add more spec stuff, fix format

Author: markgeejw

source/python-api/api-reference/models.rst

@@ -31,3 +31,35 @@ BoltzGen
 .. autoclass:: openprotein.models.foundation.boltzgen.BoltzGenFuture
    :members:
    :inherited-members:
+     
+.. autoclass:: openprotein.models.foundation.boltzgen_schema.BoltzGenDesignSpec
+   :members:
+   :exclude-members: model_config
+
+.. autoclass:: openprotein.models.foundation.boltzgen_schema.Entity
+   :members:
+   :exclude-members: model_config
+
+.. autoclass:: openprotein.models.foundation.boltzgen_schema.ProteinEntity
+   :members:
+   :exclude-members: model_config
+
+.. autoclass:: openprotein.models.foundation.boltzgen_schema.LigandEntity
+   :members:
+   :exclude-members: model_config
+
+.. autoclass:: openprotein.models.foundation.boltzgen_schema.FileEntity
+   :members:
+   :exclude-members: model_config
+
+.. autoclass:: openprotein.models.foundation.boltzgen_schema.Constraint
+   :members:
+   :exclude-members: model_config
+
+.. autoclass:: openprotein.models.foundation.boltzgen_schema.BondConstraint
+   :members:
+   :exclude-members: model_config
+
+.. autoclass:: openprotein.models.foundation.boltzgen_schema.TotalLengthConstraint
+   :members:
+   :exclude-members: model_config

source/python-api/structure-generation/index.rst

@@ -8,10 +8,8 @@ Get started using Structure Generation
 --------------------------------------
 **Tutorials**:
 
-- `Using RFdiffusion <./Using_RFdiffusion.ipynb>`_
-  - `API Reference <../api-reference/models.rst#RFdiffusion>`_
-- `Using BoltzGen <./Using_BoltzGen.ipynb>`_
-  - `API Reference <../api-reference/models.rst#BoltzGen>`_
+- `Using RFdiffusion <./Using_RFdiffusion.ipynb>`_ (`API Reference <../api-reference/models.rst#RFdiffusion>`_)
+- `Using BoltzGen <./Using_BoltzGen.ipynb>`_ (`API Reference <../api-reference/models.rst#BoltzGen>`_)
 
 .. toctree::
    :maxdepth: 2