diff options
| -rw-r--r-- | scripts/quick-ligand-protein.py | 73 |
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.") |