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

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cmelab · Jan 23, 2025 · b32109a · b32109a
1 parent 7fe124d
commit b32109a
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Showing 2 changed files with 37 additions and 35 deletions.
diff --git a/grits/finegrain.py b/grits/finegrain.py
@@ -23,41 +23,41 @@ def backmap_snapshot_to_compound(
 ):
     """Backmap a fine-grained snapshot onto a coarse one.
 
-    Creates a fine-grained compound from a coarse one using the given parameters.
+        Creates a fine-grained compound from a coarse one using the given parameters.
 
-    Parameters
-    ----------
-    snapshot : gsd.hoomd.Frame
-        one frame of gsd trajectory
+        Parameters
+        ----------
+        snapshot : gsd.hoomd.Frame
+            one frame of gsd trajectory
 
-    bead_mapping : string, default None
-        SMILES string of fine-grain monomer
+        bead_mapping : string, default None
+            SMILES string of fine-grain monomer
 
-    bond_head_index : list of int, default None
-        index of polymer reaction, choose head to orient chain
+        bond_head_index : list of int, default None
+            index of polymer reaction, choose head to orient chain
 
-    bond_tail_index : list of int, default None
-        index of polymer reaction, choose tail to orient chain
+        bond_tail_index : list of int, default None
+            index of polymer reaction, choose tail to orient chain
 
-    library_key : string, default None
-        key to dictionary, reactant_dict, with known bead_mapping, bond_head_index, and bond_tail_index
+        library_key : string, default None
+            key to dictionary, reactant_dict, with known bead_mapping, bond_head_index, and bond_tail_index
 
-    ref_distance : float, default None
-        distance between monomers
+        ref_distance : float, default None
+            distance between monomers
 
-<<<<<<< HEAD
-    energy_minimize (bool) : Option to run a mbuild energy minimization.
+    <<<<<<< HEAD
+        energy_minimize (bool) : Option to run a mbuild energy minimization.
 
-=======
-    energy_minimize : bool, default False
-        Option to run a mbuild energy minimization.
-    
->>>>>>> 2785a5d (updating format for doc strings)
+    =======
+        energy_minimize : bool, default False
+            Option to run a mbuild energy minimization.
 
-    Returns
-    -------
-    :py:class:`mbuild.Compound`
-        The atomistic structure mapped onto the coarse-grained one.
+    >>>>>>> 2785a5d (updating format for doc strings)
+
+        Returns
+        -------
+        :py:class:`mbuild.Compound`
+            The atomistic structure mapped onto the coarse-grained one.
     """
     # TODO
     # assert all 3 dicts have the same keys
@@ -98,7 +98,9 @@ def backmap_snapshot_to_compound(
                     for l, particle in enumerate(comp.particles()):
                         if l == k:
                             remove_atoms.append(particle)
-            if len(bond_head_index[mapping]) > 1: #repeated if statement if reacting group is listed for head index
+            if (
+                len(bond_head_index[mapping]) > 1
+            ):  # repeated if statement if reacting group is listed for head index
                 extra_head_particles = []
                 extra_head_particles = bond_head_index[mapping][1:]
                 for k in extra_head_particles:

diff --git a/grits/tests/test_finegrain.py b/grits/tests/test_finegrain.py
@@ -29,7 +29,7 @@ def test_backmap_snap_smiles(snap):
         bead_mapping = {"A": "C=CC1=CC=CC=C1"} # Mapping one A bead to 1 Polystyrene monomer
         head_indices = {"A": [10]}
         tail_indices = {"A": [9]}
-        
+
         fg_comp = backmap_snapshot_to_compound(
             snapshot=snap,
             bead_mapping=bead_mapping,
@@ -38,7 +38,7 @@ def test_backmap_snap_smiles(snap):
             ref_distance=0.3438,
             energy_minimize=False
         )
-        
+
         assert fg_comp.particles == snap.particles
         assert fg_comp.bonds == snap.bonds
 
@@ -49,15 +49,15 @@ def test_backmap_snap_library(snap):
             ref_distance=0.3438,
             energy_minimize=False
         )
-        
+
         assert fg_comp.particles == snap.particles
         assert fg_comp.bonds == snap.bonds
-        
+
     def test_backmap_snap_lists(snap):
         bead_mapping = {"A": "C[C@@H](C(=O)O)N"} # Mapping one A bead to 1 Polyalanine monomer
         head_indices = {"A":[4,10]}
         tail_indices = {"A":[12]}
-        
+
         fg_comp = backmap_snapshot_to_compound(
             snapshot=snap,
             bead_mapping=bead_mapping,
@@ -66,7 +66,7 @@ def test_backmap_snap_lists(snap):
             ref_distance=0.3438,
             energy_minimize=False
         )
-        
+
         assert fg_comp.particles == snap.particles
         assert fg_comp.bonds == snap.bonds
 
@@ -75,7 +75,7 @@ def test_backmap_snap_not_int(snap):
         bead_mapping = {"A": "C[C@@H](C(=O)O)N"} # Mapping one A bead to 1 Polyalanine monomer
         head_indices = {"A":[4.5,10]}
         tail_indices = {"A":[12]}
-        
+
         fg_comp = backmap_snapshot_to_compound(
             snapshot=snap,
             bead_mapping=bead_mapping,
@@ -84,4 +84,4 @@ def test_backmap_snap_not_int(snap):
             ref_distance=0.3438,
             energy_minimize=False
         )
-        pass #non-int should break code
+        pass #non-int should break code