openprotein-python 0.8.2__1-py3-none-any.whl

openprotein_python-0.8.2.dist-info/METADATA

@@ -0,0 +1,176 @@
+Metadata-Version: 2.4
+Name: openprotein-python
+Version: 0.8.2
+Summary: OpenProtein Python interface.
+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: Programming Language :: Python :: 3
+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/)
+[![Coverage](https://dev.docs.openprotein.ai/api-python/_images/coverage.svg)](https://pypi.org/project/openprotein-python/)
+[![Conda version](https://anaconda.org/openprotein/openprotein-python/badges/version.svg)](https://anaconda.org/openprotein/openprotein-python)
+
+
+# openprotein-python
+The OpenProtein.AI Python Interface provides a user-friendly library to interact with the OpenProtein.AI REST API, enabling various tasks related to protein analysis and modeling.
+
+
+
+# Table of Contents
+
+|   | Workflow                                           | Description                                          |
+|---|----------------------------------------------------|------------------------------------------------------|
+| 0 | [`Quick start`](#Quick-start)                    | Quick start guide                     |
+| 1 | [`Installation`](https://docs.openprotein.ai/api-python/installation.html)                    | Install guide for pip and conda.                     |
+| 2 | [`Session management`](https://docs.openprotein.ai/api-python/overview.html)        | An overview of the OpenProtein Python Client & the asynchronous jobs system. |
+| 3 | [`Asssay-based Sequence Learning`](https://docs.openprotein.ai/api-python/core_workflow.html) | Covers core tasks such as data upload, model training & prediction, and sequence design. |
+| 4 | [`De Novo prediction & generative models (PoET)`](https://docs.openprotein.ai/api-python/poet_workflow.html) | Covers PoET, a protein LLM for *de novo* scoring, as well as sequence generation. |
+| 5 | [`Protein Language Models & Embeddings`](https://docs.openprotein.ai/api-python/embedding_workflow.html) | Covers methods for creating sequence embeddings with proprietary & open-source models. |
+
+
+# Quick-start
+
+Get started with our quickstart README! You can peruse the [official documentation](https://docs.openprotein.ai/api-python/) for more details!
+## Installation 
+
+To install the python interface using pip, run the following command: 
+```
+pip install openprotein-python
+```
+
+or with conda:
+```
+conda install -c openprotein openprotein-python
+```
+
+### Requirements
+
+- Python 3.8 or higher.
+- pydantic version 1.0 or newer.
+- requests version 2.0 or newer.
+- tqdm version 4.0 or newer.
+- pandas version 1.0 or newer.
+
+# Getting started
+
+
+Read on below for the quick-start guide, or see the [docs](https://docs.openprotein.ai/api-python/) for more information!
+
+To begin, create a session using your login credentials.
+```
+import openprotein
+
+# replace USERNAME and PASSWORD with your actual login credentials
+session = openprotein.connect(USERNAME, PASSWORD)
+```
+## Job Status
+
+The interface offers `AsyncJobFuture` objects for asynchronous calls, allowing tracking of job status and result retrieval when ready. Given a future, you can check its status and retrieve results.
+
+### Checking Job Status
+Check the status of an `AsyncJobFuture` using the following methods:
+```
+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
+```
+
+### Retrieving Job Results
+Once the job has finished, retrieve the results using the following methods:
+```
+result = future.wait()     # wait until done and then fetch results
+
+#verbosity is controlled with verbose arg
+result = future.get(verbose=True)  # get the result from a finished job
+```
+
+## Jobs Interface
+
+### Listing Jobs
+To view all jobs associated with each session, the following method is available, providing an option to filter results by date, job type, or status.
+```
+session.jobs.list() 
+```
+
+### Retrieving Specific Job
+For detailed information about a particular job, use the following command with the corresponding job ID:
+``` 
+session.jobs.get(JOB_ID)  # Replace JOB_ID with the ID of the specific job to be retrieved
+```
+
+### Resuming Jobs
+Jobs from prior workflows can be resumed using the load_job method provided by each API. 
+```
+session.load_job(JOB_ID)  # Replace JOB_ID with the ID of the training job to resume
+```
+
+## PoET interface
+The PoET Interface allows scoring, generating, and retrieving sequences using the PoET model.
+
+### Scoring Sequences
+To score sequences, use the score function. Provide a prompt and a list of queries. The results will be a list of (sequence, score) pydantic objects.
+
+```
+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
+```
+
+### Scoring Single Site Variants
+For scoring single site variants, use the `single_site function`, providing the original sequence and setting `prompt_is_seed` to True if the prompt is a seed sequence.
+```
+sequence = "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN"
+future = session.poet.single_site(prompt, sequence, prompt_is_seed=True) 
+result = future.wait()
+# result is a dictionary of {variant: score}
+```
+
+### Generating Sequences
+To generate sequences from the PoET model, use the `generate` function with relevant parameters. The result will be a list of generated samples.
+```
+future = session.poet.generate(
+    prompt,
+    max_seqs_from_msa=1024,
+    num_samples=100,
+    temperature=1.0,
+    topk=15
+)
+samples = future.wait()
+```
+
+### Retrieving Input Sequences
+You can retrieve the prompt, MSA, or seed sequences for a PoET job using the `get_input` function or the individual functions for each type.
+```
+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/)

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openprotein_python-0.8.2.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any

openprotein_python-0.8.2.dist-info/licenses/LICENSE.txt

@@ -0,0 +1,30 @@
+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.