Format code with Black

1 files changed, 157 insertions, 77 deletions

diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index 49b69f0..2a32d29 100644
--- a/scripts/makeReport.py
+++ b/scripts/makeReport.py
@@ -1,8 +1,8 @@
 #!/usr/bin/python3
-import argparse 
+import argparse
 
 parser = argparse.ArgumentParser(description="Make Report Helper Script")
-parser.add_argument("-i","--input",help="Path to report folder")
+parser.add_argument("-i", "--input", help="Path to report folder")
 
 args = parser.parse_args()
 
@@ -11,68 +11,72 @@ if args.input == None:
     exit(1)
 
 path = args.input
-#path = '/Users/navanchauhan/Desktop/nCOV-19/scripts/pymol/test/'
+# path = '/Users/navanchauhan/Desktop/nCOV-19/scripts/pymol/test/'
 
 import untangle
 from tabulate import tabulate
 
-#import sys
-#report = path + "report.md"
-#sys.stdout = open(report, 'w')
+# import sys
+# report = path + "report.md"
+# sys.stdout = open(report, 'w')
 
 from os import listdir
 from os.path import isfile, join
+
 onlyfiles = [f for f in listdir(path) if isfile(join(path, f))]
 image = ""
 for x in onlyfiles:
-    if '.png' in x and 'UNL' in x:
+    if ".png" in x and "UNL" in x:
         image = x
 import os
-fname = os.path.join(path,'report.xml')
+
+fname = os.path.join(path, "report.xml")
 
 doc = untangle.parse(fname)
 
-hi, hb, wb, sb, ps, pc, hab, mc = 0,0,0,0,0,0,0,0
+hi, hb, wb, sb, ps, pc, hab, mc = 0, 0, 0, 0, 0, 0, 0, 0
 
 indexForUNL = 0
 
 for x in doc.report.bindingsite:
-    if x.identifiers.longname.cdata == 'UNL':
+    if x.identifiers.longname.cdata == "UNL":
         break
     else:
         indexForUNL += 1
 
 
 name = doc.report.pdbid.cdata
-#print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
+# print(("# " + (name.replace("_"," ")).replace("PROTEIN","")), end="\n\n")
 fallback = 0
 
-print("## Visualisation", end="\n\n")    
-print(f'![]({image})', end="\n\n")
+print("## Visualisation", end="\n\n")
+print(f"![]({image})", end="\n\n")
 
 natural_ligands = []
 showNaturalLigands = True
 
 try:
     for x in range(len(doc.report.bindingsite)):
-        if doc.report.bindingsite[x]['has_interactions'] == 'True' and x != indexForUNL:
+        if doc.report.bindingsite[x]["has_interactions"] == "True" and x != indexForUNL:
             natural_ligands.append(x)
 except:
-    fallback==1
+    fallback == 1
 
 if natural_ligands == []:
     showNaturalLigands == False
 
 for ligand in natural_ligands:
-    print("### Natural Ligand " + str(x),end="\n\n")
-    if doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.cdata == '':
-        print("No Hydrophobic Interactions Found",end="\n\n")
+    print("### Natural Ligand " + str(x), end="\n\n")
+    if doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.cdata == "":
+        print("No Hydrophobic Interactions Found", end="\n\n")
     else:
-        print("#### Hydrophobic Interactions",end="\n\n")
+        print("#### Hydrophobic Interactions", end="\n\n")
         tableBody = []
-        tableHeaders = ['No.','Res.','AA','Dist','Ligand Atom','Proton Atom']
+        tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for x in doc.report.bindingsite[ligand].interactions.hydrophobic_interactions.hydrophobic_interaction:
+        for x in doc.report.bindingsite[
+            ligand
+        ].interactions.hydrophobic_interactions.hydrophobic_interaction:
             l = []
             l.append(i)
             l.append(x.resnr.cdata)
@@ -83,14 +87,27 @@ for ligand in natural_ligands:
             i += 1
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
-    if doc.report.bindingsite[ligand].interactions.hydrogen_bonds.cdata == '':
+    if doc.report.bindingsite[ligand].interactions.hydrogen_bonds.cdata == "":
         print("No Hydrogen Bonds Found", end="\n\n")
     else:
-        print("## Hydrogen Bonds",end="\n\n")
+        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:
+        for x in doc.report.bindingsite[
+            ligand
+        ].interactions.hydrogen_bonds.hydrogen_bond:
             l = []
             l.append(i)
             l.append(x.resnr.cdata)
@@ -104,111 +121,122 @@ for ligand in natural_ligands:
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
             tableBody.append(l)
-            #print(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, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+            # print(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, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
 
 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")
         hi = 1
 except AttributeError:
-    fallback=1
+    fallback = 1
 
-if fallback==0:
-    if doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.cdata == '':
+if fallback == 0:
+    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")
         hi = 1
-    if doc.report.bindingsite[indexForUNL].interactions.hydrogen_bonds.cdata == '':
+    if doc.report.bindingsite[indexForUNL].interactions.hydrogen_bonds.cdata == "":
         print("No Hydrogen Bonds Found", end="\n\n")
     else:
         print("**Hydrogen Bonds Found**", end="\n\n")
         hb = 1
-    if doc.report.bindingsite[indexForUNL].interactions.water_bridges.cdata == '':
+    if doc.report.bindingsite[indexForUNL].interactions.water_bridges.cdata == "":
         print("No Water Bridges Found", end="\n\n")
     else:
         print("**Water Bridges Found**", end="\n\n")
         wb = 1
-    if doc.report.bindingsite[indexForUNL].interactions.salt_bridges.cdata == '':
+    if doc.report.bindingsite[indexForUNL].interactions.salt_bridges.cdata == "":
         print("No Salt Bridges Found", end="\n\n")
     else:
         print("**Salt Bridges Found**", end="\n\n")
         sb = 1
-    if doc.report.bindingsite[indexForUNL].interactions.pi_stacks.cdata == '':
+    if doc.report.bindingsite[indexForUNL].interactions.pi_stacks.cdata == "":
         print("No Pi Stacks Found", end="\n\n")
     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")
         pc = 1
-    if doc.report.bindingsite[indexForUNL].interactions.halogen_bonds.cdata == '':
+    if doc.report.bindingsite[indexForUNL].interactions.halogen_bonds.cdata == "":
         print("No Halogen Bonds Found", end="\n\n")
     else:
         print("** Halogen Bonds Found**", end="\n\n")
         hab = 1
-    if doc.report.bindingsite[indexForUNL].interactions.metal_complexes.cdata == '':
-        print("No Metal Complexes Found", end="\n\n")    
+    if doc.report.bindingsite[indexForUNL].interactions.metal_complexes.cdata == "":
+        print("No Metal Complexes Found", end="\n\n")
     else:
         print("**Metal Complexes Found**", end="\n\n")
         mc = 1
 
 if fallback == 1:
-    if doc.report.bindingsite.interactions.hydrophobic_interactions.cdata == '':
+    if doc.report.bindingsite.interactions.hydrophobic_interactions.cdata == "":
         print("No Hydrophobic Interactions Found", end="\n\n")
     else:
         print("**Hydrophobic Interactions Found**", end="\n\n")
         hi = 1
-    if doc.report.bindingsite.interactions.hydrogen_bonds.cdata == '':
+    if doc.report.bindingsite.interactions.hydrogen_bonds.cdata == "":
         print("No Hydrogen Bonds Found", end="\n\n")
     else:
         print("**Hydrogen Bonds Found**", end="\n\n")
         hb = 1
-    if doc.report.bindingsite.interactions.water_bridges.cdata == '':
+    if doc.report.bindingsite.interactions.water_bridges.cdata == "":
         print("No Water Bridges Found", end="\n\n")
     else:
         print("**Water Bridges Found**", end="\n\n")
         wb = 1
-    if doc.report.bindingsite.interactions.salt_bridges.cdata == '':
+    if doc.report.bindingsite.interactions.salt_bridges.cdata == "":
         print("No Salt Bridges Found", end="\n\n")
     else:
         print("**Salt Bridges Found**", end="\n\n")
         sb = 1
-    if doc.report.bindingsite.interactions.pi_stacks.cdata == '':
+    if doc.report.bindingsite.interactions.pi_stacks.cdata == "":
         print("No Pi Stacks Found", end="\n\n")
     else:
         print("**Pi Stacks Found**", end="\n\n")
         ps = 1
-    if doc.report.bindingsite.interactions.pi_cation_interactions.cdata == '':
+    if doc.report.bindingsite.interactions.pi_cation_interactions.cdata == "":
         print("No Pi Cation Interactions Found", end="\n\n")
     else:
         print("**Pi Cation Interactions Found**", end="\n\n")
         pc = 1
-    if doc.report.bindingsite.interactions.halogen_bonds.cdata == '':
+    if doc.report.bindingsite.interactions.halogen_bonds.cdata == "":
         print("No Halogen Bonds Found", end="\n\n")
     else:
         print("** Halogen Bonds Found**", end="\n\n")
         hab = 1
-    if doc.report.bindingsite.interactions.metal_complexes.cdata == '':
-        print("No Metal Complexes Found", end="\n\n")    
+    if doc.report.bindingsite.interactions.metal_complexes.cdata == "":
+        print("No Metal Complexes Found", end="\n\n")
     else:
         print("**Metal Complexes Found**", end="\n\n")
         mc = 1
 
 if fallback == 0:
     if hi == 1:
-        print("## Hydrophobic Interactions",end="\n\n")
+        print("## Hydrophobic Interactions", end="\n\n")
         tableBody = []
-        tableHeaders = ['No.','Res.','AA','Dist','Ligand Atom','Proton Atom']
+        tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for x in doc.report.bindingsite[indexForUNL].interactions.hydrophobic_interactions.hydrophobic_interaction:
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.hydrophobic_interactions.hydrophobic_interaction:
             l = []
             l.append(i)
             l.append(x.resnr.cdata)
@@ -221,11 +249,24 @@ if fallback == 0:
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
 
     if hb == 1:
-        print("## Hydrogen Bonds",end="\n\n")
+        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:
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.hydrogen_bonds.hydrogen_bond:
             l = []
             l.append(i)
             l.append(x.resnr.cdata)
@@ -239,15 +280,25 @@ if fallback == 0:
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
             tableBody.append(l)
-            #print(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, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+            # print(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, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
 
     if sb == 1:
-        print("## Salt Bridges",end="\n\n")
+        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:
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.salt_bridges.salt_bridge:
             l = []
             l.append(i)
             l.append(x.resnr.cdata)
@@ -263,12 +314,14 @@ if fallback == 0:
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
 
-    if pc==1:
-        print("## Pi Cation Interactions",end="\n\n")
+    if pc == 1:
+        print("## Pi Cation Interactions", end="\n\n")
         tableBody = []
-        tableHeaders = ['Index','Residue','AA','Distance','Prot charged?','Atoms']
+        tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
         i = 1
-        for x in doc.report.bindingsite[indexForUNL].interactions.pi_cation_interactions.pi_cation_interaction:
+        for x in doc.report.bindingsite[
+            indexForUNL
+        ].interactions.pi_cation_interactions.pi_cation_interaction:
             l = []
             l.append(i)
             l.append(x.resnr.cdata)
@@ -285,11 +338,15 @@ if fallback == 0:
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
 elif fallback == 1:
     if hi == 1:
-        print("## Hydrophobic Interactions",end="\n\n")
+        print("## Hydrophobic Interactions", end="\n\n")
         tableBody = []
-        tableHeaders = ['No.','Res.','AA','Dist','Ligand Atom','Proton Atom']
+        tableHeaders = ["No.", "Res.", "AA", "Dist", "Ligand Atom", "Proton Atom"]
         i = 1
-        for x in doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction:
+        for (
+            x
+        ) in (
+            doc.report.bindingsite.interactions.hydrophobic_interactions.hydrophobic_interaction
+        ):
             l = []
             l.append(i)
             l.append(x.resnr.cdata)
@@ -302,9 +359,20 @@ elif fallback == 1:
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
 
     if hb == 1:
-        print("## Hydrogen Bonds",end="\n\n")
+        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 = []
@@ -320,13 +388,21 @@ elif fallback == 1:
             l.append((x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
             i += 1
             tableBody.append(l)
-            #print(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, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
+            # print(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, (x.donoridx.cdata + "[" + x.donortype.cdata + "]"), (x.acceptoridx.cdata + "[" + x.acceptortype.cdata + "]"))
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
 
     if sb == 1:
-        print("## Salt Bridges",end="\n\n")
+        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 = []
@@ -344,12 +420,16 @@ elif fallback == 1:
             tableBody.append(l)
         print(tabulate(tableBody, headers=tableHeaders), end="\n\n")
 
-    if pc==1:
-        print("## Pi Cation Interactions",end="\n\n")
+    if pc == 1:
+        print("## Pi Cation Interactions", end="\n\n")
         tableBody = []
-        tableHeaders = ['Index','Residue','AA','Distance','Prot charged?','Atoms']
+        tableHeaders = ["Index", "Residue", "AA", "Distance", "Prot charged?", "Atoms"]
         i = 1
-        for x in doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction:
+        for (
+            x
+        ) in (
+            doc.report.bindingsite.interactions.pi_cation_interactions.pi_cation_interaction
+        ):
             l = []
             l.append(i)
             l.append(x.resnr.cdata)
@@ -367,7 +447,7 @@ elif fallback == 1:
 
 print("## Figures", end="\n\n")
 
-print(f'![](output-back.png)', end="\n\n")
-print(f'![](output-front.png)', end="\n\n")
-print(f'![](closeup-back.png)', end="\n\n")
-print(f'![](closeup-front.png)', end="\n\n")
+print(f"![](output-back.png)", end="\n\n")
+print(f"![](output-front.png)", end="\n\n")
+print(f"![](closeup-back.png)", end="\n\n")
+print(f"![](closeup-front.png)", end="\n\n")