Format code with Blackdeepsource-transform-b65b5545

4 files changed, 195 insertions, 104 deletions

diff --git a/scripts/get-best.py b/scripts/get-best.py
index a10c2d2..c0185e4 100644
--- a/scripts/get-best.py
+++ b/scripts/get-best.py
@@ -11,13 +11,14 @@ version = "1.0"
 desc_text = "PyMol Quick Visualtion " + version
 
 parser = argparse.ArgumentParser(description=desc_text)
-parser.add_argument("-p","--protein",help="Path to protein file")
-parser.add_argument("-l","--ligand",help="Path to ligand_out file")
+parser.add_argument("-p", "--protein", help="Path to protein file")
+parser.add_argument("-l", "--ligand", help="Path to ligand_out file")
 
 args = parser.parse_args()
 
+
 def li(s):
-    #log.info(s)
+    # log.info(s)
     None
 
 
@@ -35,10 +36,10 @@ ligand = args.ligand
 session = pymol2.PyMOL()
 session.start()
 cmd = session.cmd
-cmd.load(protein,'pro')
-cmd.load(ligand,'lig')
-cmd.split_states('lig')
+cmd.load(protein, "pro")
+cmd.load(ligand, "lig")
+cmd.split_states("lig")
 
-#fname = re.sub(r'^.*?/', '', protein.replace(".pdbqt","")) + "-" + re.sub(r'^.*?/', '', ligand.replace(".pdbqt","")) + ".pdb" 
+# fname = re.sub(r'^.*?/', '', protein.replace(".pdbqt","")) + "-" + re.sub(r'^.*?/', '', ligand.replace(".pdbqt","")) + ".pdb"
 
-cmd.save("best.pdb","pro lig_0001")
+cmd.save("best.pdb", "pro lig_0001")
diff --git a/scripts/get_dock_score.py b/scripts/get_dock_score.py
index c8b87d5..1cc0412 100644
--- a/scripts/get_dock_score.py
+++ b/scripts/get_dock_score.py
@@ -3,8 +3,8 @@
 import argparse
 
 parser = argparse.ArgumentParser(description="Get Docking Score")
-parser.add_argument("-p","--protein",help="Path to protein file")
-parser.add_argument("-l","--ligand",help="Path to ligand_out file")
+parser.add_argument("-p", "--protein", help="Path to protein file")
+parser.add_argument("-l", "--ligand", help="Path to ligand_out file")
 
 args = parser.parse_args()
 
@@ -21,7 +21,13 @@ ligand = args.ligand
 
 from os.path import basename
 
-print("# " + str(basename(protein)).replace(".pdbqt","") + "-" + str(basename(ligand)).replace("_out.pdbqt",""), end="\n\n")
+print(
+    "# "
+    + str(basename(protein)).replace(".pdbqt", "")
+    + "-"
+    + str(basename(ligand)).replace("_out.pdbqt", ""),
+    end="\n\n",
+)
 
 from tabulate import tabulate
 
@@ -31,7 +37,7 @@ results = []
 i = 1
 for line in lines:
     ta = []
-    if line.find('REMARK VINA') == 0 and line.split()[3] != "":
+    if line.find("REMARK VINA") == 0 and line.split()[3] != "":
         l = line.split()
         ta.append(i)
         ta.append(l[3])
@@ -41,6 +47,6 @@ for line in lines:
     if ta != []:
         results.append(ta)
 
-print("## Docking Scores",end="\n\n")
-print(tabulate(results,headers=["No.","Affinity","rmsd l.b","rmsd u.b"]))
-print("",end="\n\n")
+print("## Docking Scores", end="\n\n")
+print(tabulate(results, headers=["No.", "Affinity", "rmsd l.b", "rmsd u.b"]))
+print("", end="\n\n")
diff --git a/scripts/makeReport.py b/scripts/makeReport.py
index 79d9c70..fc53381 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()
 
@@ -11,147 +11,160 @@ 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")
 
-print("## Visualisation", end="\n\n")    
-print(f'![]({image})', end="\n\n")
+print("## Visualisation", end="\n\n")
+print(f"![]({image})", end="\n\n")
 
 print("## Interactions", end="\n\n")
 
 fallback = 0
 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)
@@ -164,11 +177,24 @@ 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)
@@ -182,15 +208,25 @@ 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)
@@ -206,12 +242,14 @@ 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)
@@ -228,11 +266,15 @@ 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)
@@ -245,9 +287,20 @@ 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 = []
@@ -263,13 +316,21 @@ 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 = []
@@ -287,12 +348,16 @@ 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)
@@ -310,7 +375,7 @@ 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")
diff --git a/scripts/quick-ligand-protein.py b/scripts/quick-ligand-protein.py
index faff403..e211844 100644
--- a/scripts/quick-ligand-protein.py
+++ b/scripts/quick-ligand-protein.py
@@ -1,12 +1,14 @@
 #!/usr/bin/python3
 import argparse
-#import logzero
-#import logging
-#from logzero import logger as log
+
+# import logzero
+# import logging
+# from logzero import logger as log
 import pymol2
 import time
 
 import os
+
 print(os.getcwd())
 
 #################
@@ -17,7 +19,7 @@ startTime = time.time()
 version = "1.0"
 desc_text = "PyMol Quick Visualtion " + version
 ligandColor = "red"
-#logzero.loglevel(logging.INFO)
+# logzero.loglevel(logging.INFO)
 height = 1000
 width = 800
 dpi = 300
@@ -28,9 +30,9 @@ m1 = "target"
 m2 = "ligand"
 
 parser = argparse.ArgumentParser(description=desc_text)
-parser.add_argument("-p","--protein",help="Path to protein file")
-parser.add_argument("-l","--ligand",help="Path to ligand_out file")
-parser.add_argument("-c","--color",help="Color for ligand in visualisation")
+parser.add_argument("-p", "--protein", help="Path to protein file")
+parser.add_argument("-l", "--ligand", help="Path to ligand_out file")
+parser.add_argument("-c", "--color", help="Color for ligand in visualisation")
 
 args = parser.parse_args()
 
@@ -47,38 +49,55 @@ protein = args.protein
 print("Protein: ", protein)
 ligand = args.ligand
 
+
 def loadMol(filename, name):
     print("Loading " + filename + " as " + name)
-    cmd.load(filename,name)
+    cmd.load(filename, name)
+
+
 def changeColor(name, colorName):
     print("Changed " + name + "'s color to " + colorName)
-    cmd.color(colorName,name)
+    cmd.color(colorName, name)
+
+
 def orientEtZoom():
     cmd.orient()
     cmd.zoom()
+
+
 def showSurface(name):
-    cmd.show("surface",name)
+    cmd.show("surface", name)
+
+
 def surfaceTransparency(amount):
-    print("Changed surface transparency to " + str(amount*100) + "%")
-    cmd.set("transparency",amount)
-def generatePNG(filename,height=height,width=width,dpi=dpi,ray=ray):
+    print("Changed surface transparency to " + str(amount * 100) + "%")
+    cmd.set("transparency", amount)
+
+
+def generatePNG(filename, height=height, width=width, dpi=dpi, ray=ray):
     print("Generating " + filename + ".png")
-    cmd.png(filename,height,width,dpi=dpi,ray=ray)
+    cmd.png(filename, height, width, dpi=dpi, ray=ray)
+
+
 def flipHorizontal():
-    cmd.rotate("y",180)
+    cmd.rotate("y", 180)
+
+
 def zoomTo(name):
     cmd.zoom(name)
+
+
 def generatePictures():
-    generatePNG('output-front')
+    generatePNG("output-front")
     flipHorizontal()
-    generatePNG('output-back')
+    generatePNG("output-back")
     zoomTo(m2)
-    generatePNG('closeup-back')
+    generatePNG("closeup-back")
     orientEtZoom()
     flipHorizontal()
     zoomTo(m2)
-    generatePNG('closeup-front')
-    
+    generatePNG("closeup-front")
+
 
 print("Initialising PyMol")
 session = pymol2.PyMOL()
@@ -86,10 +105,10 @@ print("Starting PyMol Session")
 session.start()
 cmd = session.cmd
 
-loadMol(protein,m1)
-loadMol(ligand,m2)
-changeColor(m1,"grey60")
-changeColor(m2,ligandColor)
+loadMol(protein, m1)
+loadMol(ligand, m2)
+changeColor(m1, "grey60")
+changeColor(m2, ligandColor)
 orientEtZoom()
 showSurface(m1)
 surfaceTransparency(0.6)
@@ -97,4 +116,4 @@ surfaceTransparency(0.6)
 generatePictures()
 
 endTime = time.time()
-print("Finished Execution in " + str(round((endTime - startTime),2)) + " seconds.")
+print("Finished Execution in " + str(round((endTime - startTime), 2)) + " seconds.")