From 2e80d172f52f2a84f22eea5e1d4fe24d180b5d81 Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Sun, 26 Oct 2025 15:15:17 +0000 Subject: [PATCH 1/2] fix links --- mise.dev.toml | 1 + mise.toml | 2 +- source/python-api/api-reference/embedding.rst | 2 +- source/python-api/foundation-models/SVD-embeddings.ipynb | 2 +- source/python-api/foundation-models/attention-maps.ipynb | 2 +- source/python-api/foundation-models/logits.ipynb | 2 +- source/python-api/poet/creating-MSA.ipynb | 6 +++--- source/python-api/poet/scoring-sequences.ipynb | 4 ++-- source/python-api/poet/single-site-analysis.ipynb | 5 ++--- 9 files changed, 13 insertions(+), 13 deletions(-) diff --git a/mise.dev.toml b/mise.dev.toml index 305f044..a728c46 100644 --- a/mise.dev.toml +++ b/mise.dev.toml @@ -4,3 +4,4 @@ _.python.venv = ".pixi/envs/dev" [tools] dprint = "latest" +pandoc = "latest" diff --git a/mise.toml b/mise.toml index 64dfb9f..2794511 100644 --- a/mise.toml +++ b/mise.toml @@ -3,4 +3,4 @@ pandoc = "latest" pixi = "latest" [env] -# _.python.venv = ".pixi/envs/default" +_.python.venv = ".pixi/envs/default" diff --git a/source/python-api/api-reference/embedding.rst b/source/python-api/api-reference/embedding.rst index 40cfc37..2740765 100644 --- a/source/python-api/api-reference/embedding.rst +++ b/source/python-api/api-reference/embedding.rst @@ -3,7 +3,7 @@ openprotein.embeddings Create embeddings for your protein sequences using open-source and proprietary models! -Note that for PoET Models, you will also need to utilize our :doc:`align `. workflow. +Note that for PoET Models, you will also need to utilize our :doc:`align ` workflow. Interface --------- diff --git a/source/python-api/foundation-models/SVD-embeddings.ipynb b/source/python-api/foundation-models/SVD-embeddings.ipynb index 8b7aed1..75477fb 100644 --- a/source/python-api/foundation-models/SVD-embeddings.ipynb +++ b/source/python-api/foundation-models/SVD-embeddings.ipynb @@ -207,7 +207,7 @@ "source": [ "## Next steps\n", "\n", - "For more information, visit the [Embeddings API](https://docs.openprotein.ai/api-python/embedding.html) reference." + "For more information, visit the [Embeddings API](../api-reference/embedding.html) reference." ] } ], diff --git a/source/python-api/foundation-models/attention-maps.ipynb b/source/python-api/foundation-models/attention-maps.ipynb index 3ef7ef4..fc345c8 100644 --- a/source/python-api/foundation-models/attention-maps.ipynb +++ b/source/python-api/foundation-models/attention-maps.ipynb @@ -180,7 +180,7 @@ "source": [ "## Next steps\n", "\n", - "For more information, visit the [Embeddings API](https://docs.openprotein.ai/api-python/embedding.html) reference." + "For more information, visit the [Embeddings API](../api-reference/embedding.html) reference." ] } ], diff --git a/source/python-api/foundation-models/logits.ipynb b/source/python-api/foundation-models/logits.ipynb index 5b0f4af..60a0fae 100644 --- a/source/python-api/foundation-models/logits.ipynb +++ b/source/python-api/foundation-models/logits.ipynb @@ -397,7 +397,7 @@ "source": [ "## Next steps\n", "\n", - "For more information, visit the [Embeddings API](https://docs.openprotein.ai/api-python/embedding.html) reference." + "For more information, visit the [Embeddings API](../api-reference/embedding.html) reference." ] } ], diff --git a/source/python-api/poet/creating-MSA.ipynb b/source/python-api/poet/creating-MSA.ipynb index 48f02fb..2f79b05 100644 --- a/source/python-api/poet/creating-MSA.ipynb +++ b/source/python-api/poet/creating-MSA.ipynb @@ -222,11 +222,11 @@ "source": [ "## Next steps\n", "\n", - "Learn more about the MSAs on our [MSA API](https://docs.openprotein.ai/api-python/align.html) page.\n", + "Learn more about the MSAs on our [MSA API](../api-reference/align.html#openprotein.align.AlignAPI.create_msa) page.\n", "\n", - "You can use your MSA to create a prompt and start generating, scoring, and analyzing sequences with our state-of-the-art PoET model. See [Creating a prompt](https://colab.research.google.com/drive/1BTuPVz4B5jLNvnsEXSJhSjBrOEWJ_ygj?usp=drive_link) for instructions.\n", + "You can use your MSA to create a prompt and start generating, scoring, and analyzing sequences with our state-of-the-art PoET model. See [Creating a prompt](./creating-prompt.ipynb) for instructions.\n", "\n", - "You can also use your MSA with our structure prediction tool to visualize the 3D structure of sequence. See [Structure prediction](https://docs.openprotein.ai/api-python/demos/fold_demo.html) for more information." + "You can also use your MSA with our structure prediction tool to visualize the 3D structure of sequence. See [Using AlphaFold2](../structure-prediction/Using_AlphaFold2.html) for more information." ] } ], diff --git a/source/python-api/poet/scoring-sequences.ipynb b/source/python-api/poet/scoring-sequences.ipynb index f5a3e98..ec3a08c 100644 --- a/source/python-api/poet/scoring-sequences.ipynb +++ b/source/python-api/poet/scoring-sequences.ipynb @@ -16,7 +16,7 @@ "\n", "## What you need before getting started\n", "\n", - "You need a previously generated multiple sequence alignment (MSA) and a prompt. See [Creating an MSA](https://colab.research.google.com/drive/1uoX7g6CBYU_PQzh5mEI6WAR8MbVDLq9A#scrollTo=kB3_IJ-HZh-g) and [Creating a prompt](https://colab.research.google.com/drive/1BTuPVz4B5jLNvnsEXSJhSjBrOEWJ_ygj#scrollTo=XnXhgmXVbMxD) for more information.\n", + "You need a previously generated multiple sequence alignment (MSA) and a prompt. See [Creating an MSA](./creating-MSA.ipynb) and [Creating a prompt](./creating-prompt.ipynb) for more information.\n", "\n", "## Scoring your sequences\n", "\n", @@ -129,7 +129,7 @@ "source": [ "## Next steps\n", "\n", - "Learn more about the `score` function in our [PoET API](https://docs.openprotein.ai/api-python/embedding.html#openprotein.api.embedding.PoETModel.score) page.\n", + "Learn more about the `score` function in our [PoET Model API](../api-reference/embedding.html#openprotein.embeddings.PoETModel.score) page.\n", "\n", "Now that you have a list of sequence variants of interest, you can use the PoET model to perform a [single site analysis] to score all single substitution variants of your parent sequence conditioned on the prompt. See [Using PoET single site analysis](https://colab.research.google.com/drive/1iWZkoQtQxbLoxrzhUeHFTNO5TtWoMIvX?usp=drive_link) for more information." ] diff --git a/source/python-api/poet/single-site-analysis.ipynb b/source/python-api/poet/single-site-analysis.ipynb index 841fb48..daf7d44 100644 --- a/source/python-api/poet/single-site-analysis.ipynb +++ b/source/python-api/poet/single-site-analysis.ipynb @@ -10,11 +10,11 @@ "\n", "This tutorial shows you how to perform a single site analysis using PoET, which scores all single substitution variants of an input sequence with a given prompt. Use this as a starting point to design single mutant or combinatorial variant libraries and predict the strength of protein activity.\n", "\n", - "Find more information about the PoET model on our [PoET API](https://docs.openprotein.ai/api-python/embedding.html#openprotein.api.embedding.PoETModel) page.\n", + "Find more information about the PoET model on our [PoET model API](../api-reference/embedding.html#openprotein.embeddings.PoETModel) page.\n", "\n", "## What you need before getting started\n", "\n", - "You need a prompt and a multiple sequence alignment (MSA). For more information, see [Creating a multiple sequence alignment](https://colab.research.google.com/drive/1uoX7g6CBYU_PQzh5mEI6WAR8MbVDLq9A?usp=drive_link) and [Creating a prompt](https://colab.research.google.com/drive/1BTuPVz4B5jLNvnsEXSJhSjBrOEWJ_ygj?usp=drive_link)." + "You need a prompt and a multiple sequence alignment (MSA). For more information, see [Creating a multiple sequence alignment](./creating-MSA.ipynb) and [Creating a prompt](./creating-prompt.ipynb)." ] }, { @@ -36,7 +36,6 @@ }, "outputs": [], "source": [ - "\n", "poet = session.embedding.get_model(\"poet\")\n", "sspjob = poet.single_site(prompt=prompt, sequence=\"MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM\".encode())" ] From e896fe0bde37a9381da55e9ddfb3e987421b67b1 Mon Sep 17 00:00:00 2001 From: Mark Gee Date: Sun, 26 Oct 2025 15:20:54 +0000 Subject: [PATCH 2/2] fix link in scoring sequences --- source/python-api/poet/scoring-sequences.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/python-api/poet/scoring-sequences.ipynb b/source/python-api/poet/scoring-sequences.ipynb index ec3a08c..517b778 100644 --- a/source/python-api/poet/scoring-sequences.ipynb +++ b/source/python-api/poet/scoring-sequences.ipynb @@ -131,7 +131,7 @@ "\n", "Learn more about the `score` function in our [PoET Model API](../api-reference/embedding.html#openprotein.embeddings.PoETModel.score) page.\n", "\n", - "Now that you have a list of sequence variants of interest, you can use the PoET model to perform a [single site analysis] to score all single substitution variants of your parent sequence conditioned on the prompt. See [Using PoET single site analysis](https://colab.research.google.com/drive/1iWZkoQtQxbLoxrzhUeHFTNO5TtWoMIvX?usp=drive_link) for more information." + "Now that you have a list of sequence variants of interest, you can use the PoET model to perform a [single site analysis] to score all single substitution variants of your parent sequence conditioned on the prompt. See [Using PoET single site analysis](./single-site-analysis.ipynb) for more information." ] } ],