diff --git a/TODO b/TODO index e527688c..ea22b19b 100644 --- a/TODO +++ b/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 diff --git a/automol/geom/ts.py b/automol/geom/ts.py index 0c89d23b..fa262627 100644 --- a/automol/geom/ts.py +++ b/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 diff --git a/automol/graph/base/_geom.py b/automol/graph/base/_geom.py index 585d7754..919c3762 100644 --- a/automol/graph/base/_geom.py +++ b/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: diff --git a/automol/graph/base/_stereo.py b/automol/graph/base/_stereo.py index a23d23b5..16239f97 100644 --- a/automol/graph/base/_stereo.py +++ b/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, diff --git a/automol/tests/test_graph.py b/automol/tests/test_graph.py index 4292a8ef..972f84b9 100644 --- a/automol/tests/test_graph.py +++ b/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: diff --git a/phydat/phycon.py b/phydat/phycon.py index 873ba327..b76420b8 100644 --- a/phydat/phycon.py +++ b/phydat/phycon.py @@ -1,7 +1,6 @@ """ Library of physical constants """ -import numpy from qcelemental import constants as qcc