Format code with Black

1 files changed, 46 insertions, 27 deletions

diff --git a/scripts/quick-ligand-protein.py b/scripts/quick-ligand-protein.py
index a300800..5873270 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()
@@ -86,12 +105,12 @@ print("Starting PyMol Session")
 session.start()
 cmd = session.cmd
 
-loadMol(protein,m1)
-cmd.remove("resn hoh") # remove water
-cmd.color("blue","hetatm") # color heteroatoms
-loadMol(ligand,m2)
-changeColor(m1,"grey60")
-changeColor(m2,ligandColor)
+loadMol(protein, m1)
+cmd.remove("resn hoh")  # remove water
+cmd.color("blue", "hetatm")  # color heteroatoms
+loadMol(ligand, m2)
+changeColor(m1, "grey60")
+changeColor(m2, ligandColor)
 orientEtZoom()
 showSurface(m1)
 surfaceTransparency(0.6)
@@ -99,4 +118,4 @@ 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.")