Merge pull request #20 from andrewtarzia/development_august

Development august commit: Adding some features: * Refactor topology graphs for other usage * Write to chemiscope output
andrewtarzia · Oct 10, 2024 · 76a0304 · 76a0304
2 parents 90acb3b + b70743d
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diff --git a/docs/source/_autosummary/cgexplore.rst b/docs/source/_autosummary/cgexplore.rst
@@ -35,5 +35,6 @@
    optimisation
    systems_optimisation
    terms
+   topologies
    utilities
 
diff --git a/docs/source/_autosummary/cgexplore.topologies.CGM12L24.rst b/docs/source/_autosummary/cgexplore.topologies.CGM12L24.rst
@@ -0,0 +1,26 @@
+cgexplore.topologies.CGM12L24
+=============================
+
+.. currentmodule:: cgexplore.topologies
+
+.. autoclass:: CGM12L24
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+      ~CGM12L24.get_vertex_alignments
+
+
+
+
+
+
diff --git a/docs/source/_autosummary/cgexplore.topologies.CGM4L8.rst b/docs/source/_autosummary/cgexplore.topologies.CGM4L8.rst
@@ -0,0 +1,25 @@
+cgexplore.topologies.CGM4L8
+===========================
+
+.. currentmodule:: cgexplore.topologies
+
+.. autoclass:: CGM4L8
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+
diff --git a/docs/source/_autosummary/cgexplore.topologies.M4L82.rst b/docs/source/_autosummary/cgexplore.topologies.M4L82.rst
@@ -0,0 +1,34 @@
+cgexplore.topologies.M4L82
+==========================
+
+.. currentmodule:: cgexplore.topologies
+
+.. autoclass:: M4L82
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~M4L82.paired_wall_1_coord
+      ~M4L82.paired_wall_2_coord
+      ~M4L82.wall_1_shift
+      ~M4L82.wall_2_shift
+
+
diff --git a/docs/source/_autosummary/cgexplore.topologies.rst b/docs/source/_autosummary/cgexplore.topologies.rst
@@ -0,0 +1,35 @@
+cgexplore.topologies
+====================
+
+.. automodule:: cgexplore.topologies
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+      :toctree:
+      :template: class.rst
+      :nosignatures:
+
+      CGM12L24
+      CGM4L8
+      M4L82
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/source/_autosummary/cgexplore.utilities.AtomliteDatabase.rst b/docs/source/_autosummary/cgexplore.utilities.AtomliteDatabase.rst
@@ -20,6 +20,7 @@ cgexplore.utilities.AtomliteDatabase
       ~AtomliteDatabase.add_entries
       ~AtomliteDatabase.add_molecule
       ~AtomliteDatabase.add_properties
+      ~AtomliteDatabase.get_database
       ~AtomliteDatabase.get_entries
       ~AtomliteDatabase.get_entry
       ~AtomliteDatabase.get_molecule

diff --git a/docs/source/_autosummary/cgexplore.utilities.extract_property.rst b/docs/source/_autosummary/cgexplore.utilities.extract_property.rst
@@ -0,0 +1,6 @@
+cgexplore.utilities.extract\_property
+=====================================
+
+.. currentmodule:: cgexplore.utilities
+
+.. autofunction:: extract_property
diff --git a/docs/source/_autosummary/cgexplore.utilities.rst b/docs/source/_autosummary/cgexplore.utilities.rst
@@ -35,6 +35,7 @@ cgexplore.utilities
       check_directory
       convert_pyramid_angle
       draw_pie
+      extract_property
       get_supramolecule
       get_unforced_supramolecule
       optimise_ligand
@@ -43,6 +44,7 @@ cgexplore.utilities
       run_soft_md_cycle
       shift_beads
       soften_forcefield
+      write_chemiscope_json
       yield_near_models
       yield_shifted_models
 

diff --git a/docs/source/_autosummary/cgexplore.utilities.write_chemiscope_json.rst b/docs/source/_autosummary/cgexplore.utilities.write_chemiscope_json.rst
@@ -0,0 +1,6 @@
+cgexplore.utilities.write\_chemiscope\_json
+===========================================
+
+.. currentmodule:: cgexplore.utilities
+
+.. autofunction:: write_chemiscope_json
diff --git a/docs/source/databasing.rst b/docs/source/databasing.rst
@@ -1,5 +1,8 @@
-Databasing
-==========
+Sharing with collaborators
+==========================
+
+Databasing with atomlite
+------------------------
 
 .. seealso::
 
@@ -9,3 +12,17 @@ Databasing
   :maxdepth: 1
 
   AtomliteDatabase <_autosummary/cgexplore.utilities.AtomliteDatabase>
+
+
+Mapping with chemiscope
+-----------------------
+
+.. seealso::
+
+    chemiscope: https://chemiscope.org/
+
+.. toctree::
+  :maxdepth: 1
+
+  write_chemiscope_json <_autosummary/cgexplore.utilities.write_chemiscope_json>
+  extract_property <_autosummary/cgexplore.utilities.extract_property>
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -4,15 +4,16 @@
    :maxdepth: 2
 
    Analysis <analysis>
-   Databasing <databasing>
+   Sharing with collaborators <databasing>
    Forcefields <forcefields>
    Molecular <molecular>
    Optimisation <optimisation>
-   Systems Optimisation <systems_optimisation>
+   Systems optimisation <systems_optimisation>
    Terms <terms>
    Utilities <utilities>
    Executables <executables>
-   First Paper Example <first_paper_example>
+   Topologies <topologies>
+   First paper example <first_paper_example>
 
 .. toctree::
   :hidden:

diff --git a/docs/source/topologies.rst b/docs/source/topologies.rst
@@ -0,0 +1,14 @@
+Topologies
+==========
+
+A package of the classes for handling topology graphs in `CGExplore`.
+
+New topology graphs
+-------------------
+
+.. toctree::
+  :maxdepth: 1
+
+  CGM12L24 <_autosummary/cgexplore.topologies.CGM12L24>
+  CGM4L8 <_autosummary/cgexplore.topologies.CGM4L8>
+  M4L82 <_autosummary/cgexplore.topologies.M4L82>