Merge pull request #57 from coltonbh/feature-conf-search-view-grid-view

coltonbh · Aug 17, 2024 · 96c7da4 · 96c7da4
2 parents 11b0da6 + c069b94
commit 96c7da4
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Showing 12 changed files with 1,725 additions and 542 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -7,8 +7,10 @@
         "classmethod",
         "cmdline",
         "conformerid",
+        "Dmol",
         "dtype",
         "ETKDG",
+        "figsize",
         "freqs",
         "getfixturevalue",
         "HARTREE",
@@ -49,6 +51,7 @@
         "terachem",
         "traceback",
         "vibmodes",
+        "viewergrid",
         "wavenumber",
         "wavenumbers"
     ]

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [unreleased]
 
+### Changed
+
+- `Structure` views now use `GridViewer` when laying out multiple structures with `py3Dmol` so as to use only one WebGL context for all images. This dramatically improves performance and reduces lag.
+- Added `view_2d` option for viewing a `2D` image of a molecule rather than the `3D` viewer.
+
+### Added
+
+- View for `ConformerSearchResults`.
+
 ## [0.11.8] - 2024-08-13
 
 ### Added

diff --git a/docs/visualizations/U1-_confsearch-crest.json b/docs/visualizations/U1-_confsearch-crest.json
diff --git a/docs/visualizations/coreviews.ipynb b/docs/visualizations/coreviews.ipynb
diff --git a/docs/visualizations/programoutputs.ipynb b/docs/visualizations/programoutputs.ipynb
diff --git a/docs/visualizations/structure.ipynb b/docs/visualizations/structure.ipynb
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -117,4 +117,5 @@ nav:
       - Overview: visualizations/overview.md
       - Structure: visualizations/structure.ipynb
       - ProgramOutputs: visualizations/programoutputs.ipynb
+      - Core Views: visualizations/coreviews.ipynb
   - Changelog: https://github.com/coltonbh/qcio/blob/master/CHANGELOG.md
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -29,7 +29,7 @@ openbabel-wheel = { version = "^3.1.1.19", optional = true }
 [tool.poetry.extras]
 rdkit = ["rdkit"]
 openbabel = ["openbabel-wheel"]
-view = ["matplotlib", "ipython", "py3Dmol"]
+view = ["matplotlib", "ipython", "py3Dmol", "rdkit"]
 all = ["rdkit", "openbabel-wheel", "matplotlib", "ipython", "py3Dmol"]
 
 [tool.poetry.group.dev.dependencies]

diff --git a/qcio/utils.py b/qcio/utils.py
@@ -9,7 +9,13 @@
 # Helper Structures
 water = Structure(
     symbols=["O", "H", "H"],
-    geometry=np.array([0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0, 1.0, 0.0]),
+    geometry=np.array(
+        [
+            [0.0253397, 0.01939466, -0.00696322],
+            [0.22889176, 1.84438441, 0.16251426],
+            [1.41760224, -0.62610794, -1.02954938],
+        ]
+    ),
     charge=0,
     multiplicity=1,
     connectivity=[(0, 1, 1.0), (0, 2, 1.0)],