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1 files changed, 99 insertions, 0 deletions

diff --git a/scripts/quick-ligand-protein.py b/scripts/quick-ligand-protein.py
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+++ b/scripts/quick-ligand-protein.py
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+import argparse
+#import logzero
+#import logging
+#from logzero import logger as log
+import pymol2
+import time
+
+import os
+print(os.getcwd())
+
+#################
+# Configuration #
+#################
+
+startTime = time.time()
+version = "1.0"
+desc_text = "PyMol Quick Visualtion " + version
+ligandColor = "red"
+#logzero.loglevel(logging.INFO)
+height = 1000
+width = 800
+dpi = 300
+ray = 0
+
+
+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")
+
+args = parser.parse_args()
+
+if args.protein == None:
+    print("Error: Please specify protein file")
+    exit(1)
+if args.ligand == None:
+    print("Error: Please specify ligand file")
+    exit(1)
+if args.color == None:
+    print("No color was speciifed, using default settings.")
+
+protein = args.protein
+print("Protein: ", protein)
+ligand = args.ligand
+
+def loadMol(filename, name):
+    print("Loading " + filename + " as " + name)
+    cmd.load(filename,name)
+def changeColor(name, colorName):
+    print("Changed " + name + "'s color to " + colorName)
+    cmd.color(colorName,name)
+def orientEtZoom():
+    cmd.orient()
+    cmd.zoom()
+def showSurface(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("Generating " + filename + ".png")
+    cmd.png(filename,height,width,dpi=dpi,ray=ray)
+def flipHorizontal():
+    cmd.rotate("y",180)
+def zoomTo(name):
+    cmd.zoom(name)
+def generatePictures():
+    generatePNG('output-front')
+    #flipHorizontal()
+    #generatePNG('output-back')
+    #zoomTo(m2)
+    #generatePNG('closeup-back')
+    #orientEtZoom()
+    #flipHorizontal()
+    #zoomTo(m2)
+    #generatePNG('closeup-front')
+    
+
+print("Initialising PyMol")
+session = pymol2.PyMOL()
+print("Starting PyMol Session")
+session.start()
+cmd = session.cmd
+
+loadMol(protein,m1)
+loadMol(ligand,m2)
+changeColor(m1,"grey60")
+changeColor(m2,ligandColor)
+orientEtZoom()
+showSurface(m1)
+surfaceTransparency(0.6)
+
+generatePictures()
+
+endTime = time.time()
+print("Finished Execution in " + str(round((endTime - startTime),2)) + " seconds.")
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