openprotein-python 0.1.1b4__tar.gz

openprotein_python-0.1.1b4/LICENSE.txt

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+Copyright (c) 2021-2023, OpenProtein.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+
+    * Redistributions in binary form must reproduce the above
+       copyright notice, this list of conditions and the following
+       disclaimer in the documentation and/or other materials provided
+       with the distribution.
+
+    * Neither the name of the OPenProtein Developers nor the names of any
+       contributors may be used to endorse or promote products derived
+       from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

openprotein_python-0.1.1b4/PKG-INFO

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+Metadata-Version: 2.1
+Name: openprotein-python
+Version: 0.1.1b4
+Summary: OpenProtein Python interface.
+Home-page: https://docs.openprotein.ai/
+License: MIT
+Author: OpenProtein
+Author-email: info@ne47.bio
+Requires-Python: >=3.7,<4.0
+Classifier: Development Status :: 4 - Beta
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+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 (>=1.2,<2.0)
+Requires-Dist: pydantic (>=1.8,<2.0)
+Requires-Dist: requests (>=2.25,<3.0)
+Requires-Dist: tqdm (>=4.61,<5.0)
+Description-Content-Type: text/markdown
+
+# openprotein-python
+Python interface for the OpenProtein.AI REST API.
+
+## Installation 
+
+You can install with pip: 
+
+```
+pip install openprotein-python
+```
+## Getting started
+
+First, create a session using your login credentials.
+```
+import openprotein
+session = openprotein.connect(USERNAME, PASSWORD)
+```
+
+Async calls return `AsyncJobFuture` objects that allow tracking the status of the job and retrieving the result when it's ready.
+
+Given a future, check its status and retrieve results
+```
+future.refresh() # call the backend to update the job status
+future.done() # returns True if the job is done, meaning the status could be SUCCESS, FAILED, or CANCELLED
+future.wait() # wait until done and then fetch results, verbosity is controlled with verbose arg.
+result = future.get() # get the result from a finished job
+```
+
+
+### Jobs interface
+
+List your jobs, optionally filtered by date, job type, and status.
+```
+session.jobs.list() # list all jobs
+session.jobs.get(JOB_ID) # get a specific job
+```
+
+Resume an `AsyncJobFuture` from where you left off with each API's load_job:
+
+For example for training jobs:
+
+```
+session.train.load_job(JOB_ID)
+```
+### PoET interface
+
+Score sequences using the PoET interface.
+```
+prompt_seqs = b'MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN'
+
+prompt = session.poet.upload_prompt(prompt_seqs)
+```
+
+```
+queries = [
+    b'MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN',
+    b'MALWMRLLPLLVLLALWGPDPASAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN',
+    b'MALWTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEGPQVGALELAGGPGAGGLEGPPQKRGIVEQCCASVCSLYQLENYCN',
+    b'MALWIRSLPLLALLVFSGPGTSYAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDVEQPLVSSPLRGEAGVLPFQQEEYEKVKRGIVEQCCHNTCSLYQLENYCN',
+    b'MALWMRLLPLLALLALWAPAPTRAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEDLQVRDVELAGAPGEGGLQPLALEGALQKRGIVEQCCTSICSLYQLENYCN',
+]
+```
+
+```
+future = session.poet.score(prompt, queries)
+result = future.wait()
+# result is a list of (sequence, score) pydantic objects
+```
+
+Score single site variants using the PoET interface.
+```
+sequence = "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
+future = session.poet.single_site(prompt, sequence, prompt_is_seed=True) 
+result = future.wait()
+# result is a dictionary of {variant: score}
+```
+
+Generate sequences from the PoET model.
+```
+
+future = session.poet.generate(
+    prompt,
+    max_seqs_from_msa=1024,
+    num_samples=100,
+    temperature=1.0,
+    topk=15
+)
+samples = future.wait()
+```
+
+Retrieve the prompt, MSA, or input (seed) sequences for a PoET job.
+```
+future.get_input(INPUT_TYPE)
+# or, functions for each type
+future.get_prompt()
+future.get_msa()
+future.get_seed()
+```
+
+See more at our [Homepage](https://docs.openprotein.ai/)

openprotein_python-0.1.1b4/README.md

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+# openprotein-python
+Python interface for the OpenProtein.AI REST API.
+
+## Installation 
+
+You can install with pip: 
+
+```
+pip install openprotein-python
+```
+## Getting started
+
+First, create a session using your login credentials.
+```
+import openprotein
+session = openprotein.connect(USERNAME, PASSWORD)
+```
+
+Async calls return `AsyncJobFuture` objects that allow tracking the status of the job and retrieving the result when it's ready.
+
+Given a future, check its status and retrieve results
+```
+future.refresh() # call the backend to update the job status
+future.done() # returns True if the job is done, meaning the status could be SUCCESS, FAILED, or CANCELLED
+future.wait() # wait until done and then fetch results, verbosity is controlled with verbose arg.
+result = future.get() # get the result from a finished job
+```
+
+
+### Jobs interface
+
+List your jobs, optionally filtered by date, job type, and status.
+```
+session.jobs.list() # list all jobs
+session.jobs.get(JOB_ID) # get a specific job
+```
+
+Resume an `AsyncJobFuture` from where you left off with each API's load_job:
+
+For example for training jobs:
+
+```
+session.train.load_job(JOB_ID)
+```
+### PoET interface
+
+Score sequences using the PoET interface.
+```
+prompt_seqs = b'MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN'
+
+prompt = session.poet.upload_prompt(prompt_seqs)
+```
+
+```
+queries = [
+    b'MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN',
+    b'MALWMRLLPLLVLLALWGPDPASAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN',
+    b'MALWTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEGPQVGALELAGGPGAGGLEGPPQKRGIVEQCCASVCSLYQLENYCN',
+    b'MALWIRSLPLLALLVFSGPGTSYAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDVEQPLVSSPLRGEAGVLPFQQEEYEKVKRGIVEQCCHNTCSLYQLENYCN',
+    b'MALWMRLLPLLALLALWAPAPTRAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEDLQVRDVELAGAPGEGGLQPLALEGALQKRGIVEQCCTSICSLYQLENYCN',
+]
+```
+
+```
+future = session.poet.score(prompt, queries)
+result = future.wait()
+# result is a list of (sequence, score) pydantic objects
+```
+
+Score single site variants using the PoET interface.
+```
+sequence = "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
+future = session.poet.single_site(prompt, sequence, prompt_is_seed=True) 
+result = future.wait()
+# result is a dictionary of {variant: score}
+```
+
+Generate sequences from the PoET model.
+```
+
+future = session.poet.generate(
+    prompt,
+    max_seqs_from_msa=1024,
+    num_samples=100,
+    temperature=1.0,
+    topk=15
+)
+samples = future.wait()
+```
+
+Retrieve the prompt, MSA, or input (seed) sequences for a PoET job.
+```
+future.get_input(INPUT_TYPE)
+# or, functions for each type
+future.get_prompt()
+future.get_msa()
+future.get_seed()
+```
+
+See more at our [Homepage](https://docs.openprotein.ai/)

openprotein_python-0.1.1b4/openprotein_python/__init__.py

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+from openprotein._version import __version__
+
+from openprotein.base import APISession
+from openprotein.api.jobs import JobsAPI, Job
+from openprotein.api.data import DataAPI
+from openprotein.api.poet import PoetAPI
+from openprotein.api.embedding import EmbeddingAPI
+from openprotein.api.train import TrainingAPI
+from openprotein.api.design import DesignAPI
+from openprotein.api.predict import PredictAPI
+class OpenProtein(APISession):
+    """
+    The base class for accessing OpenProtein API functionality.
+    """
+
+    def wait(self, job: Job, *args, **kwargs):
+        return job.wait(self, *args, **kwargs)
+    
+    wait_until_done = wait
+
+    @property
+    def jobs(self):
+        """
+        The jobs submodule gives access to functionality for listing jobs and checking their status.
+        """
+        return JobsAPI(self)
+    
+    @property
+    def data(self):
+        """
+        The data submodule gives access to functionality for uploading and accessing user data. 
+        """
+        return DataAPI(self)
+    
+    @property 
+    def train(self):
+        """
+        The train submodule gives access to functionality for training and validating ML models. 
+        """
+        return TrainingAPI(self)
+
+    @property
+    def poet(self):
+        """
+        The PoET submodule gives access to the PoET generative model and MSA and prompt creation interfaces.
+        """
+        return PoetAPI(self)
+    
+    @property
+    def embedding(self):
+        """
+        The embedding submodule gives access to protein embedding models and their inference endpoints.
+        """
+        return EmbeddingAPI(self)
+
+    @property 
+    def predict(self):
+        """
+        The predict submodule gives access to sequence predictions using models from train. 
+        """
+        return PredictAPI(self)
+    
+    @property
+    def design(self):
+        """
+        The design submodule gives access to functionality for designing new sequences using models from train. 
+        """
+        return DesignAPI(self)
+
+connect = OpenProtein

openprotein_python-0.1.1b4/openprotein_python/_version.py

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+__version_tuple__ = version_tuple = (0, 1, 1, 'b3')
+__version__ = version = '.'.join(str(x) for x in __version_tuple__)

openprotein_python-0.1.1b4/openprotein_python/api/__init__.py

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+from . import data 
+from . import design
+from . import train 
+from . import predict
+from . import poet 
+from . import embedding