Format code with Blackdeepsource-transform-b65b5545

1 files changed, 37 insertions, 25 deletions

diff --git a/plip/visualization/visualize.py b/plip/visualization/visualize.py
index 4cd7a14..a551798 100644
--- a/plip/visualization/visualize.py
+++ b/plip/visualization/visualize.py
@@ -20,54 +20,63 @@ def visualize_in_pymol(plcomplex):
     lig_members = plcomplex.lig_members
     chain = plcomplex.chain
     if config.PEPTIDES:
-        vis.ligname = 'PeptideChain%s' % plcomplex.chain
+        vis.ligname = "PeptideChain%s" % plcomplex.chain
     if config.INTRA is not None:
-        vis.ligname = 'Intra%s' % plcomplex.chain
+        vis.ligname = "Intra%s" % plcomplex.chain
 
     ligname = vis.ligname
     hetid = plcomplex.hetid
 
     metal_ids = plcomplex.metal_ids
-    metal_ids_str = '+'.join([str(i) for i in metal_ids])
+    metal_ids_str = "+".join([str(i) for i in metal_ids])
 
     ########################
     # Basic visualizations #
     ########################
 
-    start_pymol(run=True, options='-pcq', quiet=not config.VERBOSE and not config.SILENT)
+    start_pymol(
+        run=True, options="-pcq", quiet=not config.VERBOSE and not config.SILENT
+    )
     vis.set_initial_representations()
 
     cmd.load(plcomplex.sourcefile)
-    current_name = cmd.get_object_list(selection='(all)')[0]
-    logger.debug(f'setting current_name to {current_name} and pdbid to {pdbid}')
+    current_name = cmd.get_object_list(selection="(all)")[0]
+    logger.debug(f"setting current_name to {current_name} and pdbid to {pdbid}")
     cmd.set_name(current_name, pdbid)
-    cmd.hide('everything', 'all')
+    cmd.hide("everything", "all")
     if config.PEPTIDES:
-        cmd.select(ligname, 'chain %s and not resn HOH' % plcomplex.chain)
+        cmd.select(ligname, "chain %s and not resn HOH" % plcomplex.chain)
     else:
-        cmd.select(ligname, 'resn %s and chain %s and resi %s*' % (hetid, chain, plcomplex.position))
-    logger.debug(f'selecting ligand for PDBID {pdbid} and ligand name {ligname}')
-    logger.debug(f'resn {hetid} and chain {chain} and resi {plcomplex.position}')
+        cmd.select(
+            ligname,
+            "resn %s and chain %s and resi %s*" % (hetid, chain, plcomplex.position),
+        )
+    logger.debug(f"selecting ligand for PDBID {pdbid} and ligand name {ligname}")
+    logger.debug(f"resn {hetid} and chain {chain} and resi {plcomplex.position}")
 
     # Visualize and color metal ions if there are any
     if not len(metal_ids) == 0:
         vis.select_by_ids(ligname, metal_ids, selection_exists=True)
-        cmd.show('spheres', 'id %s and %s' % (metal_ids_str, pdbid))
+        cmd.show("spheres", "id %s and %s" % (metal_ids_str, pdbid))
 
     # Additionally, select all members of composite ligands
     if len(lig_members) > 1:
         for member in lig_members:
             resid, chain, resnr = member[0], member[1], str(member[2])
-            cmd.select(ligname, '%s or (resn %s and chain %s and resi %s)' % (ligname, resid, chain, resnr))
-
-    cmd.show('sticks', ligname)
-    cmd.color('myblue')
-    cmd.color('myorange', ligname)
-    cmd.util.cnc('all')
+            cmd.select(
+                ligname,
+                "%s or (resn %s and chain %s and resi %s)"
+                % (ligname, resid, chain, resnr),
+            )
+
+    cmd.show("sticks", ligname)
+    cmd.color("myblue")
+    cmd.color("myorange", ligname)
+    cmd.util.cnc("all")
     if not len(metal_ids) == 0:
-        cmd.color('hotpink', 'id %s' % metal_ids_str)
-        cmd.hide('sticks', 'id %s' % metal_ids_str)
-        cmd.set('sphere_scale', 0.3, ligname)
+        cmd.color("hotpink", "id %s" % metal_ids_str)
+        cmd.hide("sticks", "id %s" % metal_ids_str)
+        cmd.set("sphere_scale", 0.3, ligname)
     cmd.deselect()
 
     vis.make_initial_selections()
@@ -91,9 +100,9 @@ def visualize_in_pymol(plcomplex):
     vis.additional_cleanup()
     if config.DNARECEPTOR:
         # Rename Cartoon selection to Line selection and change repr.
-        cmd.set_name('%sCartoon' % plcomplex.pdbid, '%sLines' % plcomplex.pdbid)
-        cmd.hide('cartoon', '%sLines' % plcomplex.pdbid)
-        cmd.show('lines', '%sLines' % plcomplex.pdbid)
+        cmd.set_name("%sCartoon" % plcomplex.pdbid, "%sLines" % plcomplex.pdbid)
+        cmd.hide("cartoon", "%sLines" % plcomplex.pdbid)
+        cmd.show("lines", "%sLines" % plcomplex.pdbid)
 
     if config.PEPTIDES:
         filename = "%s_PeptideChain%s" % (pdbid.upper(), plcomplex.chain)
@@ -104,7 +113,10 @@ def visualize_in_pymol(plcomplex):
         if config.PYMOL:
             vis.save_session(config.OUTPATH, override=filename)
     else:
-        filename = '%s_%s' % (pdbid.upper(), "_".join([hetid, plcomplex.chain, plcomplex.position]))
+        filename = "%s_%s" % (
+            pdbid.upper(),
+            "_".join([hetid, plcomplex.chain, plcomplex.position]),
+        )
         if config.PYMOL:
             vis.save_session(config.OUTPATH)
     if config.PICS: