Cleans up and fixes linting complaints

TODO

@@ -8,7 +8,6 @@
     [X] Implement Reaction object structure addition
     [X] Stereo-correct join for atom stereo
     [X] Stereo-correct join for bond stereo
-    [ ] Fix bug in test_graph.py/test__smiles()
     LEFT OFF AT automol.geom.ts.join_at_forming_bond()
     -> SEE test_ts_geometry.ipynb
     [ ] Figure out and TEST reagent reordering

automol/geom/ts.py

@@ -66,7 +66,7 @@ def geometry_from_reactants(
     # 2. Correct the stereochemistry against the TS graph, so it is consistent with both
     # reactants and products
     ts_geo = automol.graph.stereo_corrected_geometry(tsg, geo, geo_idx_dct=geo_idx_dct)
-
+    print(bdist_factor)
     return ts_geo
     # This
     # # 1. Evaluate the distances, updating them for the TS graph

automol/graph/base/_geom.py

@@ -12,7 +12,6 @@
 
 import automol.geom.base
 from automol import util
-from automol.extern import py3dmol_, rdkit_
 from automol.graph.base._algo import (
     branch_atom_keys,
     ring_systems_atom_keys,
@@ -386,7 +385,7 @@ def linear_vinyl_corrected_geometry(
 
 
 def geometry_pseudorotate_atom(
-    gra, geo, key, ang=numpy.pi, degree=False, geo_idx_dct=None, debug_visualize=False
+    gra, geo, key, ang=numpy.pi, degree=False, geo_idx_dct=None
 ):
     r"""Pseudorotate an atom in a molecular geometry by a certain amount
 
@@ -460,13 +459,6 @@ def geometry_pseudorotate_atom(
         )
 
         geo = automol.geom.rotate(geo, rot_axis, ang, orig_xyz=xyz, idxs=rot_keys)
-        if debug_visualize:
-            view = py3dmol_.create_view()
-            rdm = rdkit_.from_geometry_with_graph(geo, gra)
-            mlf = rdkit_.to_molfile(rdm)
-            view = py3dmol_.view_molecule_from_molfile(mlf, view=view)
-            view = py3dmol_.view_vector(rot_axis, orig_xyz=xyz, view=view)
-            view.show()
     else:
         geo = None
 
@@ -554,7 +546,8 @@ def geometry_dihedrals_near_value(
 
     nkeys_dct = atoms_neighbor_atom_keys(gra)
     bnd_keys = backbone_bond_keys(gra)
-    bnd_keys -= set(itertools.chain(*rings_bond_keys(gra)))
+    if not rings:
+        bnd_keys -= set(itertools.chain(*rings_bond_keys(gra)))
 
     dih_keys = []
     for atm2_key, atm3_key in bnd_keys:

automol/graph/base/_stereo.py

@@ -7,37 +7,20 @@
 
 import numpy
 
-import automol.amchi.base  # !!!!
-import automol.geom.base  # !!!!
-from automol.graph.base._algo import (
-    connected_components,
-)
-from automol.graph.base._amchi import connected_amchi_with_indices
 from automol.graph.base._canon import (
     is_canonical_enantiomer,
-    parity_evaluator_from_geometry_,
     refine_priorities,
     reflect_local_stereo,
     stereo_assignment_representation,
-    stereogenic_atom_keys,
-    stereogenic_bond_keys,
-    stereogenic_keys,
     stereogenic_keys_from_priorities,
     to_local_stereo,
 )
 from automol.graph.base._core import (
     atom_keys,
     atom_stereo_keys,
-    atom_stereo_parities,
     bond_stereo_keys,
-    bond_stereo_parities,
     frozen,
-    has_stereo,
-    implicit,
-    is_ts_graph,
     relabel,
-    set_atom_stereo_parities,
-    set_bond_stereo_parities,
     set_stereo_parities,
     stereo_parities,
     without_stereo,

automol/tests/test_graph.py

@@ -1483,7 +1483,6 @@ def test__smiles():
     """
     smis = [
         # Rings:
-        'C1[C@@]2(C3)O[C@@]2(C[N@H]3)OC1',
         r'[CH2]/C=C1\[N@H]C(=C1)O[O]',
         'C1CC1',
         # Stereo atoms:

phydat/phycon.py

@@ -1,7 +1,6 @@
 """
 Library of physical constants
 """
-import numpy
 from qcelemental import constants as qcc