Backend selection

spyrmsd/graph.py

@@ -1,43 +1,30 @@
+import numpy as np
+import sys
+
+from spyrmsd import constants
+
+## Checking and initializing the available backends
+graph_backends = []
+
 try:
-    from spyrmsd.graphs.gt import (
-        cycle,
-        graph_from_adjacency_matrix,
-        lattice,
-        match_graphs,
-        num_edges,
-        num_vertices,
-        vertex_property,
-    )
+    import spyrmsd.graphs.gt
+    graph_backends.append("graph_tool")
 
 except ImportError:
-    try:
-        from spyrmsd.graphs.nx import (
-            cycle,
-            graph_from_adjacency_matrix,
-            lattice,
-            match_graphs,
-            num_edges,
-            num_vertices,
-            vertex_property,
-        )
-    except ImportError:
-        raise ImportError("graph_tool or NetworkX libraries not found.")
-
-__all__ = [
-    "graph_from_adjacency_matrix",
-    "match_graphs",
-    "vertex_property",
-    "num_vertices",
-    "num_edges",
-    "lattice",
-    "cycle",
-    "adjacency_matrix_from_atomic_coordinates",
-]
-
-import numpy as np
+    print("Graph Tool backend not found")
+
+try:
+   import spyrmsd.graphs.nx
+   graph_backends.append("networkx")
+
+except ImportError:
+    print("NetworkX backend not found")
 
-from spyrmsd import constants
+if len(graph_backends) == 0:
+    sys.exit("No valid graph backends were found, please make sure atleast one of the supported backends is installed correctly")
 
+def get_backends():
+    return graph_backends
 
 def adjacency_matrix_from_atomic_coordinates(
     aprops: np.ndarray, coordinates: np.ndarray

spyrmsd/graphs/nx.py

@@ -190,3 +190,4 @@ def cycle(n):
         Cycle graph
     """
     return nx.cycle_graph(n)
+

spyrmsd/molecule.py

@@ -186,7 +186,7 @@ def strip(self) -> None:
 
             self.stripped = True
 
-    def to_graph(self):
+    def to_graph(self, backend: str = "default"):
         """
         Convert molecule to graph.
 
@@ -202,9 +202,44 @@ def to_graph(self):
 
         The molecular graph is cached.
         """
-        if self.G is None:
+
+        ## Check if the graph exists and is in the correct backend type
+        if self.G is None or not backend.lower() in self.current_backend:
+            # Check the backend
+            available_backends = graph.get_backends()
+
+            gt_backends = ["graphtool", "graph-tool", "graph_tool", "gt"]
+            nx_backends = ["networkx", "nx"]
+
+            if backend.lower() in gt_backends:
+                if "graph_tool" in available_backends:
+                    import spyrmsd.graphs.gt as graph_backend
+                    self.current_backend = gt_backends      
+
+                else:
+                    raise ImportError("Graph_tools backend not present")
+            elif backend.lower() in nx_backends:      
+                if "networkx" in available_backends:
+                    import spyrmsd.graphs.nx as graph_backend
+                    self.current_backend = nx_backends    
+                else:
+                    raise ImportError("NetworkX backend not present")
+            elif backend.lower() == "default":
+
+                if len(available_backends) == 0:
+                    raise ValueError("No valid backends were found, please ensure one of the supported backends is installed correctly")
+                if "graph_tool" in available_backends:
+                    import spyrmsd.graphs.gt as graph_backend
+                    self.current_backend = gt_backends
+
+                else:
+                    import spyrmsd.graphs.nx as graph_backend
+                    self.current_backend = nx_backends
+            else:
+                raise ValueError(f"Didn't recognize backend '{backend}'")
+            print(graph_backend)    
             try:
-                self.G = graph.graph_from_adjacency_matrix(
+                self.G = graph_backend.graph_from_adjacency_matrix(
                     self.adjacency_matrix, self.atomicnums
                 )
             except AttributeError:
@@ -218,7 +253,7 @@ def to_graph(self):
                     self.atomicnums, self.coordinates
                 )
 
-                self.G = graph.graph_from_adjacency_matrix(
+                self.G = graph_backend.graph_from_adjacency_matrix(
                     self.adjacency_matrix, self.atomicnums
                 )
 

spyrmsd/rmsd.py

@@ -125,6 +125,7 @@ def _rmsd_isomorphic_core(
     minimize: bool = False,
     isomorphisms: Optional[List[Tuple[List[int], List[int]]]] = None,
     atol: float = 1e-9,
+    backend: str = "default",
 ) -> Tuple[float, List[Tuple[List[int], List[int]]]]:
     """
     Compute RMSD using graph isomorphism.
@@ -158,6 +159,29 @@ def _rmsd_isomorphic_core(
         RMSD (after graph matching) and graph isomorphisms
     """
 
+    available_backends = graph.get_backends()
+
+    # Check the backend
+    if backend.lower() in ["graphtool", "graph-tool", "graph_tool", "graph tool", "gt"]:
+        if "graph_tool" in available_backends:
+            import spyrmsd.graphs.gt as graph_backend        
+        else:
+            raise ImportError("Graph_tools backend not present")
+    elif backend.lower() in ["networkx", "nx"]:
+        if "networkx" in available_backends:
+            import spyrmsd.graphs.nx as graph_backend           
+        else:
+            raise ImportError("NetworkX backend not present")
+    elif backend.lower() == "default":      
+        if len(available_backends) == 0:
+            raise ValueError("No valid backends were found, please ensure one of the supported backends is installed correctly")
+        if "graph_tool" in available_backends:
+            import spyrmsd.graphs.gt as graph_backend           
+        else:
+            import spyrmsd.graphs.nx as graph_backend           
+    else:
+        raise ValueError(f"Didn't recognize backend '{backend}'")
+
     assert coords1.shape == coords2.shape
 
     n = coords1.shape[0]
@@ -169,11 +193,11 @@ def _rmsd_isomorphic_core(
     # No cached isomorphisms
     if isomorphisms is None:
         # Convert molecules to graphs
-        G1 = graph.graph_from_adjacency_matrix(am1, aprops1)
-        G2 = graph.graph_from_adjacency_matrix(am2, aprops2)
+        G1 = graph_backend.graph_from_adjacency_matrix(am1, aprops1)
+        G2 = graph_backend.graph_from_adjacency_matrix(am2, aprops2)
 
         # Get all the possible graph isomorphisms
-        isomorphisms = graph.match_graphs(G1, G2)
+        isomorphisms = graph_backend.match_graphs(G1, G2)
 
     # Minimum result
     # Squared displacement (not minimize) or RMSD (minimize)
@@ -214,6 +238,7 @@ def symmrmsd(
     minimize: bool = False,
     cache: bool = True,
     atol: float = 1e-9,
+    backend: str = "default",
 ) -> Any:
     """
     Compute RMSD using graph isomorphism for multiple coordinates.
@@ -240,7 +265,9 @@ def symmrmsd(
         Cache graph isomorphisms
     atol: float
         Absolute tolerance parameter for QCP (see :func:`qcp_rmsd`)
-
+    backend: str
+        Which backend to use (default, graph_tool or networkx)
+
     Returns
     -------
     float: Union[float, List[float]]
@@ -276,6 +303,7 @@ def symmrmsd(
                 minimize=minimize,
                 isomorphisms=isomorphism,
                 atol=atol,
+                backend=backend,
             )
 
             RMSD.append(srmsd)
@@ -292,6 +320,7 @@ def symmrmsd(
             minimize=minimize,
             isomorphisms=None,
             atol=atol,
+            backend=backend,
         )
 
     return RMSD
@@ -305,9 +334,10 @@ def rmsdwrapper(
     minimize: bool = False,
     strip: bool = True,
     cache: bool = True,
+    backend: str = "default",
 ) -> Any:
     """
-    Compute RMSD between two molecule.
+    Compute RMSD between two molecules.
 
     Parameters
     ----------
@@ -323,6 +353,8 @@ def rmsdwrapper(
         Minimised RMSD (using the quaternion polynomial method)
     strip: bool, optional
         Strip hydrogen atoms
+    backend: str
+        Which backend to use (default, graph_tool or networkx)
 
     Returns
     -------
@@ -358,6 +390,7 @@ def rmsdwrapper(
             center=center,
             minimize=minimize,
             cache=cache,
+            backend=backend,
         )
     else:  # No symmetry
         for c in cmols: