Update docs.

andrewtarzia · Dec 17, 2024 · 47e3ded · 47e3ded
1 parent 5900299
commit 47e3ded
Show file tree

Hide file tree

Showing 11 changed files with 90 additions and 13 deletions.
diff --git a/docs/source/_autosummary/cgexplore.atomistic.extract_ditopic_ensemble.rst b/docs/source/_autosummary/cgexplore.atomistic.extract_ditopic_ensemble.rst
@@ -0,0 +1,6 @@
+cgexplore.atomistic.extract\_ditopic\_ensemble
+==============================================
+
+.. currentmodule:: cgexplore.atomistic
+
+.. autofunction:: extract_ditopic_ensemble
diff --git a/docs/source/_autosummary/cgexplore.atomistic.extract_ensemble.rst b/docs/source/_autosummary/cgexplore.atomistic.extract_ensemble.rst
diff --git a/docs/source/_autosummary/cgexplore.atomistic.get_ditopic_aligned_bb.rst b/docs/source/_autosummary/cgexplore.atomistic.get_ditopic_aligned_bb.rst
@@ -0,0 +1,6 @@
+cgexplore.atomistic.get\_ditopic\_aligned\_bb
+=============================================
+
+.. currentmodule:: cgexplore.atomistic
+
+.. autofunction:: get_ditopic_aligned_bb
diff --git a/docs/source/_autosummary/cgexplore.atomistic.rst b/docs/source/_autosummary/cgexplore.atomistic.rst
@@ -30,7 +30,8 @@ cgexplore.atomistic
       :nosignatures:
 
       cgx_optimisation_sequence
-      extract_ensemble
+      extract_ditopic_ensemble
+      get_ditopic_aligned_bb
       run_conformer_analysis
 
 

diff --git a/...lore.scram.HomolepticTopologyIterator.rst → ...tosummary/cgexplore.molecular.SixBead.rst b/...lore.scram.HomolepticTopologyIterator.rst → ...tosummary/cgexplore.molecular.SixBead.rst
@@ -1,9 +1,9 @@
-cgexplore.scram.HomolepticTopologyIterator
-==========================================
+cgexplore.molecular.SixBead
+===========================
 
-.. currentmodule:: cgexplore.scram
+.. currentmodule:: cgexplore.molecular
 
-.. autoclass:: HomolepticTopologyIterator
+.. autoclass:: SixBead
    :members:
    :inherited-members:
    :undoc-members:

diff --git a/docs/source/_autosummary/cgexplore.molecular.StericSixBead.rst b/docs/source/_autosummary/cgexplore.molecular.StericSixBead.rst
@@ -0,0 +1,25 @@
+cgexplore.molecular.StericSixBead
+=================================
+
+.. currentmodule:: cgexplore.molecular
+
+.. autoclass:: StericSixBead
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+
diff --git a/docs/source/_autosummary/cgexplore.molecular.rst b/docs/source/_autosummary/cgexplore.molecular.rst
@@ -26,8 +26,10 @@ cgexplore.molecular
       LinearPrecursor
       Precursor
       PrecursorGenerator
+      SixBead
       SpindryConformer
       SquarePrecursor
+      StericSixBead
       ThreeC0Arm
       ThreeC1Arm
       ThreeC2Arm

diff --git a/docs/source/_autosummary/cgexplore.scram.BuildingBlockConfiguration.rst b/docs/source/_autosummary/cgexplore.scram.BuildingBlockConfiguration.rst
@@ -0,0 +1,35 @@
+cgexplore.scram.BuildingBlockConfiguration
+==========================================
+
+.. currentmodule:: cgexplore.scram
+
+.. autoclass:: BuildingBlockConfiguration
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+      ~BuildingBlockConfiguration.get_building_block_dictionary
+      ~BuildingBlockConfiguration.get_hashable_bbidx_dict
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~BuildingBlockConfiguration.idx
+      ~BuildingBlockConfiguration.building_block_idx_map
+      ~BuildingBlockConfiguration.building_block_idx_dict
+
+
diff --git a/docs/source/_autosummary/cgexplore.scram.IHomolepticTopologyIterator.rst b/docs/source/_autosummary/cgexplore.scram.IHomolepticTopologyIterator.rst
@@ -17,9 +17,10 @@ cgexplore.scram.IHomolepticTopologyIterator
    .. autosummary::
       :nosignatures:
 
-      ~IHomolepticTopologyIterator.get_graphs
+      ~IHomolepticTopologyIterator.count_graphs
       ~IHomolepticTopologyIterator.get_num_building_blocks
       ~IHomolepticTopologyIterator.get_vertex_prototypes
+      ~IHomolepticTopologyIterator.yield_graphs
 
 
 

diff --git a/docs/source/_autosummary/cgexplore.scram.get_custom_bb_configurations.rst b/docs/source/_autosummary/cgexplore.scram.get_custom_bb_configurations.rst
@@ -0,0 +1,6 @@
+cgexplore.scram.get\_custom\_bb\_configurations
+===============================================
+
+.. currentmodule:: cgexplore.scram
+
+.. autofunction:: get_custom_bb_configurations
diff --git a/docs/source/_autosummary/cgexplore.scram.rst b/docs/source/_autosummary/cgexplore.scram.rst
@@ -16,8 +16,8 @@ cgexplore.scram
       :template: class.rst
       :nosignatures:
 
+      BuildingBlockConfiguration
       Constructed
-      HomolepticTopologyIterator
       IHomolepticTopologyIterator
       TopologyCode
       TopologyIterator
@@ -33,6 +33,7 @@ cgexplore.scram
       :toctree:
       :nosignatures:
 
+      get_custom_bb_configurations
       get_potential_bb_dicts
       graph_optimise_cage
       optimise_cage