Lower default PyMOL surface quality

Author: kfuku52

csubst/csubst

@@ -561,6 +561,8 @@ def _build_parser():
                       help='default=%(default)s: Gray value for no-substitution sites. 0=black, 100=white')
     site.add_argument('--pymol_transparency', metavar='FLOAT', default=0.65, required=False, type=float,
                       help='default=%(default)s: Surface transparency. 0=non-transparent, 1=completely transparent')
+    site.add_argument('--pymol_surface_quality', metavar='INT', default=-1, required=False, type=int,
+                      help='default=%(default)s: PyMOL surface quality setting. Lower values speed up surface generation at the cost of smoothness.')
     site.add_argument('--pymol_img', metavar='yes|no', default='yes', type=strtobool,
                       help='default=%(default)s: Whether to generate a rendered 6-view image file of protein structure.')
     site.add_argument('--pymol_max_num_chain', metavar='INT', default=20, required=False, type=int,

csubst/param.py

@@ -863,6 +863,8 @@ def get_global_parameters(args):
         )
         if (g['pymol_transparency'] < 0) or (g['pymol_transparency'] > 1):
             raise ValueError('--pymol_transparency should satisfy 0 <= value <= 1.')
+    if 'pymol_surface_quality' in g.keys():
+        g['pymol_surface_quality'] = int(g['pymol_surface_quality'])
     if 'pymol_max_num_chain' in g.keys():
         g['pymol_max_num_chain'] = int(g['pymol_max_num_chain'])
         if g['pymol_max_num_chain'] < 1:

csubst/parser_pymol.py

@@ -905,6 +905,7 @@ def set_substitution_colors(df, g, object_names, N_sub_cols):
 def write_pymol_session(df, g):
     df = df.reset_index(drop=True)
     _cmd_set('seq_view', 1)
+    _cmd_set('surface_quality', int(g.get('pymol_surface_quality', -1)))
     if g['remove_solvent']:
         _cmd_remove('solvent')
     if g['remove_ligand']:

tests/test_param_backend.py

@@ -823,6 +823,7 @@ def test_get_global_parameters_validates_site_database_and_pymol_ranges():
             mafft_ep=0.2,
             pymol_gray=80,
             pymol_transparency=0.65,
+            pymol_surface_quality=-1,
             pymol_max_num_chain=20,
         )
     )
@@ -832,6 +833,7 @@ def test_get_global_parameters_validates_site_database_and_pymol_ranges():
     assert g["mafft_ep"] == pytest.approx(0.2)
     assert g["pymol_gray"] == 80
     assert g["pymol_transparency"] == pytest.approx(0.65)
+    assert g["pymol_surface_quality"] == -1
     assert g["pymol_max_num_chain"] == 20
 
     with pytest.raises(ValueError, match="database_evalue_cutoff"):

tests/test_parser_pymol.py

@@ -740,14 +740,18 @@ def test_write_pymol_session_skips_ligand_preset_without_organic_atoms(tmp_path,
         "remove_ligand": "",
         "pymol_transparency": 0.1,
         "pymol_gray": 80,
+        "pymol_surface_quality": -1,
         "mask_subunit": False,
         "session_file_path": str(tmp_path / "out.pse"),
     }
     parser_pymol.write_pymol_session(df=df, g=g)
     assert not any("preset.ligand_sites_trans_hq" in cmd for cmd in commands)
     assert not any("util.cbag organic" in cmd for cmd in commands)
+    surface_quality_index = next(i for i, cmd in enumerate(commands) if "set surface_quality" in cmd)
     set_index = next(i for i, cmd in enumerate(commands) if "set transparency" in cmd)
     show_surface_index = next(i for i, cmd in enumerate(commands) if cmd == "show surface")
+    assert "set surface_quality, -1" in commands[surface_quality_index]
+    assert surface_quality_index < show_surface_index
     assert set_index < show_surface_index
 
 
@@ -770,9 +774,11 @@ def test_write_pymol_session_keeps_ligand_preset_with_organic_atoms(tmp_path, mo
         "remove_ligand": "",
         "pymol_transparency": 0.1,
         "pymol_gray": 80,
+        "pymol_surface_quality": 0,
         "mask_subunit": False,
         "session_file_path": str(tmp_path / "out.pse"),
     }
     parser_pymol.write_pymol_session(df=df, g=g)
     assert any("preset.ligand_sites_trans_hq" in cmd for cmd in commands)
     assert any("util.cbag organic" in cmd for cmd in commands)
+    assert any("set surface_quality, 0" in cmd for cmd in commands)