Fix linting issues

automol/geom/_extra.py

@@ -254,10 +254,10 @@ def is_unique(geo, geo_lst, check_dct=None):
 
 # def hydrogen_bonded_structure(geo, grxn=None,
 #                               dist_thresh=4.55, angle_thresh=1.92):
-def hydrogen_bonded_structure(geo, grxn=None,
-                              dist_thresh=4.92, angle_thresh=1.92):
 # def hydrogen_bonded_structure(geo, grxn=None,
 #                               dist_thresh=5.3, angle_thresh=1.92):
+def hydrogen_bonded_structure(geo, grxn=None,
+                              dist_thresh=4.92, angle_thresh=1.92):
     """ Compare bond lengths in structure to determine if there
         is a hydrogen bond
 

automol/inchi/_conv.py

@@ -186,7 +186,7 @@ def add_stereo(ich):
         :rtype: str
     """
     geo = geometry(ich)
-    print ('geometry test:',automol.geom.string(geo))
+    print('geometry test:', automol.geom.string(geo))
     ich = automol.geom.inchi(geo, stereo=True)
     return ich
 

automol/par.py

@@ -102,9 +102,9 @@ def string(rxn_class):
     cls_str = typ(rxn_class)
 
     out_str = ''
-    for string in (isc_str, radrad_str, spin_str, cls_str):
-        if string:
-            out_str += '{} '.format(string)
+    for str_ in (isc_str, radrad_str, spin_str, cls_str):
+        if str_:
+            out_str += '{} '.format(str_)
 
     return out_str.strip()
 

automol/reac/_enum.py

@@ -100,7 +100,10 @@ def hydrogen_migrations(rct_gras, viable_only=True):
 
 
 # 2. Homolytic scissions
-def homolytic_scissions(rct_gras, viable_only=True):
+# AVC comment: replaced commented-out if statement by changing the default here
+# to False. Is the viability check broken for this case?
+# def homolytic_scissions(rct_gras, viable_only=True):
+def homolytic_scissions(rct_gras, viable_only=False):
     """ find all possible homolytic scission reactions for these reactants
 
     :param rct_gras: graphs for the reactants, without stereo and without
@@ -149,8 +152,8 @@ def homolytic_scissions(rct_gras, viable_only=True):
                     prds_keys=list(map(atom_keys, prd_gras)),
                 ))
     # filter removes all reactions
-    # if viable_only:
-    #    rxns = filter_viable_reactions(rxns)
+    if viable_only:
+        rxns = filter_viable_reactions(rxns)
 
     return ts_unique(rxns)
 

automol/reac/_scan.py

@@ -233,7 +233,7 @@ def elimination_grid(zrxn, zma, npoints=(7, 5)):
 
     grid1 = numpy.linspace(r1min, r1max, npoints1)
     grid2 = numpy.linspace(r2min, r2max, npoints2)
-    
+
     print(automol.zmat.string(zma))
     print(frm_name, frm_bnd_len)
     print(grid1)

automol/reac/_zmat.py

@@ -385,5 +385,5 @@ def _zma_names(zma, bnd_keys):
 
     frm_bnd_keys = ts.forming_bond_keys(zrxn.forward_ts_graph)
     brk_bnd_keys = ts.breaking_bond_keys(zrxn.forward_ts_graph)
-  
+
     return (_zma_names(zma, frm_bnd_keys), _zma_names(zma, brk_bnd_keys))

automol/rotor/_rotor.py

@@ -119,7 +119,8 @@ def grids(rotor_lst,
     for rotor in rotor_lst:
         rotor_grids = ()
         for torsion in rotor:
-            print('rotor grids input test:', torsion.zma, torsion.name, span, torsion.symmetry, increment)
+            print('rotor grids input test:', torsion.zma, torsion.name,
+                  span, torsion.symmetry, increment)
             rotor_grids += (
                 automol.pot.grid(
                     torsion.zma, torsion.name,

automol/tests/test_reac.py

@@ -4,7 +4,7 @@
 import numpy
 import automol
 from automol.par import ReactionClass
-from automol.graph import ts
+# from automol.graph import ts
 
 SUBSTITUTION_RXN_STR = """
 reaction class: substitution
@@ -894,8 +894,8 @@ def _check_reaction(rxn_obj,
     # print(automol.zmat.string(zma))
     # print(zrxn)
 
-    frm_bnd_keys = ts.forming_bond_keys(zrxn.forward_ts_graph)
-    brk_bnd_keys = ts.breaking_bond_keys(zrxn.forward_ts_graph)
+    # frm_bnd_keys = ts.forming_bond_keys(zrxn.forward_ts_graph)
+    # brk_bnd_keys = ts.breaking_bond_keys(zrxn.forward_ts_graph)
     # print('keys')
     # print(frm_bnd_keys)
     # print(brk_bnd_keys)
@@ -918,7 +918,7 @@ def _check_reaction(rxn_obj,
     gbnd_keys = automol.reac.rotational_bond_keys(grxn)
     assert len(gbnd_keys) == len(bnd_keys)
 
-    zaxes = sorted(map(sorted, bnd_keys))
+    # zaxes = sorted(map(sorted, bnd_keys))
     axes = sorted(map(sorted, gbnd_keys))
     tors_symms = [automol.reac.rotational_symmetry_number(grxn, *a)
                   for a in axes]

phydat/phycon.py

@@ -15,9 +15,9 @@
 SOL = (qcc.get('speed of light in vacuum') *
        qcc.conversion_factor('meter / second', 'bohr hartree / h'))
 SOLMS = qcc.get('speed of light in vacuum')
-KB = qcc.get('kb') # The Boltzmann constant (JK$^{-1}$)
-H = qcc.get('h') # The Planck constant (Js)
-HBAR = qcc.get('hbar') # The Planck constant (Js) over 2pi
+KB = qcc.get('kb')  # The Boltzmann constant (JK$^{-1}$)
+H = qcc.get('h')  # The Planck constant (Js)
+HBAR = qcc.get('hbar')  # The Planck constant (Js) over 2pi
 
 # Energy Conversion factors
 KCAL2CAL = qcc.conversion_factor('kcal/mol', 'cal/mol')