add more examples everywhere

ginkgobioworks · Dec 16, 2024 · 9bcfb2c · 9bcfb2c
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diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -19,5 +19,14 @@ AA0 model
 ~~~~~~~~~~~
 
 .. literalinclude:: ../../examples/3utr_model.py
+   :language: python
+   :linenos:
+
+
+
+Boltz structure inference
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. literalinclude:: ../../examples/boltz_structure_inference/gfp.py
    :language: python
    :linenos:
diff --git a/docs/source/ref.rst b/docs/source/ref.rst
@@ -10,12 +10,40 @@ GinkgoAIClient
 Mean embedding Queries
 ~~~~~~~~~~~~~~~~~~~~~~
 
+Used to get embedding vectors for protein or nucleotide sequences, using models such as ESM, Ginkgo-AA0, etc.
 
 .. autoclass:: ginkgo_ai_client.queries.MeanEmbeddingQuery
 .. autoclass:: ginkgo_ai_client.queries.EmbeddingResponse
 
 Masked inference queries
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
+Used to get maximum-likelihood predictions for masked  protein or nucleotide sequences, using models such as ESM, Ginkgo-AA0, etc.
+
 .. autoclass:: ginkgo_ai_client.queries.MaskedInferenceQuery
-.. autoclass:: ginkgo_ai_client.queries.SequenceResponse
+.. autoclass:: ginkgo_ai_client.queries.SequenceResponse
+
+
+Promoter activity prediction queries
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Used to predict the activity of promoters in various human tissues, using Borzoi and Ginkgo's Promoter-0
+
+.. autoclass:: ginkgo_ai_client.queries.PromoterActivityQuery
+.. autoclass:: ginkgo_ai_client.queries.PromoterActivityResponse
+
+Diffusion queries
+~~~~~~~~~~~~~~~~~
+
+Used to generate protein or nucleotide sequences using Ginkgo-devloped diffusion models LCDNA and AB-Diffusion.
+
+.. autoclass:: ginkgo_ai_client.queries.DiffusionMaskedQuery
+.. autoclass:: ginkgo_ai_client.queries.DiffusionMaskedResponse
+
+Boltz structure inference queries
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Used to predict the 3D structure of a protein sequence using Boltz.
+
+.. autoclass:: ginkgo_ai_client.queries.BoltzStructurePredictionQuery
+.. autoclass:: ginkgo_ai_client.queries.BoltzStructurePredictionResponse
diff --git a/examples/boltz_structure_inference/gfp.py b/examples/boltz_structure_inference/gfp.py
@@ -1,3 +1,5 @@
+"""Simple example where we predict the 3D structure of the GFP protein."""
+
 from ginkgo_ai_client import GinkgoAIClient, BoltzStructurePredictionQuery
 
 client = GinkgoAIClient()