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#!/usr/bin/python3
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)
cmd.remove("resn hoh") # remove water
loadMol(ligand, m2)
changeColor(m1, "grey60")
changeColor(m2, ligandColor)
cmd.color("blue", "hetatm") # color heteroatoms
orientEtZoom()
showSurface(m1)
surfaceTransparency(0.6)
generatePictures()
endTime = time.time()
print("Finished Execution in " + str(round((endTime - startTime), 2)) + " seconds.")
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