openprotein-python 0.4.1__tar.gz → 0.8.0__tar.gz

openprotein_python-0.8.0/.gitignore

@@ -0,0 +1,365 @@
+
+# SECRETS FILE
+secrets.config
+poetry.lock
+/htmlcov
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+
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+
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+develop-eggs/
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+
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+
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+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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+# Environments
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+.venv
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+.mypy_cache/
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+dmypy.json
+
+# Pyre type checker
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+
+/.quarto/
+poet_demo.ipynb
+*chorismate_mutase_combined_seqs.fasta
+
+nohup.out
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+notebooks
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+
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+lib/
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+parts/
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+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
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+
+# Installer logs
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+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
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+
+# Sphinx documentation
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+
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+target/
+
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+
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+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
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+
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+
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+
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+*.sage.py
+
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+.env
+.envrc
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+ENV/
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+
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+
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+
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+/site
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+
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+/data/

{openprotein_python-0.4.1 → openprotein_python-0.8.0}/PKG-INFO

@@ -1,24 +1,19 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: openprotein-python
-Version: 0.4.1
+Version: 0.8.0
 Summary: OpenProtein Python interface.
-Home-page: https://docs.openprotein.ai/
-License: MIT
-Author: OpenProtein
-Author-email: info@ne47.bio
-Requires-Python: >=3.8,<4.0
+Author-email: Mark Gee <markgee@ne47.bio>, "Timothy Truong Jr." <ttruong@ne47.bio>, Tristan Bepler <tbepler@ne47.bio>
+License-Expression: MIT
+License-File: LICENSE.txt
 Classifier: Development Status :: 4 - Beta
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3
-Requires-Dist: pandas (>=1)
-Requires-Dist: pydantic (>=1)
-Requires-Dist: requests (>=2)
-Requires-Dist: tqdm (>=4)
+Requires-Python: >=3.10
+Requires-Dist: gemmi<0.8,>=0.7.0
+Requires-Dist: numpy<3,>=1.9
+Requires-Dist: pandas<3,>=2.2.2
+Requires-Dist: pydantic<3,>=2.5
+Requires-Dist: requests<3,>=2.32.3
+Requires-Dist: tqdm<5,>=4.66.5
 Description-Content-Type: text/markdown
 
 [![PyPI version](https://badge.fury.io/py/openprotein-python.svg)](https://pypi.org/project/openprotein-python/)

{openprotein_python-0.4.1 → openprotein_python-0.8.0}/README.md

@@ -155,4 +155,4 @@ future.get_msa()
 future.get_seed()
 ```
 
-See more at our [Homepage](https://docs.openprotein.ai/)
+See more at our [Homepage](https://docs.openprotein.ai/)

openprotein_python-0.8.0/openprotein/__init__.py

@@ -0,0 +1,153 @@
+"""
+OpenProtein Python client.
+
+A pythonic interface for interacting with our cutting-edge protein engineering platform.
+
+isort:skip_file
+"""
+
+from typing import TYPE_CHECKING
+import warnings
+
+from openprotein._version import __version__
+from openprotein.data import DataAPI
+from openprotein.errors import DeprecationError
+from openprotein.jobs import JobsAPI
+from openprotein.align import AlignAPI
+from openprotein.prompt import PromptAPI
+from openprotein.embeddings import EmbeddingsAPI
+from openprotein.fold import FoldAPI
+from openprotein.svd import SVDAPI
+from openprotein.umap import UMAPAPI
+from openprotein.predictor import PredictorAPI
+from openprotein.design import DesignAPI
+from openprotein.jobs import Future
+from openprotein.base import APISession
+
+
+class OpenProtein(APISession):
+    """
+    The base class for accessing OpenProtein API functionality.
+    """
+
+    _data = None
+    _jobs = None
+    _align = None
+    _prompt = None
+    _embeddings = None
+    _svd = None
+    _umap = None
+    _fold = None
+    _predictor = None
+    _design = None
+
+    def wait(self, future: Future, *args, **kwargs):
+        return future.wait(*args, **kwargs)
+
+    wait_until_done = wait
+
+    def load_job(self, job_id):
+        return self.jobs.get(job_id=job_id)
+
+    @property
+    def data(self) -> DataAPI:
+        """
+        The data submodule gives access to functionality for uploading and accessing user data.
+        """
+        if self._data is None:
+            self._data = DataAPI(self)
+        return self._data
+
+    @property
+    def jobs(self) -> JobsAPI:
+        """
+        The jobs submodule gives access to functionality for listing jobs and checking their status.
+        """
+        if self._jobs is None:
+            self._jobs = JobsAPI(self)
+        return self._jobs
+
+    @property
+    def align(self) -> AlignAPI:
+        """
+        The Align submodule gives access to the sequence alignment capabilities by building MSAs and prompts that can be used with PoET.
+        """
+        if self._align is None:
+            self._align = AlignAPI(self)
+        return self._align
+
+    @property
+    def prompt(self) -> PromptAPI:
+        """
+        The Align submodule gives access to the sequence alignment capabilities by building MSAs and prompts that can be used with PoET.
+        """
+        if self._prompt is None:
+            self._prompt = PromptAPI(self)
+        return self._prompt
+
+    @property
+    def embedding(self) -> EmbeddingsAPI:
+        """
+        The embedding submodule gives access to protein embedding models and their inference endpoints.
+        """
+        if self._embeddings is None:
+            self._embeddings = EmbeddingsAPI(self)
+        return self._embeddings
+
+    embeddings = embedding
+
+    @property
+    def svd(self) -> SVDAPI:
+        """
+        The embedding submodule gives access to protein embedding models and their inference endpoints.
+        """
+        if self._svd is None:
+            self._svd = SVDAPI(
+                session=self,
+            )
+        return self._svd
+
+    @property
+    def umap(self) -> UMAPAPI:
+        """
+        The embedding submodule gives access to protein embedding models and their inference endpoints.
+        """
+        if self._umap is None:
+            self._umap = UMAPAPI(
+                session=self,
+            )
+        return self._umap
+
+    @property
+    def predictor(self) -> PredictorAPI:
+        """
+        The predictor submodule gives access to training and predicting with predictors built on top of embeddings.
+        """
+        if self._predictor is None:
+            self._predictor = PredictorAPI(
+                session=self,
+            )
+        return self._predictor
+
+    @property
+    def design(self) -> DesignAPI:
+        """
+        The designer submodule gives access to functionality for designing new sequences using models from predictor train.
+        """
+        if self._design is None:
+            self._design = DesignAPI(
+                session=self,
+            )
+        return self._design
+
+    @property
+    def fold(self) -> FoldAPI:
+        """
+        The fold submodule gives access to functionality for folding sequences and returning PDBs.
+        """
+        if self._fold is None:
+            self._fold = FoldAPI(self)
+        return self._fold
+
+
+connect = OpenProtein

{openprotein_python-0.4.1 → openprotein_python-0.8.0}/openprotein/_version.py

@@ -1,10 +1,9 @@
 try:
     from importlib.metadata import version
 except ModuleNotFoundError:
-    from importlib_metadata import version # py37
+    from importlib_metadata import version  # type: ignore - py37
 
 try:
     __version__ = version("openprotein-python")
-except: 
+except:
     __version__ = "None"
-

openprotein_python-0.8.0/openprotein/align/__init__.py

@@ -0,0 +1,8 @@
+"""
+Align module for creating and searching alignments on OpenProtein.
+
+isort:skip_file
+"""
+
+from .msa import MSAFuture
+from .align import AlignAPI