Add method for removing embedded images to utils __init__.py.

Author: Oliver Scott

scaffoldgraph/vis/base.py

@@ -9,6 +9,8 @@
 from scaffoldgraph.core import ScaffoldGraph
 from scaffoldgraph.utils import canonize_smiles
 
+from .utils import remove_node_mol_images
+
 
 class Visualizer(ABC):
     """Base class for ScaffoldGraph visualizers.
@@ -21,7 +23,7 @@ class Visualizer(ABC):
     scaffoldgraph.vis.notebook.cytoscape.CytoscapeVisualizer
 
     """
-    def __init__(self, graph, requires_tree=False):
+    def __init__(self, graph, requires_tree=False, refresh_images=False):
         """Initialize the visualizer.
 
         Parameters
@@ -31,9 +33,14 @@ def __init__(self, graph, requires_tree=False):
         requires_tree : bool, optional
             Whether the visualizer requires a tree
             structure to create a visualization.
+        refresh_images: bool, optional
+            If True remove all embeded images from the
+            input graph and regenerate when required.
+            The default is False.
 
         """
         self._requires_tree = requires_tree
+        self._refresh = refresh_images
         self._graph = self._validate_graph(graph)
 
     @property
@@ -56,6 +63,8 @@ def _validate_graph(self, graph):
                 msg = '{} requires a tree/forest structured graph'
                 msg.format(self.__class__.__name__)
                 raise ValueError(msg)
+        if self._refresh is True:
+            remove_node_mol_images(graph)
         return graph
 
     def _subgraph_from_mol(self, molecule):

scaffoldgraph/vis/notebook/cytoscape.py

@@ -89,7 +89,7 @@ class CytoscapeVisualizer(Visualizer):
     >>> visualizer.draw_for_scaffold('c1ccc(CNc2ccccc2)cc1')
 
     """
-    def __init__(self, graph, style=None):
+    def __init__(self, graph, style=None, refresh_images=False):
         """Initialize the cytoscape visualizer.
 
         Parameters
@@ -102,9 +102,17 @@ def __init__(self, graph, style=None):
             see the ipycytoscape documentation. If None
             a default style is used and can be updated
             after initialization.
+        refresh_images: bool, optional
+            If True remove all embeded images from the
+            input graph and regenerate when required.
+            The default is False.
 
         """
-        super(CytoscapeVisualizer, self).__init__(graph, requires_tree=False)
+        super(CytoscapeVisualizer, self).__init__(
+            graph,
+            requires_tree=False,
+            refresh_images=refresh_images,
+        )
         self._style = style if style else read_style_file(DEFAULT_STYLE)
 
     @property