Format code with Black

1 files changed, 180 insertions, 26 deletions

diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index cab6b78..c83928d 100644
--- a/scripts/makeReport.py
+++ b/scripts/makeReport.py
@@ -74,8 +74,17 @@ for ligand in natural_ligands:
         tableBody = []
         tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for x in doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.hydrophobic_interaction:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.ligcarbonidx.cdata,x.protcarbonidx.cdata]
+        for x in doc.report.bindingsite[
+            ligand
+        ].interactions.hydrophobic_interactions.hydrophobic_interaction:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.ligcarbonidx.cdata,
+                x.protcarbonidx.cdata,
+            ]
             i += 1
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
@@ -84,10 +93,32 @@ for ligand in natural_ligands:
     else:
         print("## Hydrogen Bonds", end="\n\n")
         tableBody = []
-        tableHeaders = ["No.","Res.","AA","Dist H-A","Dist D-A","Don Angle","Protisdon?","Sidechain?","D. Atom","A. Atom",]
+        tableHeaders = [
+            "No.",
+            "Res.",
+            "AA",
+            "Dist H-A",
+            "Dist D-A",
+            "Don Angle",
+            "Protisdon?",
+            "Sidechain?",
+            "D. Atom",
+            "A. Atom",
+        ]
         i = 1
-        for x in doc.report.bindingsite[ligand].interactions.hydrogen_bonds.hydrogen_bond:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist_h_a.cdata,x.dist_d_a.cdata,x.don_angle.cdata,x.protisdon.cdata,x.sidechain.cdata]
+        for x in doc.report.bindingsite[
+            ligand
+        ].interactions.hydrogen_bonds.hydrogen_bond:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist_h_a.cdata,
+                x.dist_d_a.cdata,
+                x.don_angle.cdata,
+                x.protisdon.cdata,
+                x.sidechain.cdata,
+            ]
             l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
@@ -98,7 +129,10 @@ for ligand in natural_ligands:
 print("## Ligand Interactions", end="\n\n")
 
 try:
-    if doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata== "":
+    if (
+        doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata
+        == ""
+    ):
         print("No Hydrophobic Interactions Found", end="\n\n")
     else:
         print("**Hydrophobic Interactions Found**", end="\n\n")
@@ -107,7 +141,10 @@ except AttributeError:
     fallback = 1
 
 if fallback == 0:
-    if doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata== "":
+    if (
+        doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata
+        == ""
+    ):
         print("No Hydrophobic Interactions Found", end="\n\n")
     else:
         print("**Hydrophobic Interactions Found**", end="\n\n")
@@ -132,7 +169,10 @@ if fallback == 0:
     else:
         print("**Pi Stacks Found**", end="\n\n")
         ps = 1
-    if doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.cdata== "":
+    if (
+        doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.cdata
+        == ""
+    ):
         print("No Pi Cation Interactions Found", end="\n\n")
     else:
         print("**Pi Cation Interactions Found**", end="\n\n")
@@ -196,8 +236,17 @@ if fallback == 0:
         tableBody = []
         tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for x in doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.hydrophobic_interaction:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.ligcarbonidx.cdata,x.protcarbonidx.cdata]
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.hydrophobic_interactions.hydrophobic_interaction:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.ligcarbonidx.cdata,
+                x.protcarbonidx.cdata,
+            ]
             i += 1
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
@@ -205,10 +254,32 @@ if fallback == 0:
     if hb == 1:
         print("## Hydrogen Bonds", end="\n\n")
         tableBody = []
-        tableHeaders = ["No.","Res.","AA","Dist H-A","Dist D-A","Don Angle","Protisdon?","Sidechain?","D. Atom","A. Atom"]
+        tableHeaders = [
+            "No.",
+            "Res.",
+            "AA",
+            "Dist H-A",
+            "Dist D-A",
+            "Don Angle",
+            "Protisdon?",
+            "Sidechain?",
+            "D. Atom",
+            "A. Atom",
+        ]
         i = 1
-        for x in doc.report.bindingsite[indexForUNL].interactions.hydrogen_bonds.hydrogen_bond:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist_h_a.cdata,x.dist_d_a.cdata,x.don_angle.cdata,x.protisdon.cdata,x.sidechain.cdata]
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.hydrogen_bonds.hydrogen_bond:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist_h_a.cdata,
+                x.dist_d_a.cdata,
+                x.don_angle.cdata,
+                x.protisdon.cdata,
+                x.sidechain.cdata,
+            ]
             l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
@@ -219,10 +290,27 @@ if fallback == 0:
     if sb == 1:
         print("## Salt Bridges", end="\n\n")
         tableBody = []
-        tableHeaders = ["Index","Residue","AA","Distance","Protein positive?","Ligand Group","Ligand Atoms"]
+        tableHeaders = [
+            "Index",
+            "Residue",
+            "AA",
+            "Distance",
+            "Protein positive?",
+            "Ligand Group",
+            "Ligand Atoms",
+        ]
         i = 1
-        for x in doc.report.bindingsite[indexForUNL].interactions.salt_bridges.salt_bridge:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.protispos.cdata,x.lig_group.cdata]
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.salt_bridges.salt_bridge:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.protispos.cdata,
+                x.lig_group.cdata,
+            ]
             atoms = []
             for y in x.lig_idx_list.idx:
                 atoms.append(y.cdata)
@@ -236,8 +324,17 @@ if fallback == 0:
         tableBody = []
         tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
         i = 1
-        for x in doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.pi_cation_interaction:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.offset.cdata,x.protcharged.cdata]
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.pi_cation_interactions.pi_cation_interaction:
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.offset.cdata,
+                x.protcharged.cdata,
+            ]
             atoms = []
             for y in x.lig_idx_list.idx:
                 atoms.append(y.cdata)
@@ -251,8 +348,19 @@ elif fallback == 1:
         tableBody = []
         tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for x in doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.ligcarbonidx.cdata,x.protcarbonidx.cdata]
+        for (
+            x
+        ) in (
+            doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction
+        ):
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.ligcarbonidx.cdata,
+                x.protcarbonidx.cdata,
+            ]
             i += 1
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
@@ -260,10 +368,30 @@ elif fallback == 1:
     if hb == 1:
         print("## Hydrogen Bonds", end="\n\n")
         tableBody = []
-        tableHeaders = ["No.","Res.","AA","Dist H-A","Dist D-A","Don Angle","Protisdon?","Sidechain?","D. Atom","A. Atom"]
+        tableHeaders = [
+            "No.",
+            "Res.",
+            "AA",
+            "Dist H-A",
+            "Dist D-A",
+            "Don Angle",
+            "Protisdon?",
+            "Sidechain?",
+            "D. Atom",
+            "A. Atom",
+        ]
         i = 1
         for x in doc.report.bindingsite.interactions.hydrogen_bonds.hydrogen_bond:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist_h_a.cdata,x.dist_d_a.cdata,x.don_angle.cdata,x.protisdon.cdata,x.sidechain.cdata]
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist_h_a.cdata,
+                x.dist_d_a.cdata,
+                x.don_angle.cdata,
+                x.protisdon.cdata,
+                x.sidechain.cdata,
+            ]
             l.append((x.donoridx.cdata + "[" + x.donortype.cdata + "]"))
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
@@ -274,10 +402,25 @@ elif fallback == 1:
     if sb == 1:
         print("## Salt Bridges", end="\n\n")
         tableBody = []
-        tableHeaders = ["Index","Residue","AA","Distance","Protein positive?","Ligand Group","Ligand Atoms"]
+        tableHeaders = [
+            "Index",
+            "Residue",
+            "AA",
+            "Distance",
+            "Protein positive?",
+            "Ligand Group",
+            "Ligand Atoms",
+        ]
         i = 1
         for x in doc.report.bindingsite.interactions.salt_bridges.salt_bridge:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.protispos.cdata,x.lig_group.cdata]
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.protispos.cdata,
+                x.lig_group.cdata,
+            ]
             atoms = []
             for y in x.lig_idx_list.idx:
                 atoms.append(y.cdata)
@@ -291,8 +434,19 @@ elif fallback == 1:
         tableBody = []
         tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
         i = 1
-        for x in doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction:
-            l = [i,x.resnr.cdata,x.restype.cdata,x.dist.cdata,x.offset.cdata,x.protcharged.cdata]
+        for (
+            x
+        ) in (
+            doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction
+        ):
+            l = [
+                i,
+                x.resnr.cdata,
+                x.restype.cdata,
+                x.dist.cdata,
+                x.offset.cdata,
+                x.protcharged.cdata,
+            ]
             atoms = []
             for y in x.lig_idx_list.idx:
                 atoms.append(y.cdata)