdb`, `.ent`), PDBQT, PQR, GRO, XYZ, SDF / MOL /
+  MOL2, LAMMPS data/dump
+- **Volumes:** CCP4 / MRC / MAP (`.map`, `.mrc`, `.ccp4` — EMDB maps), DSN6 / BRIX,
+  DX, Cube, density server CIF, MTZ
+- **Trajectories and topologies:** DCD, XTC, TRR, NetCDF, PSF, PRMTOP, TOP
+- **Other:** PLY / OBJ meshes, MolViewSpec (`.mvsj`, `.mvsx`), Mol* sessions (`.molj`, `.molx`)
+
+Unsupported files are skipped with a warning in the Mol* log panel.
+
+Maps open at Mol*'s default isovalue (2σ) — the EMDB-recommended contour level is not
+stored in the map file. Adjust it in the Volume panel on the right.
+
+### Remote machines
+
+With `--no-browser`, or on a Linux machine without a display (e.g. over SSH), `molstar`
+doesn't start a browser; it prints an `ssh -L` command instead:
+
+```console
+server$ molstar model.cif
+Mol* viewer: http://127.0.0.1:41235/Xy.../
+On a remote machine? Run `ssh -L 41235:127.0.0.1:41235 server` on your computer, then open the URL above there.
+Press Ctrl-C to stop.
+```
+
+Use `--port` to keep the same forwarded port between runs.
+
+### Security
+
+The server listens on `127.0.0.1` only, every URL carries a random token, and only the
+files named on the command line can be read — no directory listing, no other paths.
+
+## Development
+
+```console
+$ python -m venv .venv && .venv/bin/pip install -e . pytest
+$ .venv/bin/pytest
+```
+
+### Updating the bundled Mol*
+
+The prebuilt viewer from the [`molstar` npm package](https://www.npmjs.com/package/molstar)
+is vendored in `molstar_cli/static/molstar/` (no Node.js needed):
+
+```console
+$ python scripts/update_molstar.py 5.11.0
+```
+
+Check that it loads, then commit the result.
+
+### Releasing
+
+Create a GitHub release with a tag like `v0.0.2`. The package version is taken from the
+tag, so there is nothing to bump. The *Publish to PyPI* workflow builds and uploads it
+using [trusted publishing](https://docs.pypi.org/trusted-publishers/) (PyPI publisher:
+owner `aozalevsky`, repository `molstar_cli`, workflow `publish.yml`, environment `pypi`).
+
+## Citing Mol*
+
+If you use Mol* in your work, please cite:
+
+> D. Sehnal, S. Bittrich, M. Deshpande, R. Svobodová, K. Berka, V. Bazgier, S. Velankar,
+> S.K. Burley, J. Koča, A.S. Rose. Mol* Viewer: modern web app for 3D visualization and
+> analysis of large biomolecular structures. *Nucleic Acids Research* 49(W1), W431–W437
+> (2021). [doi:10.1093/nar/gkab314](https://doi.org/10.1093/nar/gkab314)
+
+## License
+
+MIT. The bundled Mol* viewer is © Mol* contributors, also MIT —
+see [`LICENSE.molstar`](molstar_cli/static/molstar/LICENSE.molstar).

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molstar_cli-0.0.1.dist-info/WHEEL

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+Generator: hatchling 1.32.4
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+Tag: py3-none-any

molstar_cli-0.0.1.dist-info/entry_points.txt

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+[console_scripts]
+molstar = molstar_cli.cli:main

molstar_cli-0.0.1.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 Arthur Zalevsky
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

molstar_cli-0.0.1.dist-info/licenses/molstar_cli/static/molstar/LICENSE.molstar

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+The MIT License
+
+    Copyright (c) 2017 - now, Mol* contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.