Merge pull request #21 from fekad/spacegroup

using args and kwargs fot the quickview method

examples/4 - Interface for pymatgen.ipynb

@@ -38,7 +38,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "quick_view(struct)"
@@ -47,7 +49,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": false
+   },
    "outputs": [],
    "source": [
     "quick_view(struct, conventional=True)"
@@ -71,12 +75,39 @@
     "quick_view(struct, conventional=True, supercell=[2,2,2])"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Using extra parameters"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "All positional arguments will be passed to jsmol's load command."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
+   "source": [
+    "quick_view(struct, \"packed\", conventional=True)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "?quick_view"
+   ]
   }
  ],
  "metadata": {
@@ -95,7 +126,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.8"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,

js/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jupyter-jsmol",
-  "version": "0.2.5",
+  "version": "0.2.6",
   "author": {
     "name": "Adam Fekete",
     "email": "adam@fekete.co.uk"

jupyter_jsmol/_frontend.py

@@ -9,4 +9,4 @@
 """
 
 module_name = "jupyter-jsmol"
-module_version = "^0.2.5"
+module_version = "^0.2.6"

jupyter_jsmol/_version.py

@@ -4,5 +4,5 @@
 # Copyright (c) Adam Fekete.
 # Distributed under the terms of the Modified BSD License.
 
-version_info = (0, 2, 5)
+version_info = (0, 2, 6)
 __version__ = ".".join(map(str, version_info))

jupyter_jsmol/pymatgen.py

@@ -4,29 +4,50 @@
 try:
     from pymatgen import Structure
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+    from pymatgen.io.cif import CifWriter
+
     pymatgen_loaded = True
 except ImportError:
-    raise RuntimeError('To use quick_view, you need to have pymatgen installed.')
+    raise RuntimeError("To use quick_view, you need to have pymatgen installed.")
 
 from jupyter_jsmol import JsmolView
 
-def quick_view(structure: Structure, conventional: bool = False, supercell: list = None) -> JsmolView:
+
+def quick_view(
+    structure: Structure,
+    *args,
+    conventional: bool = False,
+    supercell: list = [1, 1, 1],
+    symprec: float = 0.01,
+    angle_tolerance: float = 5.0
+) -> JsmolView:
     """A function to visualize pymatgen Structure objects in jupyter notebook using jupyter_jsmol package.
 
     Args:
         structure: pymatgen Structure object.
+        *args: Extra arguments for JSmol's load command. Eg. "{2 2 2}", "packed"
         conventional: use conventional cell. Defaults to False.
-        transform: can be used to make supercells with pymatgen.Structure.make_supercell method.
+        supercell: can be used to make supercells with pymatgen.Structure.make_supercell method.
+        symprec: If not none, finds the symmetry of the structure
+            and writes the cif with symmetry information. Passes symprec
+            to the SpacegroupAnalyzer.
+        angle_tolerance: Angle tolerance for symmetry finding. Passes
+            angle_tolerance to the SpacegroupAnalyzer. Used only if symprec
+            is not None.
 
     Returns:
         A jupyter widget object.
     """
 
     s = structure.copy()
     if conventional:
-        s = SpacegroupAnalyzer(s).get_conventional_standard_structure()
+        spga = SpacegroupAnalyzer(s, symprec=symprec, angle_tolerance=angle_tolerance)
+        s = spga.get_conventional_standard_structure()
+
+    cif = CifWriter(
+        s, symprec=symprec, angle_tolerance=angle_tolerance, refine_struct=False
+    )
 
-    if supercell:
-        s.make_supercell(supercell)
+    supercell_str = "{" + " ".join(map(str, supercell)) + "}"
 
-    return JsmolView.from_str(s.to('cif'))
+    return JsmolView.from_str(str(cif), supercell_str, *args)

setup.py

@@ -28,7 +28,7 @@
     description='JSmol viewer widget for Jupyter',
     long_description=long_description,
     long_description_content_type="text/markdown",
-    version='0.2.5',
+    version='0.2.6',
     author='Adam Fekete',
     author_email='adam@fekete.co.uk',
     url='https://github.com/fekad/jupyter-jsmol',