updated sphinx docs

docs/index.rst

@@ -10,14 +10,11 @@ Welcome to Protein Design Tools's documentation!
    :maxdepth: 2
    :caption: Contents:
 
-   core/index
-   alignment/index
-   io/index
-   utils/index
+   modules
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
+* :ref:`search`

docs/modules.rst

@@ -0,0 +1,7 @@
+protein_design_tools
+====================
+
+.. toctree::
+   :maxdepth: 4
+
+   protein_design_tools

docs/protein_design_tools.alignment.rst

@@ -0,0 +1,21 @@
+protein\_design\_tools.alignment package
+========================================
+
+Submodules
+----------
+
+protein\_design\_tools.alignment.superpose module
+-------------------------------------------------
+
+.. automodule:: protein_design_tools.alignment.superpose
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protein_design_tools.alignment
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/protein_design_tools.core.rst

@@ -0,0 +1,45 @@
+protein\_design\_tools.core package
+===================================
+
+Submodules
+----------
+
+protein\_design\_tools.core.atom module
+---------------------------------------
+
+.. automodule:: protein_design_tools.core.atom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protein\_design\_tools.core.chain module
+----------------------------------------
+
+.. automodule:: protein_design_tools.core.chain
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protein\_design\_tools.core.protein\_structure module
+-----------------------------------------------------
+
+.. automodule:: protein_design_tools.core.protein_structure
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protein\_design\_tools.core.residue module
+------------------------------------------
+
+.. automodule:: protein_design_tools.core.residue
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protein_design_tools.core
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/protein_design_tools.io.rst

@@ -0,0 +1,21 @@
+protein\_design\_tools.io package
+=================================
+
+Submodules
+----------
+
+protein\_design\_tools.io.pdb module
+------------------------------------
+
+.. automodule:: protein_design_tools.io.pdb
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protein_design_tools.io
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/protein_design_tools.metrics.rst

@@ -0,0 +1,45 @@
+protein\_design\_tools.metrics package
+======================================
+
+Submodules
+----------
+
+protein\_design\_tools.metrics.gdt module
+-----------------------------------------
+
+.. automodule:: protein_design_tools.metrics.gdt
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protein\_design\_tools.metrics.lddt module
+------------------------------------------
+
+.. automodule:: protein_design_tools.metrics.lddt
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protein\_design\_tools.metrics.rmsd module
+------------------------------------------
+
+.. automodule:: protein_design_tools.metrics.rmsd
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protein\_design\_tools.metrics.tmscore module
+---------------------------------------------
+
+.. automodule:: protein_design_tools.metrics.tmscore
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protein_design_tools.metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/protein_design_tools.rst

@@ -0,0 +1,22 @@
+protein\_design\_tools package
+==============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   protein_design_tools.alignment
+   protein_design_tools.core
+   protein_design_tools.io
+   protein_design_tools.metrics
+   protein_design_tools.utils
+
+Module contents
+---------------
+
+.. automodule:: protein_design_tools
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/protein_design_tools.utils.rst

@@ -0,0 +1,29 @@
+protein\_design\_tools.utils package
+====================================
+
+Submodules
+----------
+
+protein\_design\_tools.utils.analysis module
+--------------------------------------------
+
+.. automodule:: protein_design_tools.utils.analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+protein\_design\_tools.utils.helpers module
+-------------------------------------------
+
+.. automodule:: protein_design_tools.utils.helpers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: protein_design_tools.utils
+   :members:
+   :undoc-members:
+   :show-inheritance: