Format code with Blackdeepsource-transform-b65b5545

1 files changed, 56 insertions, 28 deletions

diff --git a/plip/visualization/chimera.py b/plip/visualization/chimera.py
index a37fffb..436d0e3 100644
--- a/plip/visualization/chimera.py
+++ b/plip/visualization/chimera.py
@@ -5,8 +5,8 @@ class ChimeraVisualizer:
         self.chimera = chimera_module
         self.tid = tid
         self.uid = plcomplex.uid
-        self.plipname = 'PLIP-%i' % self.tid
-        self.hetid, self.chain, self.pos = self.uid.split(':')
+        self.plipname = "PLIP-%i" % self.tid
+        self.hetid, self.chain, self.pos = self.uid.split(":")
         self.pos = int(self.pos)
         self.colorbyname = self.chimera.colorTable.getColorByName
         self.rc = self.chimera.runCommand
@@ -32,7 +32,10 @@ class ChimeraVisualizer:
         self.update_model_dict()
         self.rc("background solid white")
         self.rc("setattr g display 0")  # Hide all pseudobonds
-        self.rc("~display #%i & :/isHet & ~:%s" % (self.model_dict[self.plipname], self.hetid))
+        self.rc(
+            "~display #%i & :/isHet & ~:%s"
+            % (self.model_dict[self.plipname], self.hetid)
+        )
 
     def update_model_dict(self):
         """Updates the model dictionary"""
@@ -51,39 +54,47 @@ class ChimeraVisualizer:
 
     def show_hydrophobic(self):
         """Visualizes hydrophobic contacts."""
-        grp = self.getPseudoBondGroup("Hydrophobic Interactions-%i" % self.tid, associateWith=[self.model])
+        grp = self.getPseudoBondGroup(
+            "Hydrophobic Interactions-%i" % self.tid, associateWith=[self.model]
+        )
         grp.lineType = self.chimera.Dash
         grp.lineWidth = 3
-        grp.color = self.colorbyname('gray')
+        grp.color = self.colorbyname("gray")
         for i in self.plcomplex.hydrophobic_contacts.pairs_ids:
             self.bs_res_ids.append(i[0])
 
     def show_hbonds(self):
         """Visualizes hydrogen bonds."""
-        grp = self.getPseudoBondGroup("Hydrogen Bonds-%i" % self.tid, associateWith=[self.model])
+        grp = self.getPseudoBondGroup(
+            "Hydrogen Bonds-%i" % self.tid, associateWith=[self.model]
+        )
         grp.lineWidth = 3
         for i in self.plcomplex.hbonds.ldon_id:
             b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
-            b.color = self.colorbyname('blue')
+            b.color = self.colorbyname("blue")
             self.bs_res_ids.append(i[0])
         for i in self.plcomplex.hbonds.pdon_id:
             b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
-            b.color = self.colorbyname('blue')
+            b.color = self.colorbyname("blue")
             self.bs_res_ids.append(i[1])
 
     def show_halogen(self):
         """Visualizes halogen bonds."""
-        grp = self.getPseudoBondGroup("HalogenBonds-%i" % self.tid, associateWith=[self.model])
+        grp = self.getPseudoBondGroup(
+            "HalogenBonds-%i" % self.tid, associateWith=[self.model]
+        )
         grp.lineWidth = 3
         for i in self.plcomplex.halogen_bonds:
             b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
-            b.color = self.colorbyname('turquoise')
+            b.color = self.colorbyname("turquoise")
 
             self.bs_res_ids.append(i.acc_id)
 
     def show_stacking(self):
         """Visualizes pi-stacking interactions."""
-        grp = self.getPseudoBondGroup("pi-Stacking-%i" % self.tid, associateWith=[self.model])
+        grp = self.getPseudoBondGroup(
+            "pi-Stacking-%i" % self.tid, associateWith=[self.model]
+        )
         grp.lineWidth = 3
         grp.lineType = self.chimera.Dash
         for i, stack in enumerate(self.plcomplex.pistacking):
@@ -101,13 +112,15 @@ class ChimeraVisualizer:
             r.addAtom(centroid_lig)
 
             b = grp.newPseudoBond(centroid_lig, centroid_prot)
-            b.color = self.colorbyname('forest green')
+            b.color = self.colorbyname("forest green")
 
             self.bs_res_ids += stack.proteinring_atoms
 
     def show_cationpi(self):
         """Visualizes cation-pi interactions"""
-        grp = self.getPseudoBondGroup("Cation-Pi-%i" % self.tid, associateWith=[self.model])
+        grp = self.getPseudoBondGroup(
+            "Cation-Pi-%i" % self.tid, associateWith=[self.model]
+        )
         grp.lineWidth = 3
         grp.lineType = self.chimera.Dash
         for i, cat in enumerate(self.plcomplex.pication):
@@ -125,7 +138,7 @@ class ChimeraVisualizer:
             r.addAtom(centroid)
 
             b = grp.newPseudoBond(centroid, chargecenter)
-            b.color = self.colorbyname('orange')
+            b.color = self.colorbyname("orange")
 
             if cat.protcharged:
                 self.bs_res_ids += cat.charge_atoms
@@ -135,7 +148,9 @@ class ChimeraVisualizer:
     def show_sbridges(self):
         """Visualizes salt bridges."""
         # Salt Bridges
-        grp = self.getPseudoBondGroup("Salt Bridges-%i" % self.tid, associateWith=[self.model])
+        grp = self.getPseudoBondGroup(
+            "Salt Bridges-%i" % self.tid, associateWith=[self.model]
+        )
         grp.lineWidth = 3
         grp.lineType = self.chimera.Dash
         for i, sbridge in enumerate(self.plcomplex.saltbridges):
@@ -153,7 +168,7 @@ class ChimeraVisualizer:
             r.addAtom(chargecenter2)
 
             b = grp.newPseudoBond(chargecenter1, chargecenter2)
-            b.color = self.colorbyname('yellow')
+            b.color = self.colorbyname("yellow")
 
             if sbridge.protispos:
                 self.bs_res_ids += sbridge.positive_atoms
@@ -162,14 +177,20 @@ class ChimeraVisualizer:
 
     def show_wbridges(self):
         """Visualizes water bridges"""
-        grp = self.getPseudoBondGroup("Water Bridges-%i" % self.tid, associateWith=[self.model])
+        grp = self.getPseudoBondGroup(
+            "Water Bridges-%i" % self.tid, associateWith=[self.model]
+        )
         grp.lineWidth = 3
         for i, wbridge in enumerate(self.plcomplex.waterbridges):
-            c = grp.newPseudoBond(self.atoms[wbridge.water_id], self.atoms[wbridge.acc_id])
-            c.color = self.colorbyname('cornflower blue')
+            c = grp.newPseudoBond(
+                self.atoms[wbridge.water_id], self.atoms[wbridge.acc_id]
+            )
+            c.color = self.colorbyname("cornflower blue")
             self.water_ids.append(wbridge.water_id)
-            b = grp.newPseudoBond(self.atoms[wbridge.don_id], self.atoms[wbridge.water_id])
-            b.color = self.colorbyname('cornflower blue')
+            b = grp.newPseudoBond(
+                self.atoms[wbridge.don_id], self.atoms[wbridge.water_id]
+            )
+            b.color = self.colorbyname("cornflower blue")
             self.water_ids.append(wbridge.water_id)
             if wbridge.protisdon:
                 self.bs_res_ids.append(wbridge.don_id)
@@ -178,16 +199,20 @@ class ChimeraVisualizer:
 
     def show_metal(self):
         """Visualizes metal coordination."""
-        grp = self.getPseudoBondGroup("Metal Coordination-%i" % self.tid, associateWith=[self.model])
+        grp = self.getPseudoBondGroup(
+            "Metal Coordination-%i" % self.tid, associateWith=[self.model]
+        )
         grp.lineWidth = 3
         for i, metal in enumerate(self.plcomplex.metal_complexes):
-            c = grp.newPseudoBond(self.atoms[metal.metal_id], self.atoms[metal.target_id])
-            c.color = self.colorbyname('magenta')
+            c = grp.newPseudoBond(
+                self.atoms[metal.metal_id], self.atoms[metal.target_id]
+            )
+            c.color = self.colorbyname("magenta")
 
-            if metal.location == 'water':
+            if metal.location == "water":
                 self.water_ids.append(metal.target_id)
 
-            if metal.location.startswith('protein'):
+            if metal.location.startswith("protein"):
                 self.bs_res_ids.append(metal.target_id)
 
     def cleanup(self):
@@ -197,13 +222,16 @@ class ChimeraVisualizer:
             # Hide all non-interacting water molecules
             water_selection = []
             for wid in self.water_ids:
-                water_selection.append('serialNumber=%i' % wid)
+                water_selection.append("serialNumber=%i" % wid)
             self.rc("~display :HOH")
             self.rc("display :@/%s" % " or ".join(water_selection))
 
         # Show all interacting binding site residues
         self.rc("~display #%i & ~:/isHet" % self.model_dict[self.plipname])
-        self.rc("display :%s" % ",".join([str(self.atoms[bsid].residue.id) for bsid in self.bs_res_ids]))
+        self.rc(
+            "display :%s"
+            % ",".join([str(self.atoms[bsid].residue.id) for bsid in self.bs_res_ids])
+        )
         self.rc("color lightblue :HOH")
 
     def zoom_to_ligand(self):