[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

mbuild/path/bias.py

@@ -58,7 +58,9 @@ def __init__(self, site_type, weight, system_coordinates, new_coordinates):
         super(TargetType, self).__init__(system_coordinates, new_coordinates)
 
     def __call__(self):
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
 
 class AvoidType(Bias):
@@ -69,7 +71,9 @@ def __init__(self, site_type, weight, system_coordinates, new_coordinates):
         super(AvoidType, self).__init__(system_coordinates, new_coordinates)
 
     def __call__(self):
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
 
 class TargetEdge(Bias):
@@ -80,7 +84,9 @@ def __init__(self, weight, system_coordinates, volume_constraint, new_coordinate
         super(TargetEdge, self).__init__(system_coordinates, new_coordinates)
 
     def __call__(self):
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
 
 class AvoidEdge(Bias):
@@ -91,7 +97,9 @@ def __init__(self, weight, system_coordinates, volume_constraint, new_coordinate
         super(AvoidEdge, self).__init__(system_coordinates, new_coordinates)
 
     def __call__(self):
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
 
 class TargetDirection(Bias):
@@ -102,7 +110,9 @@ def __init__(self, direction, weight, system_coordinates, new_coordinates):
         super(TargetDirection, self).__init__(system_coordinates, new_coordinates)
 
     def __call__(self):
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
 
 class AvoidDirection(Bias):
@@ -113,7 +123,9 @@ def __init__(self, direction, weight, system_coordinates, new_coordinates):
         super(AvoidDirection, self).__init__(system_coordinates, new_coordinates)
 
     def __call__(self):
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
 
 class TargetPath(Bias):
@@ -124,4 +136,6 @@ def __init__(self, target_path, weight, system_coordinates, new_coordinates):
         super(TargetPath, self).__init__(system_coordinates, new_coordinates)
 
     def __call__(self):
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )

mbuild/path/path.py

@@ -24,8 +24,9 @@ class Path:
     coordinates : array-like, optional
         Creates a path from a pre-defined set of coordinates
     bond_graph : networkx.Graph, optional
-       The graph defining the edges between coordinates 
+       The graph defining the edges between coordinates
     """
+
     def __init__(self, N=None, coordinates=None, bond_graph=None):
         self.bond_graph = bond_graph
         # Only N is defined, make empty coordinates array with size N
@@ -80,10 +81,12 @@ def add_edge(self, u, v):
             length=float(bond_length),
             bond_type=(u_name, v_name),
         )
-    
+
     def get_bonded_sites(self):
         """Get all bonded pairs and their bond-vector orientations."""
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
     def get_coordinates(self):
         if isinstance(self.coordinates, list):
@@ -122,7 +125,9 @@ def apply_mapping(self):
             set orientation and separation for site v tail port
 
         """
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
     def _path_history(self):
         """Maybe this is a method that can be used optionally.
@@ -131,7 +136,9 @@ def _path_history(self):
         computation time and resources.
         Might be useful for more complicated random walks/branching algorithms
         """
-        raise NotImplementedError("This feature of mBuild 2.0 has not been implemented yet.")
+        raise NotImplementedError(
+            "This feature of mBuild 2.0 has not been implemented yet."
+        )
 
 
 class HardSphereRandomWalk(Path):
@@ -182,7 +189,7 @@ def __init__(
             This path's sites are used in checking for overlapping sites.
         start_from_path_index : int, optional
             An index of `start_from_path` used as the starting point for this random walk.
-        attach_paths : bool, default = False 
+        attach_paths : bool, default = False
             If True, adds an edge between the starting point of the last path and the first
             point of this path.
         initial_point : array-like, optional
@@ -807,14 +814,15 @@ class ZigZag(Path):
         The distance between consecutive sites along the path.
     angle_deg : float, default = 120.
         The rotation applied between segments
-    sites_per_segment : int, default = 4 
+    sites_per_segment : int, default = 4
         The number of sites before rotating and beginning next segment.
     plane : str, default = "xy"
         The plane that the sites in the path occupy
     bond_graph : networkx.Graph
         Defines connectivity between sites
 
     """
+
     def __init__(
         self,
         N,

mbuild/utils/volumes.py

@@ -10,14 +10,15 @@ class Constraint:
     Notes
     -----
     Design and implement your own volume constraint by inheriting from this class
-    and implementing the constraint check in an `is_inside` method. 
+    and implementing the constraint check in an `is_inside` method.
 
     `is_inside` is expected to return a mask of booleans.
 
     The existing contraints of CuboidConstraint, SphereConstraint, and CylinderConstraint
     call numba methods from their respectice `is_inside` method, but that is not a required
     implementation to design your own constraint.
     """
+
     def __init__(self):
         pass
 
@@ -40,6 +41,7 @@ class CuboidConstraint(Constraint):
     center : array-like (1,3), default = (0, 0, 0)
         Defines the center of the volume.
     """
+
     def __init__(self, Lx, Ly, Lz, center=(0, 0, 0)):
         self.center = np.asarray(center)
         self.mins = self.center - np.array([Lx / 2, Ly / 2, Lz / 2])
@@ -74,6 +76,7 @@ class SphereConstraint(Constraint):
     center : array-like (1,3), default = (0, 0, 0)
         Defines the center point of the sphere.
     """
+
     def __init__(self, center, radius):
         self.center = np.array(center)
         self.radius = radius
@@ -109,6 +112,7 @@ class CylinderConstraint(Constraint):
     center : array-like (1,3), default = (0, 0, 0)
         Defines the center point of the sphere.
     """
+
     def __init__(self, radius, height, center=(0, 0, 0)):
         self.center = np.array(center)
         self.height = height