Format code with Blackdeepsource-transform-b65b5545

1 files changed, 384 insertions, 234 deletions

diff --git a/plip/visualization/pymol.py b/plip/visualization/pymol.py
index b97912a..2e1b0e3 100644
--- a/plip/visualization/pymol.py
+++ b/plip/visualization/pymol.py
@@ -7,7 +7,6 @@ from pymol import cmd
 
 
 class PyMOLVisualizer:
-
     def __init__(self, plcomplex):
         if plcomplex is not None:
             self.plcomplex = plcomplex
@@ -20,57 +19,86 @@ class PyMOLVisualizer:
     def set_initial_representations(self):
         """General settings for PyMOL"""
         self.standard_settings()
-        cmd.set('dash_gap', 0)  # Show not dashes, but lines for the pliprofiler
-        cmd.set('ray_shadow', 0)  # Turn on ray shadows for clearer ray-traced images
-        cmd.set('cartoon_color', 'mylightblue')
+        cmd.set("dash_gap", 0)  # Show not dashes, but lines for the pliprofiler
+        cmd.set("ray_shadow", 0)  # Turn on ray shadows for clearer ray-traced images
+        cmd.set("cartoon_color", "mylightblue")
 
         # Set clipping planes for full view
-        cmd.clip('far', -1000)
-        cmd.clip('near', 1000)
+        cmd.clip("far", -1000)
+        cmd.clip("near", 1000)
 
     def make_initial_selections(self):
         """Make empty selections for structures and interactions"""
-        for group in ['Hydrophobic-P', 'Hydrophobic-L', 'HBondDonor-P',
-                      'HBondDonor-L', 'HBondAccept-P', 'HBondAccept-L',
-                      'HalogenAccept', 'HalogenDonor', 'Water', 'MetalIons', 'StackRings-P',
-                      'PosCharge-P', 'PosCharge-L', 'NegCharge-P', 'NegCharge-L',
-                      'PiCatRing-P', 'StackRings-L', 'PiCatRing-L', 'Metal-M', 'Metal-P',
-                      'Metal-W', 'Metal-L', 'Unpaired-HBA', 'Unpaired-HBD', 'Unpaired-HAL',
-                      'Unpaired-RINGS']:
-            cmd.select(group, 'None')
+        for group in [
+            "Hydrophobic-P",
+            "Hydrophobic-L",
+            "HBondDonor-P",
+            "HBondDonor-L",
+            "HBondAccept-P",
+            "HBondAccept-L",
+            "HalogenAccept",
+            "HalogenDonor",
+            "Water",
+            "MetalIons",
+            "StackRings-P",
+            "PosCharge-P",
+            "PosCharge-L",
+            "NegCharge-P",
+            "NegCharge-L",
+            "PiCatRing-P",
+            "StackRings-L",
+            "PiCatRing-L",
+            "Metal-M",
+            "Metal-P",
+            "Metal-W",
+            "Metal-L",
+            "Unpaired-HBA",
+            "Unpaired-HBD",
+            "Unpaired-HAL",
+            "Unpaired-RINGS",
+        ]:
+            cmd.select(group, "None")
 
     def standard_settings(self):
         """Sets up standard settings for a nice visualization."""
-        cmd.set('bg_rgb', [1.0, 1.0, 1.0])  # White background
-        cmd.set('depth_cue', 0)  # Turn off depth cueing (no fog)
-        cmd.set('cartoon_side_chain_helper', 1)  # Improve combined visualization of sticks and cartoon
-        cmd.set('cartoon_fancy_helices', 1)  # Nicer visualization of helices (using tapered ends)
-        cmd.set('transparency_mode', 1)  # Turn on multilayer transparency
-        cmd.set('dash_radius', 0.05)
+        cmd.set("bg_rgb", [1.0, 1.0, 1.0])  # White background
+        cmd.set("depth_cue", 0)  # Turn off depth cueing (no fog)
+        cmd.set(
+            "cartoon_side_chain_helper", 1
+        )  # Improve combined visualization of sticks and cartoon
+        cmd.set(
+            "cartoon_fancy_helices", 1
+        )  # Nicer visualization of helices (using tapered ends)
+        cmd.set("transparency_mode", 1)  # Turn on multilayer transparency
+        cmd.set("dash_radius", 0.05)
         self.set_custom_colorset()
 
     def set_custom_colorset(self):
         """Defines a colorset with matching colors. Provided by Joachim."""
-        cmd.set_color('myorange', '[253, 174, 97]')
-        cmd.set_color('mygreen', '[171, 221, 164]')
-        cmd.set_color('myred', '[215, 25, 28]')
-        cmd.set_color('myblue', '[43, 131, 186]')
-        cmd.set_color('mylightblue', '[158, 202, 225]')
-        cmd.set_color('mylightgreen', '[229, 245, 224]')
-
-    def select_by_ids(self, selname, idlist, selection_exists=False, chunksize=20, restrict=None):
+        cmd.set_color("myorange", "[253, 174, 97]")
+        cmd.set_color("mygreen", "[171, 221, 164]")
+        cmd.set_color("myred", "[215, 25, 28]")
+        cmd.set_color("myblue", "[43, 131, 186]")
+        cmd.set_color("mylightblue", "[158, 202, 225]")
+        cmd.set_color("mylightgreen", "[229, 245, 224]")
+
+    def select_by_ids(
+        self, selname, idlist, selection_exists=False, chunksize=20, restrict=None
+    ):
         """Selection with a large number of ids concatenated into a selection
         list can cause buffer overflow in PyMOL. This function takes a selection
         name and and list of IDs (list of integers) as input and makes a careful
         step-by-step selection (packages of 20 by default)"""
         idlist = list(set(idlist))  # Remove duplicates
         if not selection_exists:
-            cmd.select(selname, 'None')  # Empty selection first
-        idchunks = [idlist[i:i + chunksize] for i in range(0, len(idlist), chunksize)]
+            cmd.select(selname, "None")  # Empty selection first
+        idchunks = [idlist[i : i + chunksize] for i in range(0, len(idlist), chunksize)]
         for idchunk in idchunks:
-            cmd.select(selname, '%s or (id %s)' % (selname, '+'.join(map(str, idchunk))))
+            cmd.select(
+                selname, "%s or (id %s)" % (selname, "+".join(map(str, idchunk)))
+            )
         if restrict is not None:
-            cmd.select(selname, '%s and %s' % (selname, restrict))
+            cmd.select(selname, "%s and %s" % (selname, restrict))
 
     def object_exists(self, object_name):
         """Checks if an object exists in the open PyMOL session."""
@@ -80,40 +108,44 @@ class PyMOLVisualizer:
         """Visualizes hydrophobic contacts."""
         hydroph = self.plcomplex.hydrophobic_contacts
         if not len(hydroph.bs_ids) == 0:
-            self.select_by_ids('Hydrophobic-P', hydroph.bs_ids, restrict=self.protname)
-            self.select_by_ids('Hydrophobic-L', hydroph.lig_ids, restrict=self.ligname)
+            self.select_by_ids("Hydrophobic-P", hydroph.bs_ids, restrict=self.protname)
+            self.select_by_ids("Hydrophobic-L", hydroph.lig_ids, restrict=self.ligname)
 
             for i in hydroph.pairs_ids:
-                cmd.select('tmp_bs', 'id %i & %s' % (i[0], self.protname))
-                cmd.select('tmp_lig', 'id %i & %s' % (i[1], self.ligname))
-                cmd.distance('Hydrophobic', 'tmp_bs', 'tmp_lig')
-            if self.object_exists('Hydrophobic'):
-                cmd.set('dash_gap', 0.5, 'Hydrophobic')
-                cmd.set('dash_color', 'grey50', 'Hydrophobic')
+                cmd.select("tmp_bs", "id %i & %s" % (i[0], self.protname))
+                cmd.select("tmp_lig", "id %i & %s" % (i[1], self.ligname))
+                cmd.distance("Hydrophobic", "tmp_bs", "tmp_lig")
+            if self.object_exists("Hydrophobic"):
+                cmd.set("dash_gap", 0.5, "Hydrophobic")
+                cmd.set("dash_color", "grey50", "Hydrophobic")
         else:
-            cmd.select('Hydrophobic-P', 'None')
+            cmd.select("Hydrophobic-P", "None")
 
     def show_hbonds(self):
         """Visualizes hydrogen bonds."""
         hbonds = self.plcomplex.hbonds
-        for group in [['HBondDonor-P', hbonds.prot_don_id],
-                      ['HBondAccept-P', hbonds.prot_acc_id]]:
+        for group in [
+            ["HBondDonor-P", hbonds.prot_don_id],
+            ["HBondAccept-P", hbonds.prot_acc_id],
+        ]:
             if not len(group[1]) == 0:
                 self.select_by_ids(group[0], group[1], restrict=self.protname)
-        for group in [['HBondDonor-L', hbonds.lig_don_id],
-                      ['HBondAccept-L', hbonds.lig_acc_id]]:
+        for group in [
+            ["HBondDonor-L", hbonds.lig_don_id],
+            ["HBondAccept-L", hbonds.lig_acc_id],
+        ]:
             if not len(group[1]) == 0:
                 self.select_by_ids(group[0], group[1], restrict=self.ligname)
         for i in hbonds.ldon_id:
-            cmd.select('tmp_bs', 'id %i & %s' % (i[0], self.protname))
-            cmd.select('tmp_lig', 'id %i & %s' % (i[1], self.ligname))
-            cmd.distance('HBonds', 'tmp_bs', 'tmp_lig')
+            cmd.select("tmp_bs", "id %i & %s" % (i[0], self.protname))
+            cmd.select("tmp_lig", "id %i & %s" % (i[1], self.ligname))
+            cmd.distance("HBonds", "tmp_bs", "tmp_lig")
         for i in hbonds.pdon_id:
-            cmd.select('tmp_bs', 'id %i & %s' % (i[1], self.protname))
-            cmd.select('tmp_lig', 'id %i & %s' % (i[0], self.ligname))
-            cmd.distance('HBonds', 'tmp_bs', 'tmp_lig')
-        if self.object_exists('HBonds'):
-            cmd.set('dash_color', 'blue', 'HBonds')
+            cmd.select("tmp_bs", "id %i & %s" % (i[1], self.protname))
+            cmd.select("tmp_lig", "id %i & %s" % (i[0], self.ligname))
+            cmd.distance("HBonds", "tmp_bs", "tmp_lig")
+        if self.object_exists("HBonds"):
+            cmd.set("dash_color", "blue", "HBonds")
 
     def show_halogen(self):
         """Visualize halogen bonds."""
@@ -122,155 +154,218 @@ class PyMOLVisualizer:
         for h in halogen:
             all_don_x.append(h.don_id)
             all_acc_o.append(h.acc_id)
-            cmd.select('tmp_bs', 'id %i & %s' % (h.acc_id, self.protname))
-            cmd.select('tmp_lig', 'id %i & %s' % (h.don_id, self.ligname))
+            cmd.select("tmp_bs", "id %i & %s" % (h.acc_id, self.protname))
+            cmd.select("tmp_lig", "id %i & %s" % (h.don_id, self.ligname))
 
-            cmd.distance('HalogenBonds', 'tmp_bs', 'tmp_lig')
+            cmd.distance("HalogenBonds", "tmp_bs", "tmp_lig")
         if not len(all_acc_o) == 0:
-            self.select_by_ids('HalogenAccept', all_acc_o, restrict=self.protname)
-            self.select_by_ids('HalogenDonor', all_don_x, restrict=self.ligname)
-        if self.object_exists('HalogenBonds'):
-            cmd.set('dash_color', 'greencyan', 'HalogenBonds')
+            self.select_by_ids("HalogenAccept", all_acc_o, restrict=self.protname)
+            self.select_by_ids("HalogenDonor", all_don_x, restrict=self.ligname)
+        if self.object_exists("HalogenBonds"):
+            cmd.set("dash_color", "greencyan", "HalogenBonds")
 
     def show_stacking(self):
         """Visualize pi-stacking interactions."""
         stacks = self.plcomplex.pistacking
         for i, stack in enumerate(stacks):
-            pires_ids = '+'.join(map(str, stack.proteinring_atoms))
-            pilig_ids = '+'.join(map(str, stack.ligandring_atoms))
-            cmd.select('StackRings-P', 'StackRings-P or (id %s & %s)' % (pires_ids, self.protname))
-            cmd.select('StackRings-L', 'StackRings-L or (id %s & %s)' % (pilig_ids, self.ligname))
-            cmd.select('StackRings-P', 'byres StackRings-P')
-            cmd.show('sticks', 'StackRings-P')
-
-            cmd.pseudoatom('ps-pistack-1-%i' % i, pos=stack.proteinring_center)
-            cmd.pseudoatom('ps-pistack-2-%i' % i, pos=stack.ligandring_center)
-            cmd.pseudoatom('Centroids-P', pos=stack.proteinring_center)
-            cmd.pseudoatom('Centroids-L', pos=stack.ligandring_center)
-
-            if stack.type == 'P':
-                cmd.distance('PiStackingP', 'ps-pistack-1-%i' % i, 'ps-pistack-2-%i' % i)
-            if stack.type == 'T':
-                cmd.distance('PiStackingT', 'ps-pistack-1-%i' % i, 'ps-pistack-2-%i' % i)
-        if self.object_exists('PiStackingP'):
-            cmd.set('dash_color', 'green', 'PiStackingP')
-            cmd.set('dash_gap', 0.3, 'PiStackingP')
-            cmd.set('dash_length', 0.6, 'PiStackingP')
-        if self.object_exists('PiStackingT'):
-            cmd.set('dash_color', 'smudge', 'PiStackingT')
-            cmd.set('dash_gap', 0.3, 'PiStackingT')
-            cmd.set('dash_length', 0.6, 'PiStackingT')
+            pires_ids = "+".join(map(str, stack.proteinring_atoms))
+            pilig_ids = "+".join(map(str, stack.ligandring_atoms))
+            cmd.select(
+                "StackRings-P",
+                "StackRings-P or (id %s & %s)" % (pires_ids, self.protname),
+            )
+            cmd.select(
+                "StackRings-L",
+                "StackRings-L or (id %s & %s)" % (pilig_ids, self.ligname),
+            )
+            cmd.select("StackRings-P", "byres StackRings-P")
+            cmd.show("sticks", "StackRings-P")
+
+            cmd.pseudoatom("ps-pistack-1-%i" % i, pos=stack.proteinring_center)
+            cmd.pseudoatom("ps-pistack-2-%i" % i, pos=stack.ligandring_center)
+            cmd.pseudoatom("Centroids-P", pos=stack.proteinring_center)
+            cmd.pseudoatom("Centroids-L", pos=stack.ligandring_center)
+
+            if stack.type == "P":
+                cmd.distance(
+                    "PiStackingP", "ps-pistack-1-%i" % i, "ps-pistack-2-%i" % i
+                )
+            if stack.type == "T":
+                cmd.distance(
+                    "PiStackingT", "ps-pistack-1-%i" % i, "ps-pistack-2-%i" % i
+                )
+        if self.object_exists("PiStackingP"):
+            cmd.set("dash_color", "green", "PiStackingP")
+            cmd.set("dash_gap", 0.3, "PiStackingP")
+            cmd.set("dash_length", 0.6, "PiStackingP")
+        if self.object_exists("PiStackingT"):
+            cmd.set("dash_color", "smudge", "PiStackingT")
+            cmd.set("dash_gap", 0.3, "PiStackingT")
+            cmd.set("dash_length", 0.6, "PiStackingT")
 
     def show_cationpi(self):
         """Visualize cation-pi interactions."""
         for i, p in enumerate(self.plcomplex.pication):
-            cmd.pseudoatom('ps-picat-1-%i' % i, pos=p.ring_center)
-            cmd.pseudoatom('ps-picat-2-%i' % i, pos=p.charge_center)
+            cmd.pseudoatom("ps-picat-1-%i" % i, pos=p.ring_center)
+            cmd.pseudoatom("ps-picat-2-%i" % i, pos=p.charge_center)
             if p.protcharged:
-                cmd.pseudoatom('Chargecenter-P', pos=p.charge_center)
-                cmd.pseudoatom('Centroids-L', pos=p.ring_center)
-                pilig_ids = '+'.join(map(str, p.ring_atoms))
-                cmd.select('PiCatRing-L', 'PiCatRing-L or (id %s & %s)' % (pilig_ids, self.ligname))
+                cmd.pseudoatom("Chargecenter-P", pos=p.charge_center)
+                cmd.pseudoatom("Centroids-L", pos=p.ring_center)
+                pilig_ids = "+".join(map(str, p.ring_atoms))
+                cmd.select(
+                    "PiCatRing-L",
+                    "PiCatRing-L or (id %s & %s)" % (pilig_ids, self.ligname),
+                )
                 for a in p.charge_atoms:
-                    cmd.select('PosCharge-P', 'PosCharge-P or (id %i & %s)' % (a, self.protname))
+                    cmd.select(
+                        "PosCharge-P",
+                        "PosCharge-P or (id %i & %s)" % (a, self.protname),
+                    )
             else:
-                cmd.pseudoatom('Chargecenter-L', pos=p.charge_center)
-                cmd.pseudoatom('Centroids-P', pos=p.ring_center)
-                pires_ids = '+'.join(map(str, p.ring_atoms))
-                cmd.select('PiCatRing-P', 'PiCatRing-P or (id %s & %s)' % (pires_ids, self.protname))
+                cmd.pseudoatom("Chargecenter-L", pos=p.charge_center)
+                cmd.pseudoatom("Centroids-P", pos=p.ring_center)
+                pires_ids = "+".join(map(str, p.ring_atoms))
+                cmd.select(
+                    "PiCatRing-P",
+                    "PiCatRing-P or (id %s & %s)" % (pires_ids, self.protname),
+                )
                 for a in p.charge_atoms:
-                    cmd.select('PosCharge-L', 'PosCharge-L or (id %i & %s)' % (a, self.ligname))
-            cmd.distance('PiCation', 'ps-picat-1-%i' % i, 'ps-picat-2-%i' % i)
-        if self.object_exists('PiCation'):
-            cmd.set('dash_color', 'orange', 'PiCation')
-            cmd.set('dash_gap', 0.3, 'PiCation')
-            cmd.set('dash_length', 0.6, 'PiCation')
+                    cmd.select(
+                        "PosCharge-L", "PosCharge-L or (id %i & %s)" % (a, self.ligname)
+                    )
+            cmd.distance("PiCation", "ps-picat-1-%i" % i, "ps-picat-2-%i" % i)
+        if self.object_exists("PiCation"):
+            cmd.set("dash_color", "orange", "PiCation")
+            cmd.set("dash_gap", 0.3, "PiCation")
+            cmd.set("dash_length", 0.6, "PiCation")
 
     def show_sbridges(self):
         """Visualize salt bridges."""
         for i, saltb in enumerate(self.plcomplex.saltbridges):
             if saltb.protispos:
                 for patom in saltb.positive_atoms:
-                    cmd.select('PosCharge-P', 'PosCharge-P or (id %i & %s)' % (patom, self.protname))
+                    cmd.select(
+                        "PosCharge-P",
+                        "PosCharge-P or (id %i & %s)" % (patom, self.protname),
+                    )
                 for latom in saltb.negative_atoms:
-                    cmd.select('NegCharge-L', 'NegCharge-L or (id %i & %s)' % (latom, self.ligname))
-                for sbgroup in [['ps-sbl-1-%i' % i, 'Chargecenter-P', saltb.positive_center],
-                                ['ps-sbl-2-%i' % i, 'Chargecenter-L', saltb.negative_center]]:
+                    cmd.select(
+                        "NegCharge-L",
+                        "NegCharge-L or (id %i & %s)" % (latom, self.ligname),
+                    )
+                for sbgroup in [
+                    ["ps-sbl-1-%i" % i, "Chargecenter-P", saltb.positive_center],
+                    ["ps-sbl-2-%i" % i, "Chargecenter-L", saltb.negative_center],
+                ]:
                     cmd.pseudoatom(sbgroup[0], pos=sbgroup[2])
                     cmd.pseudoatom(sbgroup[1], pos=sbgroup[2])
-                cmd.distance('Saltbridges', 'ps-sbl-1-%i' % i, 'ps-sbl-2-%i' % i)
+                cmd.distance("Saltbridges", "ps-sbl-1-%i" % i, "ps-sbl-2-%i" % i)
             else:
                 for patom in saltb.negative_atoms:
-                    cmd.select('NegCharge-P', 'NegCharge-P or (id %i & %s)' % (patom, self.protname))
+                    cmd.select(
+                        "NegCharge-P",
+                        "NegCharge-P or (id %i & %s)" % (patom, self.protname),
+                    )
                 for latom in saltb.positive_atoms:
-                    cmd.select('PosCharge-L', 'PosCharge-L or (id %i & %s)' % (latom, self.ligname))
-                for sbgroup in [['ps-sbp-1-%i' % i, 'Chargecenter-P', saltb.negative_center],
-                                ['ps-sbp-2-%i' % i, 'Chargecenter-L', saltb.positive_center]]:
+                    cmd.select(
+                        "PosCharge-L",
+                        "PosCharge-L or (id %i & %s)" % (latom, self.ligname),
+                    )
+                for sbgroup in [
+                    ["ps-sbp-1-%i" % i, "Chargecenter-P", saltb.negative_center],
+                    ["ps-sbp-2-%i" % i, "Chargecenter-L", saltb.positive_center],
+                ]:
                     cmd.pseudoatom(sbgroup[0], pos=sbgroup[2])
                     cmd.pseudoatom(sbgroup[1], pos=sbgroup[2])
-                cmd.distance('Saltbridges', 'ps-sbp-1-%i' % i, 'ps-sbp-2-%i' % i)
+                cmd.distance("Saltbridges", "ps-sbp-1-%i" % i, "ps-sbp-2-%i" % i)
 
-        if self.object_exists('Saltbridges'):
-            cmd.set('dash_color', 'yellow', 'Saltbridges')
-            cmd.set('dash_gap', 0.5, 'Saltbridges')
+        if self.object_exists("Saltbridges"):
+            cmd.set("dash_color", "yellow", "Saltbridges")
+            cmd.set("dash_gap", 0.5, "Saltbridges")
 
     def show_wbridges(self):
         """Visualize water bridges."""
         for bridge in self.plcomplex.waterbridges:
             if bridge.protisdon:
-                cmd.select('HBondDonor-P', 'HBondDonor-P or (id %i & %s)' % (bridge.don_id, self.protname))
-                cmd.select('HBondAccept-L', 'HBondAccept-L or (id %i & %s)' % (bridge.acc_id, self.ligname))
-                cmd.select('tmp_don', 'id %i & %s' % (bridge.don_id, self.protname))
-                cmd.select('tmp_acc', 'id %i & %s' % (bridge.acc_id, self.ligname))
+                cmd.select(
+                    "HBondDonor-P",
+                    "HBondDonor-P or (id %i & %s)" % (bridge.don_id, self.protname),
+                )
+                cmd.select(
+                    "HBondAccept-L",
+                    "HBondAccept-L or (id %i & %s)" % (bridge.acc_id, self.ligname),
+                )
+                cmd.select("tmp_don", "id %i & %s" % (bridge.don_id, self.protname))
+                cmd.select("tmp_acc", "id %i & %s" % (bridge.acc_id, self.ligname))
             else:
-                cmd.select('HBondDonor-L', 'HBondDonor-L or (id %i & %s)' % (bridge.don_id, self.ligname))
-                cmd.select('HBondAccept-P', 'HBondAccept-P or (id %i & %s)' % (bridge.acc_id, self.protname))
-                cmd.select('tmp_don', 'id %i & %s' % (bridge.don_id, self.ligname))
-                cmd.select('tmp_acc', 'id %i & %s' % (bridge.acc_id, self.protname))
-            cmd.select('Water', 'Water or (id %i & resn HOH)' % bridge.water_id)
-            cmd.select('tmp_water', 'id %i & resn HOH' % bridge.water_id)
-            cmd.distance('WaterBridges', 'tmp_acc', 'tmp_water')
-            cmd.distance('WaterBridges', 'tmp_don', 'tmp_water')
-        if self.object_exists('WaterBridges'):
-            cmd.set('dash_color', 'lightblue', 'WaterBridges')
-        cmd.delete('tmp_water or tmp_acc or tmp_don')
-        cmd.color('lightblue', 'Water')
-        cmd.show('spheres', 'Water')
+                cmd.select(
+                    "HBondDonor-L",
+                    "HBondDonor-L or (id %i & %s)" % (bridge.don_id, self.ligname),
+                )
+                cmd.select(
+                    "HBondAccept-P",
+                    "HBondAccept-P or (id %i & %s)" % (bridge.acc_id, self.protname),
+                )
+                cmd.select("tmp_don", "id %i & %s" % (bridge.don_id, self.ligname))
+                cmd.select("tmp_acc", "id %i & %s" % (bridge.acc_id, self.protname))
+            cmd.select("Water", "Water or (id %i & resn HOH)" % bridge.water_id)
+            cmd.select("tmp_water", "id %i & resn HOH" % bridge.water_id)
+            cmd.distance("WaterBridges", "tmp_acc", "tmp_water")
+            cmd.distance("WaterBridges", "tmp_don", "tmp_water")
+        if self.object_exists("WaterBridges"):
+            cmd.set("dash_color", "lightblue", "WaterBridges")
+        cmd.delete("tmp_water or tmp_acc or tmp_don")
+        cmd.color("lightblue", "Water")
+        cmd.show("spheres", "Water")
 
     def show_metal(self):
         """Visualize metal coordination."""
         metal_complexes = self.plcomplex.metal_complexes
         if not len(metal_complexes) == 0:
-            self.select_by_ids('Metal-M', self.metal_ids)
+            self.select_by_ids("Metal-M", self.metal_ids)
             for metal_complex in metal_complexes:
-                cmd.select('tmp_m', 'id %i' % metal_complex.metal_id)
-                cmd.select('tmp_t', 'id %i' % metal_complex.target_id)
-                if metal_complex.location == 'water':
-                    cmd.select('Metal-W', 'Metal-W or id %s' % metal_complex.target_id)
-                if metal_complex.location.startswith('protein'):
-                    cmd.select('tmp_t', 'tmp_t & %s' % self.protname)
-                    cmd.select('Metal-P', 'Metal-P or (id %s & %s)' % (metal_complex.target_id, self.protname))
-                if metal_complex.location == 'ligand':
-                    cmd.select('tmp_t', 'tmp_t & %s' % self.ligname)
-                    cmd.select('Metal-L', 'Metal-L or (id %s & %s)' % (metal_complex.target_id, self.ligname))
-                cmd.distance('MetalComplexes', 'tmp_m', 'tmp_t')
-                cmd.delete('tmp_m or tmp_t')
-        if self.object_exists('MetalComplexes'):
-            cmd.set('dash_color', 'violetpurple', 'MetalComplexes')
-            cmd.set('dash_gap', 0.5, 'MetalComplexes')
+                cmd.select("tmp_m", "id %i" % metal_complex.metal_id)
+                cmd.select("tmp_t", "id %i" % metal_complex.target_id)
+                if metal_complex.location == "water":
+                    cmd.select("Metal-W", "Metal-W or id %s" % metal_complex.target_id)
+                if metal_complex.location.startswith("protein"):
+                    cmd.select("tmp_t", "tmp_t & %s" % self.protname)
+                    cmd.select(
+                        "Metal-P",
+                        "Metal-P or (id %s & %s)"
+                        % (metal_complex.target_id, self.protname),
+                    )
+                if metal_complex.location == "ligand":
+                    cmd.select("tmp_t", "tmp_t & %s" % self.ligname)
+                    cmd.select(
+                        "Metal-L",
+                        "Metal-L or (id %s & %s)"
+                        % (metal_complex.target_id, self.ligname),
+                    )
+                cmd.distance("MetalComplexes", "tmp_m", "tmp_t")
+                cmd.delete("tmp_m or tmp_t")
+        if self.object_exists("MetalComplexes"):
+            cmd.set("dash_color", "violetpurple", "MetalComplexes")
+            cmd.set("dash_gap", 0.5, "MetalComplexes")
             # Show water molecules for metal complexes
-            cmd.show('spheres', 'Metal-W')
-            cmd.color('lightblue', 'Metal-W')
+            cmd.show("spheres", "Metal-W")
+            cmd.color("lightblue", "Metal-W")
 
     def selections_cleanup(self):
         """Cleans up non-used selections"""
 
         if not len(self.plcomplex.unpaired_hba_idx) == 0:
-            self.select_by_ids('Unpaired-HBA', self.plcomplex.unpaired_hba_idx, selection_exists=True)
+            self.select_by_ids(
+                "Unpaired-HBA", self.plcomplex.unpaired_hba_idx, selection_exists=True
+            )
         if not len(self.plcomplex.unpaired_hbd_idx) == 0:
-            self.select_by_ids('Unpaired-HBD', self.plcomplex.unpaired_hbd_idx, selection_exists=True)
+            self.select_by_ids(
+                "Unpaired-HBD", self.plcomplex.unpaired_hbd_idx, selection_exists=True
+            )
         if not len(self.plcomplex.unpaired_hal_idx) == 0:
-            self.select_by_ids('Unpaired-HAL', self.plcomplex.unpaired_hal_idx, selection_exists=True)
+            self.select_by_ids(
+                "Unpaired-HAL", self.plcomplex.unpaired_hal_idx, selection_exists=True
+            )
 
         selections = cmd.get_names("selections")
         for selection in selections:
@@ -281,38 +376,52 @@ class PyMOLVisualizer:
             if empty:
                 cmd.delete(selection)
         cmd.deselect()
-        cmd.delete('tmp*')
-        cmd.delete('ps-*')
+        cmd.delete("tmp*")
+        cmd.delete("ps-*")
 
     def selections_group(self):
         """Group all selections"""
-        cmd.group('Structures', '%s %s %sCartoon' % (self.protname, self.ligname, self.protname))
-        cmd.group('Interactions', 'Hydrophobic HBonds HalogenBonds WaterBridges PiCation PiStackingP PiStackingT '
-                                  'Saltbridges MetalComplexes')
-        cmd.group('Atoms', '')
-        cmd.group('Atoms.Protein', 'Hydrophobic-P HBondAccept-P HBondDonor-P HalogenAccept Centroids-P PiCatRing-P '
-                                   'StackRings-P PosCharge-P NegCharge-P AllBSRes Chargecenter-P  Metal-P')
-        cmd.group('Atoms.Ligand', 'Hydrophobic-L HBondAccept-L HBondDonor-L HalogenDonor Centroids-L NegCharge-L '
-                                  'PosCharge-L NegCharge-L ChargeCenter-L StackRings-L PiCatRing-L Metal-L Metal-M '
-                                  'Unpaired-HBA Unpaired-HBD Unpaired-HAL Unpaired-RINGS')
-        cmd.group('Atoms.Other', 'Water Metal-W')
-        cmd.order('*', 'y')
+        cmd.group(
+            "Structures",
+            "%s %s %sCartoon" % (self.protname, self.ligname, self.protname),
+        )
+        cmd.group(
+            "Interactions",
+            "Hydrophobic HBonds HalogenBonds WaterBridges PiCation PiStackingP PiStackingT "
+            "Saltbridges MetalComplexes",
+        )
+        cmd.group("Atoms", "")
+        cmd.group(
+            "Atoms.Protein",
+            "Hydrophobic-P HBondAccept-P HBondDonor-P HalogenAccept Centroids-P PiCatRing-P "
+            "StackRings-P PosCharge-P NegCharge-P AllBSRes Chargecenter-P  Metal-P",
+        )
+        cmd.group(
+            "Atoms.Ligand",
+            "Hydrophobic-L HBondAccept-L HBondDonor-L HalogenDonor Centroids-L NegCharge-L "
+            "PosCharge-L NegCharge-L ChargeCenter-L StackRings-L PiCatRing-L Metal-L Metal-M "
+            "Unpaired-HBA Unpaired-HBD Unpaired-HAL Unpaired-RINGS",
+        )
+        cmd.group("Atoms.Other", "Water Metal-W")
+        cmd.order("*", "y")
 
     def additional_cleanup(self):
         """Cleanup of various representations"""
 
         cmd.remove('not alt ""+A')  # Remove alternate conformations
-        cmd.hide('labels', 'Interactions')  # Hide labels of lines
-        cmd.disable('%sCartoon' % self.protname)
-        cmd.hide('everything', 'hydrogens')
+        cmd.hide("labels", "Interactions")  # Hide labels of lines
+        cmd.disable("%sCartoon" % self.protname)
+        cmd.hide("everything", "hydrogens")
 
     def zoom_to_ligand(self):
         """Zoom in too ligand and its interactions."""
         cmd.center(self.ligname)
         cmd.orient(self.ligname)
-        cmd.turn('x', 110)  # If the ligand is aligned with the longest axis, aromatic rings are hidden
-        if 'AllBSRes' in cmd.get_names("selections"):
-            cmd.zoom('%s or AllBSRes' % self.ligname, 3)
+        cmd.turn(
+            "x", 110
+        )  # If the ligand is aligned with the longest axis, aromatic rings are hidden
+        if "AllBSRes" in cmd.get_names("selections"):
+            cmd.zoom("%s or AllBSRes" % self.ligname, 3)
         else:
             if self.object_exists(self.ligname):
                 cmd.zoom(self.ligname, 3)
@@ -320,8 +429,10 @@ class PyMOLVisualizer:
 
     def save_session(self, outfolder, override=None):
         """Saves a PyMOL session file."""
-        filename = '%s_%s' % (self.protname.upper(), "_".join(
-            [self.hetid, self.plcomplex.chain, self.plcomplex.position]))
+        filename = "%s_%s" % (
+            self.protname.upper(),
+            "_".join([self.hetid, self.plcomplex.chain, self.plcomplex.position]),
+        )
         if override is not None:
             filename = override
         cmd.save("/".join([outfolder, "%s.pse" % filename]))
@@ -331,15 +442,15 @@ class PyMOLVisualizer:
         Use this function in case neither cmd.ray() or cmd.png() work.
         """
         sys.stdout = sys.__stdout__
-        cmd.feedback('disable', 'movie', 'everything')
+        cmd.feedback("disable", "movie", "everything")
         cmd.viewport(width, height)
-        cmd.zoom('visible', 1.5)  # Adapt the zoom to the viewport
-        cmd.set('ray_trace_frames', 1)  # Frames are raytraced before saving an image.
+        cmd.zoom("visible", 1.5)  # Adapt the zoom to the viewport
+        cmd.set("ray_trace_frames", 1)  # Frames are raytraced before saving an image.
         cmd.mpng(filepath, 1, 1)  # Use batch png mode with 1 frame only
         cmd.mplay()  # cmd.mpng needs the animation to 'run'
         cmd.refresh()
-        originalfile = "".join([filepath, '0001.png'])
-        newfile = "".join([filepath, '.png'])
+        originalfile = "".join([filepath, "0001.png"])
+        newfile = "".join([filepath, ".png"])
 
         #################################################
         # Wait for file for max. 1 second and rename it #
@@ -349,29 +460,56 @@ class PyMOLVisualizer:
         while not os.path.isfile(originalfile) and attempts <= 10:
             sleep(0.1)
             attempts += 1
-        if os.name == 'nt':  # In Windows, make sure there is no file of the same name, cannot be overwritten as in Unix
+        if (
+            os.name == "nt"
+        ):  # In Windows, make sure there is no file of the same name, cannot be overwritten as in Unix
             if os.path.isfile(newfile):
                 os.remove(newfile)
         os.rename(originalfile, newfile)  # Remove frame number in filename
 
         #  Check if imagemagick is available and crop + resize the images
-        if subprocess.call("type convert", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0:
+        if (
+            subprocess.call(
+                "type convert",
+                shell=True,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+            )
+            == 0
+        ):
             attempts, ecode = 0, 1
             # Check if file is truncated and wait if that's the case
             while ecode != 0 and attempts <= 10:
-                ecode = subprocess.call(['convert', newfile, '/dev/null'], stdout=open('/dev/null', 'w'),
-                                        stderr=subprocess.STDOUT)
+                ecode = subprocess.call(
+                    ["convert", newfile, "/dev/null"],
+                    stdout=open("/dev/null", "w"),
+                    stderr=subprocess.STDOUT,
+                )
                 sleep(0.1)
                 attempts += 1
-            trim = 'convert -trim ' + newfile + ' -bordercolor White -border 20x20 ' + newfile + ';'  # Trim the image
+            trim = (
+                "convert -trim "
+                + newfile
+                + " -bordercolor White -border 20x20 "
+                + newfile
+                + ";"
+            )  # Trim the image
             os.system(trim)
-            getwidth = 'w=`convert ' + newfile + ' -ping -format "%w" info:`;'  # Get the width of the new image
-            getheight = 'h=`convert ' + newfile + ' -ping -format "%h" info:`;'  # Get the hight of the new image
+            getwidth = (
+                "w=`convert " + newfile + ' -ping -format "%w" info:`;'
+            )  # Get the width of the new image
+            getheight = (
+                "h=`convert " + newfile + ' -ping -format "%h" info:`;'
+            )  # Get the hight of the new image
             newres = 'if [ "$w" -gt "$h" ]; then newr="${w%.*}x$w"; else newr="${h%.*}x$h"; fi;'  # Set quadratic ratio
-            quadratic = 'convert ' + newfile + ' -gravity center -extent "$newr" ' + newfile  # Fill with whitespace
+            quadratic = (
+                "convert " + newfile + ' -gravity center -extent "$newr" ' + newfile
+            )  # Fill with whitespace
             os.system(getwidth + getheight + newres + quadratic)
         else:
-            sys.stderr.write('Imagemagick not available. Images will not be resized or cropped.')
+            sys.stderr.write(
+                "Imagemagick not available. Images will not be resized or cropped."
+            )
 
     def save_picture(self, outfolder, filename):
         """Saves a picture"""
@@ -380,26 +518,26 @@ class PyMOLVisualizer:
 
     def set_fancy_ray(self):
         """Give the molecule a flat, modern look."""
-        cmd.set('light_count', 6)
-        cmd.set('spec_count', 1.5)
-        cmd.set('shininess', 4)
-        cmd.set('specular', 0.3)
-        cmd.set('reflect', 1.6)
-        cmd.set('ambient', 0)
-        cmd.set('direct', 0)
-        cmd.set('ray_shadow', 0)  # Gives the molecules a flat, modern look
-        cmd.set('ambient_occlusion_mode', 1)
-        cmd.set('ray_opaque_background', 0)  # Transparent background
+        cmd.set("light_count", 6)
+        cmd.set("spec_count", 1.5)
+        cmd.set("shininess", 4)
+        cmd.set("specular", 0.3)
+        cmd.set("reflect", 1.6)
+        cmd.set("ambient", 0)
+        cmd.set("direct", 0)
+        cmd.set("ray_shadow", 0)  # Gives the molecules a flat, modern look
+        cmd.set("ambient_occlusion_mode", 1)
+        cmd.set("ray_opaque_background", 0)  # Transparent background
 
     def adapt_for_peptides(self):
         """Adapt visualization for peptide ligands and interchain contacts"""
-        cmd.hide('sticks', self.ligname)
-        cmd.set('cartoon_color', 'lightorange', self.ligname)
-        cmd.show('cartoon', self.ligname)
-        cmd.show('sticks', "byres *-L")
+        cmd.hide("sticks", self.ligname)
+        cmd.set("cartoon_color", "lightorange", self.ligname)
+        cmd.show("cartoon", self.ligname)
+        cmd.show("sticks", "byres *-L")
         cmd.util.cnc(self.ligname)
-        cmd.remove('%sCartoon and chain %s' % (self.protname, self.plcomplex.chain))
-        cmd.set('cartoon_side_chain_helper', 0)
+        cmd.remove("%sCartoon and chain %s" % (self.protname, self.plcomplex.chain))
+        cmd.set("cartoon_side_chain_helper", 0)
 
     def adapt_for_intra(self):
         """Adapt visualization for intra-protein interactions"""
@@ -408,43 +546,55 @@ class PyMOLVisualizer:
         """Refinements for the visualization"""
 
         # Show sticks for all residues interacing with the ligand
-        cmd.select('AllBSRes', 'byres (Hydrophobic-P or HBondDonor-P or HBondAccept-P or PosCharge-P or NegCharge-P or '
-                               'StackRings-P or PiCatRing-P or HalogenAcc or Metal-P)')
-        cmd.show('sticks', 'AllBSRes')
+        cmd.select(
+            "AllBSRes",
+            "byres (Hydrophobic-P or HBondDonor-P or HBondAccept-P or PosCharge-P or NegCharge-P or "
+            "StackRings-P or PiCatRing-P or HalogenAcc or Metal-P)",
+        )
+        cmd.show("sticks", "AllBSRes")
         # Show spheres for the ring centroids
-        cmd.hide('everything', 'centroids*')
-        cmd.show('nb_spheres', 'centroids*')
+        cmd.hide("everything", "centroids*")
+        cmd.show("nb_spheres", "centroids*")
         # Show spheres for centers of charge
-        if self.object_exists('Chargecenter-P') or self.object_exists('Chargecenter-L'):
-            cmd.hide('nonbonded', 'chargecenter*')
-            cmd.show('spheres', 'chargecenter*')
-            cmd.set('sphere_scale', 0.4, 'chargecenter*')
-            cmd.color('yellow', 'chargecenter*')
+        if self.object_exists("Chargecenter-P") or self.object_exists("Chargecenter-L"):
+            cmd.hide("nonbonded", "chargecenter*")
+            cmd.show("spheres", "chargecenter*")
+            cmd.set("sphere_scale", 0.4, "chargecenter*")
+            cmd.color("yellow", "chargecenter*")
 
-        cmd.set('valence', 1)  # Show bond valency (e.g. double bonds)
+        cmd.set("valence", 1)  # Show bond valency (e.g. double bonds)
         # Optional cartoon representation of the protein
-        cmd.copy('%sCartoon' % self.protname, self.protname)
-        cmd.show('cartoon', '%sCartoon' % self.protname)
-        cmd.show('sticks', '%sCartoon' % self.protname)
-        cmd.set('stick_transparency', 1, '%sCartoon' % self.protname)
+        cmd.copy("%sCartoon" % self.protname, self.protname)
+        cmd.show("cartoon", "%sCartoon" % self.protname)
+        cmd.show("sticks", "%sCartoon" % self.protname)
+        cmd.set("stick_transparency", 1, "%sCartoon" % self.protname)
 
         # Resize water molecules. Sometimes they are not heteroatoms HOH, but part of the protein
-        cmd.set('sphere_scale', 0.2, 'resn HOH or Water')  # Needs to be done here because of the copy made
-        cmd.set('sphere_transparency', 0.4, '!(resn HOH or Water)')
-
-        if 'Centroids*' in cmd.get_names("selections"):
-            cmd.color('grey80', 'Centroids*')
-        cmd.hide('spheres', '%sCartoon' % self.protname)
-        cmd.hide('cartoon', '%sCartoon and resn DA+DG+DC+DU+DT+A+G+C+U+T' % self.protname)  # Hide DNA/RNA Cartoon
-        if self.ligname == 'SF4':  # Special case for iron-sulfur clusters, can't be visualized with sticks
-            cmd.show('spheres', '%s' % self.ligname)
-
-        cmd.hide('everything', 'resn HOH &!Water')  # Hide all non-interacting water molecules
-        cmd.hide('sticks', '%s and !%s and !AllBSRes' %
-                 (self.protname, self.ligname))  # Hide all non-interacting residues
-
-        if self.ligandtype in ['PEPTIDE', 'INTRA']:
+        cmd.set(
+            "sphere_scale", 0.2, "resn HOH or Water"
+        )  # Needs to be done here because of the copy made
+        cmd.set("sphere_transparency", 0.4, "!(resn HOH or Water)")
+
+        if "Centroids*" in cmd.get_names("selections"):
+            cmd.color("grey80", "Centroids*")
+        cmd.hide("spheres", "%sCartoon" % self.protname)
+        cmd.hide(
+            "cartoon", "%sCartoon and resn DA+DG+DC+DU+DT+A+G+C+U+T" % self.protname
+        )  # Hide DNA/RNA Cartoon
+        if (
+            self.ligname == "SF4"
+        ):  # Special case for iron-sulfur clusters, can't be visualized with sticks
+            cmd.show("spheres", "%s" % self.ligname)
+
+        cmd.hide(
+            "everything", "resn HOH &!Water"
+        )  # Hide all non-interacting water molecules
+        cmd.hide(
+            "sticks", "%s and !%s and !AllBSRes" % (self.protname, self.ligname)
+        )  # Hide all non-interacting residues
+
+        if self.ligandtype in ["PEPTIDE", "INTRA"]:
             self.adapt_for_peptides()
 
-        if self.ligandtype == 'INTRA':
+        if self.ligandtype == "INTRA":
             self.adapt_for_intra()