Dihedral Plots: RDKit Mol Object

mdpow/tests/test_automated_dihedral_analysis.py

@@ -249,13 +249,17 @@ def test_periodic_angle(self, dihedral_data):
         aug_dh2_var == pytest.approx(self.ADG_C13141520_var)
 
     # Possible ordering issue (#239)
+    # Tests using similar instances of the automated analyses
+    # will use module or class-scoped fixtures, pending #235
     def test_save_fig(self, SM25_tmp_dir):
         dihedrals.automated_dihedral_analysis(dirname=SM25_tmp_dir, figdir=SM25_tmp_dir,
                                               resname=resname, molname='SM25',
                                               solvents=('water',))
         assert (SM25_tmp_dir / 'SM25' / 'SM25_C10-C5-S4-O11_violins.pdf').exists(), 'PDF file not generated'
 
     # Possible ordering issue (#239)
+    # Tests using similar instances of the automated analyses
+    # will use module or class-scoped fixtures, pending #235
     def test_save_fig_info(self, SM25_tmp_dir, caplog):
         caplog.clear()
         caplog.set_level(logging.INFO, logger='mdpow.workflows.dihedrals')
@@ -264,13 +268,17 @@ def test_save_fig_info(self, SM25_tmp_dir, caplog):
                                               solvents=('water',))
         assert f'Figure saved as {SM25_tmp_dir}/SM25/SM25_C10-C5-S4-O11_violins.pdf' in caplog.text, 'PDF file not saved'
 
+    # Tests using similar instances of the automated analyses
+    # will use module or class-scoped fixtures, pending #235
     def test_DataFrame_input(self, SM25_tmp_dir, dihedral_data):
         df, _ = dihedral_data
         dihedrals.automated_dihedral_analysis(dirname=SM25_tmp_dir, figdir=SM25_tmp_dir,
                                               resname=resname, molname=molname,
                                               solvents=('water',), dataframe=df)
         assert (SM25_tmp_dir / 'SM25' / 'SM25_C10-C5-S4-O11_violins.pdf').exists(), 'PDF file not generated'
 
+    # Tests using similar instances of the automated analyses
+    # will use module or class-scoped fixtures, pending #235
     def test_DataFrame_input_info(self, SM25_tmp_dir, dihedral_data, caplog):
         caplog.clear()
         caplog.set_level(logging.INFO, logger='mdpow.workflows.dihedrals')

mdpow/workflows/dihedrals.py

@@ -130,6 +130,8 @@ def build_universe(dirname, solvents=SOLVENTS_DEFAULT):
 
         *solvents*
            The default solvents are documented under :data:`SOLVENTS_DEFAULT`.
+           Normally takes a two-tuple, but analysis is compatible with single solvent selections.
+           Single solvent analyses will result in a figure with fully filled violins for the single solvent.
 
        :returns:
 
@@ -187,7 +189,6 @@ def rdkit_conversion(u, resname):
         solute = u.select_atoms(f'resname {resname}')
         mol = solute.convert_to('RDKIT')
 
-    solute.unwrap(compound='residues', reference='com')
     rdCoordGen.AddCoords(mol)
 
     for atom in mol.GetAtoms():
@@ -361,6 +362,8 @@ def dihedral_groups_ensemble(dirname, atom_indices,
 
        *solvents*
            The default solvents are documented under :data:`SOLVENTS_DEFAULT`.
+           Normally takes a two-tuple, but analysis is compatible with single solvent selections.
+           Single solvent analyses will result in a figure with fully filled violins for the single solvent.
 
        *interactions*
            The default interactions are documented under :data:`INTERACTIONS_DEFAULT`.
@@ -506,6 +509,8 @@ def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None):
 
        *solvents*
            The default solvents are documented under :data:`SOLVENTS_DEFAULT`.
+           Normally takes a two-tuple, but analysis is compatible with single solvent selections.
+           Single solvent analyses will result in a figure with fully filled violins for the single solvent.
 
        *plot_title*
            generated by :func:`~mdpow.workflows.dihedrals.build_svg` using
@@ -531,19 +536,29 @@ def dihedral_violins(df, width=0.9, solvents=SOLVENTS_DEFAULT, plot_title=None):
                     len(df[df['interaction'] == "VDW"]["lambda"].unique()),
                     len(df[df['interaction'] == "Coulomb"]["lambda"].unique()) - 1]
 
-    solvs = list(solvents)
-    if len(solvs) < 2:
-        solvs.append('N/A')
-
-    g = sns.catplot(data=df, x="lambda", y="dihedral", hue="solvent", col="interaction",
-                    kind="violin", split=True, width=width, inner=None, cut=0,
-                    linewidth=0.5,
-                    hue_order=[solvs[0], solvs[1]], col_order=["Coulomb", "VDW", "Structure"],
-                    sharex=False, sharey=True,
-                    height=3.0, aspect=2.0,
-                    facet_kws={'ylim': (-180, 180),
-                               'gridspec_kws': {'width_ratios': width_ratios,
-                                                }})
+    # Usage in Jupyter causes matplotlib figure object output, not the completed figure
+    # Upcoming fix in issue #260
+    assert 0 < len(solvents) < 3, "one or two solvents must be specified, otherwise SOLVENTS_DEFAULT is used"
+    if len(list(solvents)) < 2: 
+        g = sns.catplot(data=df, x="lambda", y="dihedral", hue="solvent", col="interaction",
+                        kind="violin", split=False, width=width, inner=None, cut=0,
+                        linewidth=0.5,
+                        hue_order=list(solvents), col_order=["Coulomb", "VDW", "Structure"],
+                        sharex=False, sharey=True,
+                        height=3.0, aspect=2.0,
+                        facet_kws={'ylim': (-180, 180),
+                                'gridspec_kws': {'width_ratios': width_ratios,
+                                                    }})
+    else:
+        g = sns.catplot(data=df, x="lambda", y="dihedral", hue="solvent", col="interaction",
+                        kind="violin", split=True, width=width, inner=None, cut=0,
+                        linewidth=0.5,
+                        hue_order=list(solvents), col_order=["Coulomb", "VDW", "Structure"],
+                        sharex=False, sharey=True,
+                        height=3.0, aspect=2.0,
+                        facet_kws={'ylim': (-180, 180),
+                                'gridspec_kws': {'width_ratios': width_ratios,
+                                                    }})
 
     g.set_xlabels(r"$\lambda$")
     g.set_ylabels(r"dihedral angle $\phi$")
@@ -595,6 +610,8 @@ def build_svg(mol, molname, name_index_pairs, atom_group_selection,
 
        *solvents*
            The default solvents are documented under :data:`SOLVENTS_DEFAULT`.
+           Normally takes a two-tuple, but analysis is compatible with single solvent selections.
+           Single solvent analyses will result in a figure with fully filled violins for the single solvent.
 
        *width*
            width of the violin element (>1 overlaps)
@@ -684,6 +701,8 @@ def plot_dihedral_violins(df, resname, mol, name_index_pairs, figdir=None, molna
 
        *solvents*
            The default solvents are documented under :data:`SOLVENTS_DEFAULT`.
+           Normally takes a two-tuple, but analysis is compatible with single solvent selections.
+           Single solvent analyses will result in a figure with fully filled violins for the single solvent.
 
     '''
 
@@ -807,6 +826,8 @@ def automated_dihedral_analysis(dirname, resname,
 
        *solvents*
            The default solvents are documented under :data:`SOLVENTS_DEFAULT`.
+           Normally takes a two-tuple, but analysis is compatible with single solvent selections.
+           Single solvent analyses will result in a figure with fully filled violins for the single solvent.
 
        *interactions*
            The default interactions are documented under :data:`INTERACTIONS_DEFAULT`.