physistool 0.1.0__tar.gz

physistool-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 MorphoComputing
+
+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.

physistool-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: physistool
+Version: 0.1.0
+Summary: Open-source PhysisFold client — CLI + SDK for constraint-guided all-atom protein folding via a remote (Nitro Enclave) endpoint.
+Author: MorphoComputing
+License: MIT
+Project-URL: Homepage, https://physisfold.com
+Keywords: protein,folding,structure,bioinformatics,physisfold
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cryptography>=41
+Dynamic: license-file
+
+# physistool
+
+The open-source **PhysisFold client** — a thin, auditable CLI + SDK that speaks
+HTTP+JSON to a remote PhysisFold folding endpoint (the engine runs server-side
+inside an AWS Nitro Enclave; there is no protected IP in this package).
+
+`physistool` is the umbrella command: `physistool fold ...` today, with sibling
+verbs (engineer, msa, search, ...) joining the same command as more tools ship.
+
+## Install
+
+```
+pip install physistool
+```
+
+## SDK
+
+The pip package is `physistool`; the import module is `physis` (scikit-learn ->
+sklearn convention).
+
+```python
+from physis import fold, FoldError
+
+try:
+    report = fold("input.fasta", out_path="result.pdb",
+                  endpoint="http://127.0.0.1:8787")
+except FoldError as e:
+    ...
+```
+
+## CLI
+
+```
+physistool fold input.fasta --out result.pdb --endpoint http://127.0.0.1:8787
+# equivalently, the flat flag surface:
+physistool --sequence input.fasta --out result.pdb
+```
+
+Run `physistool --help` for the full flag set (best-of seeds, helix prior,
+Stage-C `--encrypt`, metering, attestation `--expected-pcr0`, ...).
+
+## Security model
+
+Before any input leaves your machine the client fetches and **verifies** the
+endpoint's AWS Nitro attestation (signature chain to the pinned Nitro root +
+published PCR0) and only then trusts the enclave public key. See the module
+docstrings in `physis/attestation.py` and `physis/envelope.py`.
+
+## License
+
+MIT. See `LICENSE`.

physistool-0.1.0/README.md

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+# physistool
+
+The open-source **PhysisFold client** — a thin, auditable CLI + SDK that speaks
+HTTP+JSON to a remote PhysisFold folding endpoint (the engine runs server-side
+inside an AWS Nitro Enclave; there is no protected IP in this package).
+
+`physistool` is the umbrella command: `physistool fold ...` today, with sibling
+verbs (engineer, msa, search, ...) joining the same command as more tools ship.
+
+## Install
+
+```
+pip install physistool
+```
+
+## SDK
+
+The pip package is `physistool`; the import module is `physis` (scikit-learn ->
+sklearn convention).
+
+```python
+from physis import fold, FoldError
+
+try:
+    report = fold("input.fasta", out_path="result.pdb",
+                  endpoint="http://127.0.0.1:8787")
+except FoldError as e:
+    ...
+```
+
+## CLI
+
+```
+physistool fold input.fasta --out result.pdb --endpoint http://127.0.0.1:8787
+# equivalently, the flat flag surface:
+physistool --sequence input.fasta --out result.pdb
+```
+
+Run `physistool --help` for the full flag set (best-of seeds, helix prior,
+Stage-C `--encrypt`, metering, attestation `--expected-pcr0`, ...).
+
+## Security model
+
+Before any input leaves your machine the client fetches and **verifies** the
+endpoint's AWS Nitro attestation (signature chain to the pinned Nitro root +
+published PCR0) and only then trusts the enclave public key. See the module
+docstrings in `physis/attestation.py` and `physis/envelope.py`.
+
+## License
+
+MIT. See `LICENSE`.

physistool-0.1.0/physis/__init__.py

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+"""``physis`` — the open-source PhysisFold client (CLI + SDK).
+
+This is what the customer installs and runs. It speaks HTTP+JSON to a remote
+PhysisFold folding endpoint (see ``PhysisFold/enclave/CONTRACT.md``). There is no
+protected IP here: the engine lives server-side (inside the enclave); this
+package is a thin, auditable client.
+
+SDK surface
+-----------
+    from physis import fold, FoldError
+
+``fold(...)`` is the programmatic entry point (see its docstring for the full
+parameter set). ``FoldError`` is raised on any transport failure or ``ok:false``
+server response.
+
+CLI
+---
+Installed by ``pip install physistool`` as the ``physistool`` console script
+(the import module stays ``physis``, like scikit-learn -> sklearn)::
+
+    physistool fold input.fasta --out result.pdb --endpoint http://127.0.0.1:8787
+    # or the flat flag surface:
+    physistool --sequence input.fasta --out result.pdb
+"""
+
+from __future__ import annotations
+
+from .physis_client import FoldError, fold
+
+__all__ = ["fold", "FoldError"]
+
+__version__ = "0.1.0"