add full api documentation.

SchiefLab · Feb 14, 2018 · 59c74c0 · 59c74c0
1 parent 63e036c
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diff --git a/README.rst b/README.rst
@@ -10,7 +10,7 @@ Jade
         :target: https://travis-ci.org/jadolfbr/jade
 
 .. image:: https://readthedocs.org/projects/jade/badge/?version=latest
-        :target: https://jade.readthedocs.io/en/latest/?badge=latest
+        :target: https://bio-jade.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
 
@@ -20,7 +20,7 @@ A repository for modules and applications to aid in the design and analysis of B
 
 
 * Free software: BSD license
-* Documentation: https://jade.readthedocs.io.
+* Documentation: https://bio-jade.readthedocs.io.
 
 
 Features

diff --git a/apps/pilot/__init__.py b/apps/pilot/__init__.py
diff --git a/apps/pilot/jadolfbr/__init__.py b/apps/pilot/jadolfbr/__init__.py
diff --git a/apps/public/__init__.py b/apps/public/__init__.py
diff --git a/apps/public/antibody_benchmark_utils/__init__.py b/apps/public/antibody_benchmark_utils/__init__.py
diff --git a/apps/public/antibody_utils/__init__.py b/apps/public/antibody_utils/__init__.py
diff --git a/apps/public/general/__init__.py b/apps/public/general/__init__.py
diff --git a/apps/public/pdb_utils/__init__.py b/apps/public/pdb_utils/__init__.py
diff --git a/apps/public/pyrosetta/__init__.py b/apps/public/pyrosetta/__init__.py
diff --git a/apps/public/rosetta/__init__.py b/apps/public/rosetta/__init__.py
diff --git a/apps/public/rosetta/score_analysis.py b/apps/public/rosetta/score_analysis.py
@@ -22,10 +22,8 @@
 def printVerbose(s):
     print >> sys.stderr, s
 
+def get_parser():
 
-########################################################################
-
-def main(argv):
     parser = ArgumentParser(
         "This utility parses and extracts data from score files in JSON format")
 
@@ -135,6 +133,12 @@ def main(argv):
     pymol_opts.add_argument("--super",
                             help="Super this selection instead of align all to.")
 
+    return parser
+########################################################################
+
+def main():
+
+    parser = get_parser()
     global options
     options = parser.parse_args()
 
@@ -383,4 +387,4 @@ def main(argv):
 ########################################################################
 
 if __name__ == "__main__":
-    sys.exit(main(sys.argv[1:]))
+    sys.exit(main())
diff --git a/docs/.gitignore b/docs/.gitignore
@@ -1 +1 @@
-/jade.*.rst
+
diff --git a/docs/api/jade.RAbD.AnalyzeAntibodyDesigns.rst b/docs/api/jade.RAbD.AnalyzeAntibodyDesigns.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD.AnalyzeAntibodyDesigns
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD.rst b/docs/api/jade.RAbD.rst
@@ -0,0 +1,25 @@
+jade.RAbD package
+=================
+
+.. automodule:: jade.RAbD
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+
+    jade.RAbD.window_main
+
+
+jade.RAbD.AnalyzeAntibodyDesigns module
+---------------------------------------
+
+.. automodule:: jade.RAbD.AnalyzeAntibodyDesigns
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
diff --git a/docs/api/jade.RAbD.window_main.AnalysisFrame.rst b/docs/api/jade.RAbD.window_main.AnalysisFrame.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD.window_main.AnalysisFrame
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD.window_main.CompareStrategiesFrame.rst b/docs/api/jade.RAbD.window_main.CompareStrategiesFrame.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD.window_main.CompareStrategiesFrame
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD.window_main.FeaturesFrame.rst b/docs/api/jade.RAbD.window_main.FeaturesFrame.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD.window_main.FeaturesFrame
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD.window_main.menu.rst b/docs/api/jade.RAbD.window_main.menu.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD.window_main.menu
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD.window_main.rst b/docs/api/jade.RAbD.window_main.rst
@@ -0,0 +1,42 @@
+jade.RAbD.window\_main package
+==============================
+
+.. automodule:: jade.RAbD.window_main
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+jade.RAbD.window\_main.AnalysisFrame module
+-------------------------------------------
+
+.. automodule:: jade.RAbD.window_main.AnalysisFrame
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD.window\_main.CompareStrategiesFrame module
+----------------------------------------------------
+
+.. automodule:: jade.RAbD.window_main.CompareStrategiesFrame
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD.window\_main.FeaturesFrame module
+-------------------------------------------
+
+.. automodule:: jade.RAbD.window_main.FeaturesFrame
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD.window\_main.menu module
+----------------------------------
+
+.. automodule:: jade.RAbD.window_main.menu
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
diff --git a/docs/api/jade.RAbD.window_modules.FilterSettingsWindow.rst b/docs/api/jade.RAbD.window_modules.FilterSettingsWindow.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD.window_modules.FilterSettingsWindow
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD.window_modules.rst b/docs/api/jade.RAbD.window_modules.rst
@@ -0,0 +1,20 @@
+jade.RAbD.window\_modules package
+=================================
+
+.. automodule:: jade.RAbD.window_modules
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+jade.RAbD.window\_modules.FilterSettingsWindow module
+-----------------------------------------------------
+
+.. automodule:: jade.RAbD.window_modules.FilterSettingsWindow
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
diff --git a/docs/api/jade.RAbD_BM.AnalysisInfo.rst b/docs/api/jade.RAbD_BM.AnalysisInfo.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD_BM.AnalysisInfo
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD_BM.AnalyzeRecovery.rst b/docs/api/jade.RAbD_BM.AnalyzeRecovery.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD_BM.AnalyzeRecovery
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD_BM.RunBenchmarksRAbD.rst b/docs/api/jade.RAbD_BM.RunBenchmarksRAbD.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD_BM.RunBenchmarksRAbD
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD_BM.benchmark_plotting.rst b/docs/api/jade.RAbD_BM.benchmark_plotting.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD_BM.benchmark_plotting
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD_BM.recovery_rr_tools.rst b/docs/api/jade.RAbD_BM.recovery_rr_tools.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD_BM.recovery_rr_tools
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD_BM.rst b/docs/api/jade.RAbD_BM.rst
@@ -0,0 +1,74 @@
+jade.RAbD\_BM package
+=====================
+
+.. automodule:: jade.RAbD_BM
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+jade.RAbD\_BM.AnalysisInfo module
+---------------------------------
+
+.. automodule:: jade.RAbD_BM.AnalysisInfo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD\_BM.AnalyzeRecovery module
+------------------------------------
+
+.. automodule:: jade.RAbD_BM.AnalyzeRecovery
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD\_BM.RunBenchmarksRAbD module
+--------------------------------------
+
+.. automodule:: jade.RAbD_BM.RunBenchmarksRAbD
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD\_BM.benchmark\_plotting module
+----------------------------------------
+
+.. automodule:: jade.RAbD_BM.benchmark_plotting
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD\_BM.recovery\_rr\_tools module
+----------------------------------------
+
+.. automodule:: jade.RAbD_BM.recovery_rr_tools
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD\_BM.tools module
+--------------------------
+
+.. automodule:: jade.RAbD_BM.tools
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD\_BM.tools\_ab\_db module
+----------------------------------
+
+.. automodule:: jade.RAbD_BM.tools_ab_db
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.RAbD\_BM.tools\_features\_db module
+----------------------------------------
+
+.. automodule:: jade.RAbD_BM.tools_features_db
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
diff --git a/docs/api/jade.RAbD_BM.tools.rst b/docs/api/jade.RAbD_BM.tools.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD_BM.tools
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD_BM.tools_ab_db.rst b/docs/api/jade.RAbD_BM.tools_ab_db.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD_BM.tools_ab_db
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.RAbD_BM.tools_features_db.rst b/docs/api/jade.RAbD_BM.tools_features_db.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.RAbD_BM.tools_features_db
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.antibody.CDRClusterer.rst b/docs/api/jade.antibody.CDRClusterer.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.antibody.CDRClusterer
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.antibody.ClusterData.rst b/docs/api/jade.antibody.ClusterData.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.antibody.ClusterData
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.antibody.ab_db.rst b/docs/api/jade.antibody.ab_db.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.antibody.ab_db
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.antibody.cdr_data.CDRData.rst b/docs/api/jade.antibody.cdr_data.CDRData.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.antibody.cdr_data.CDRData
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.antibody.cdr_data.CDRDataTypes.rst b/docs/api/jade.antibody.cdr_data.CDRDataTypes.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.antibody.cdr_data.CDRDataTypes
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.antibody.cdr_data.rst b/docs/api/jade.antibody.cdr_data.rst
@@ -0,0 +1,28 @@
+jade.antibody.cdr\_data package
+===============================
+
+.. automodule:: jade.antibody.cdr_data
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+jade.antibody.cdr\_data.CDRData module
+--------------------------------------
+
+.. automodule:: jade.antibody.cdr_data.CDRData
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.antibody.cdr\_data.CDRDataTypes module
+-------------------------------------------
+
+.. automodule:: jade.antibody.cdr_data.CDRDataTypes
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
diff --git a/docs/api/jade.antibody.decoy_data.DecoyData.rst b/docs/api/jade.antibody.decoy_data.DecoyData.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.antibody.decoy_data.DecoyData
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.antibody.decoy_data.DecoyDataTypes.rst b/docs/api/jade.antibody.decoy_data.DecoyDataTypes.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.antibody.decoy_data.DecoyDataTypes
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/api/jade.antibody.decoy_data.rst b/docs/api/jade.antibody.decoy_data.rst
@@ -0,0 +1,26 @@
+jade.antibody.decoy\_data package
+=================================
+
+.. automodule:: jade.antibody.decoy_data
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+jade.antibody.decoy\_data.DecoyData module
+------------------------------------------
+
+.. automodule:: jade.antibody.decoy_data.DecoyData
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+jade.antibody.decoy\_data.DecoyDataTypes module
+-----------------------------------------------
+
+.. automodule:: jade.antibody.decoy_data.DecoyDataTypes
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
diff --git a/docs/api/jade.antibody.outliers.rst b/docs/api/jade.antibody.outliers.rst
@@ -0,0 +1,4 @@
+.. automodule:: jade.antibody.outliers
+    :members:
+    :undoc-members:
+    :show-inheritance: