Style changes: Fix indentations

Author: JHKru

src/springcraft/nma.py

@@ -327,8 +327,9 @@ def dcc(enm, mode_subset=None, norm=True, tem=None, tem_factors=K_B):
     elif all_modes:
         # 3N x 3N -> N x 3 x N x 3 -> N x N x 3 x 3
         cov = enm.covariance
-        reshaped = cov.reshape(cov.shape[0]//3, 3, cov.shape[0]//3, 3
-                               ).swapaxes(1,2)
+        reshaped = cov.reshape(
+            cov.shape[0]//3, 3, cov.shape[0]//3, 3
+        ).swapaxes(1,2)
         # Accept array of any dimension 
         # -> Sum over diagonals in last two dims
         # -> Return any shape (in this case NxN)
@@ -340,8 +341,9 @@ def dcc(enm, mode_subset=None, norm=True, tem=None, tem_factors=K_B):
 
         # Reshape array of eigenvectors
         # (k,3n) -> (k,n,3) for ANMs; (k,n) -> (k,n,1) for GNMs
-        modes_reshaped = np.reshape(eig_vectors, (len(mode_subset), -1, num_dim)
-                                    )
+        modes_reshaped = np.reshape(
+            eig_vectors, (len(mode_subset), -1, num_dim)
+        )
         dcc = np.zeros((n_nodes, n_nodes))
         for ev, evec in zip(eig_values, modes_reshaped):
             dcc += (evec @ evec.T) / ev

tests/test_anm.py

@@ -189,9 +189,10 @@ def test_frequency_fluctuation_dcc(ff_name):
             # no temperature weighting
             tem_scaling = 1
             tem = 1
-            reference_fluc = np.genfromtxt(join(data_dir(), ref_fluc),
-                                            skip_header=1, delimiter=","
-                                        )
+            reference_fluc = np.genfromtxt(
+                join(data_dir(), ref_fluc),
+                skip_header=1, delimiter=","
+            )
 
         # Bio3d -> Mass- and temperature weighting
         else:
@@ -206,15 +207,19 @@ def test_frequency_fluctuation_dcc(ff_name):
                 ff_bio3d_str = "pfanm"
 
             # ENM-NMA -> Reference
-            enm_nma_bio3d = bio3d.nma(pdb=pdb_bio3d, ff=ff_bio3d_str, mass=True)
+            enm_nma_bio3d = bio3d.nma(
+                pdb=pdb_bio3d, ff=ff_bio3d_str, mass=True
+            )
             reference_masses = np.array(enm_nma_bio3d.rx2["mass"])
             reference_freq = np.array(enm_nma_bio3d.rx2["frequencies"])
             reference_fluc = np.array(enm_nma_bio3d.rx2["fluctuations"])
-            reference_fluc_subset = np.array(bio3d.fluct_nma(
-                                            enm_nma_bio3d, mode_inds=r_seq(12,33)
-                                            ))
+            reference_fluc_subset = np.array(
+                bio3d.fluct_nma(enm_nma_bio3d, mode_inds=r_seq(12,33))
+            )
             reference_dcc = np.array(bio3d.dccm(enm_nma_bio3d))
-            reference_dcc_subset = np.array(bio3d.dccm(enm_nma_bio3d, nmodes=30))
+            reference_dcc_subset = np.array(
+                bio3d.dccm(enm_nma_bio3d, nmodes=30)
+            )
 
             tem_scaling = K_B*N_A
             test_nomw = springcraft.ANM(ca, ff)