def pymolrc():
"""
startup settings, always applicable
"""
# multithreading
cmd.set('max_threads', psutil.cpu_count())
# color space
cmd.space('pymol')
# environment and color
cmd.bg_color('white')
cmd.set('depth_cue', 'off')
cmd.set('fog', 'off')
# nicer visualization
cmd.set('valence', 'on')
cmd.set('cartoon_side_chain_helper', 'on')
cmd.set('cartoon_highlight_color', 'grey50')
cmd.set('sphere_mode', '9')
# make sure trajectories are only loaded once defer_builds_mode is 3
def load_traj(*args, **kwargs):
cmd.set('defer_builds_mode', 3)
cmd.sync()
cmd.load_traj(*args, **kwargs)
cmd.extend('load_traj', load_traj)
def visualize_in_pymol(args,outfolder,clusters,interactions,pdb,cut,freq):
#(args,outfolder,clusters,interactions,pdb,cut,freq)=input_args
#print(cut)
#return
pymol.finish_launching()
cmd.reinitialize()
cmd.load(pdb)
cmd.hide("everything")
# cmd.show("ribbon")
cmd.show("cartoon")
# Create bindings and selections, and color them
bond_connections(clusters, interactions)
selections = select_clusters(clusters)
colors = color_selections(selections)
print(colors)
# colors = color_selections([sele])
#cmd.color("gray70")
#cmd.set("sphere_scale",0.75)
cmd.space("cmyk")
#cmd.set("ray_shadow","off")
#cmd.bg_color("white")
sele = "chain A and resi 131 and not name H*"
cmd.show("sticks",sele)
cmd.util.cnc(sele)
#cmd.center("chain A")
cmd.deselect()
### cut below here and paste into script ###
cmd.set_view ([\
0.185403526, -0.784912288, -0.591205537,\
-0.726189077, 0.295874894, -0.620551527,\
0.662004888, 0.544381559, -0.515144050,\
-0.001714554, -0.001769811, -125.023078918,\
30.330446243, 78.181671143, 146.038742065,\
98.763908386, 151.776306152, -20.000000000] )
outfile="{}cluster{}-{}.png".format(outfolder,cut,freq)
if args.ray or args.generate_all:
cmd.save(outfile)
### cut above here and paste into script ###
# Show clusters
if args.show[0] is None:
show_cluster(clusters)
else:
shw = [int(c) for c in args.show[0].split(',')]
for c in args.show[0]:
show_cluster(clusters[c - 1])
cmd.save(outfile)
cmd.quit()
def cspace_switch(tag):
if tag == 'PyMOL':
cmd.space('pymol')
elif tag == 'Publications':
cmd.space('rgb')
else:
cmd.space('cmyk')
def cspace_switch(tag):
if tag == 'PyMOL':
cmd.space('pymol')
elif tag == 'Publications':
cmd.space('rgb')
else:
cmd.space('cmyk')
def main():
from argparse import ArgumentParser
from sys import argv, stdin
parser = ArgumentParser(
description="Display Wordom PSN analysis clusters in PyMOL.")
parser.add_argument(
"-c", nargs=1, default=[None], metavar="float",
help="Cutoff to use (must be present in AVGfile)" +
", default=Use lowest found")
parser.add_argument(
"-f", nargs=1, default='50.0', metavar=float,
help="frequencey Cutoff to use (must be present in AVGfile)")
parser.add_argument(
"-show", nargs=1, default=[None], metavar="int[,int[...]]",
help="Show specified clusters")
parser.add_argument(
"-ray", action='store_true', help="raytrace and save fig")
parser.add_argument(
"-overwrite", action='store_true', help="overwrite if fig already exists")
parser.add_argument(
"-generate_all", action='store_true', help="generate raytraced figs for all cutoffs and frequences")
parser.add_argument(
"avg", nargs=1, metavar="AVGfile", type=str,
help="Wordom PSN avg file")
parser.add_argument(
"pdb", nargs=1, metavar="PDBfile", type=str,help="PDB file to draw")
args = parser.parse_args()
# Finish pymol launch
# pymol.finish_launching()
# cmd.feedback("disable","all","actions")
# cmd.feedback("disable","all","results")
# Set variables here
pdb = args.pdb[0]
avg = args.avg[0]
cut = args.c[0]
freq= float(args.f[0])
shw = args.show[0]
ray = args.ray or args.generate_all
outfolder=os.path.abspath(avg)
outfile = "{}cluster{}-{}.png".format(outfolder, cut, freq)
if not args.overwrite and os.path.exists(outfile):
print("\n{} already exist.\nUse -overwrite if you want to overwrite the existing file.\n".format(outfile))
sys.exit()
interactions = {}
clusters_all = {}
with open(avg, 'r') as infile:
interactions = read_avg_strength(infile)
#print(interactions)
#sys.exit()
infile.seek(0)
clusters_all = read_avg_clusters(infile)
#print(clusters)
#sys.exit()
# print("Hello")
#sys.exit(1)
# Select the cutoff
#with open("cutoffs", 'wb') as f:
# pickle.dump(list(clusters.keys()), f)
if cut is not None:
# If provided
cut = float(cut)
else:
# Default
cutoffs = list(clusters_all.keys())
cutoffs.sort()
cut = cutoffs[0]
cuts_to_sweep=[cut]
freq_to_sweep=[freq]
if args.generate_all:
cuts_to_sweep=clusters_all.keys()
freq_to_sweep=clusters_all[cut].keys()
todo=[]
for cut_ in cuts_to_sweep:
for freq_ in freq_to_sweep:
print("{} {}".format(cut_,freq_))
todo.append((args,outfolder,clusters_all[cut_][freq_],interactions,pdb,cut_,freq_))
#print(len(todo))
#sys.exit()
#pool = Pool(processes=8)
#pool.map(visualize_in_pymol,todo)
#print(todo)
#visualize_in_pymol((todo))
visualize_in_pymol(args,outfolder,clusters_all[cut][freq],interactions,pdb,cut,freq)
#for cut_ in cuts_to_sweep:
# for freq_ in freq_to_sweep:
if 1==0:
# Select clusters
print("Running for {} {}".format(cut_,freq_))
# clusters_freq = clusters_all[cut_]
# print(clusters_freq)
clusters = clusters_all[cut_][freq_]
#print(type(clusters_freq))
#print(clusters_freq.keys())
#with open("freq", 'wb') as f:
# pickle.dump(list(clusters_freq.keys()), f)
#print(type(freq))
#clusters = clusters_freq[80.0]
# print(clusters_freq)
# print(interactions)
#ys.exit()
# print(clusters)
cmd.reinitialize()
cmd.load(pdb)
cmd.hide("everything")
# cmd.show("ribbon")
cmd.show("cartoon")
# Create bindings and selections, and color them
bond_connections(clusters, interactions)
selections = select_clusters(clusters)
colors = color_selections(selections)
print(colors)
# colors = color_selections([sele])
#cmd.color("gray70")
#cmd.set("sphere_scale",0.75)
cmd.space("cmyk")
#cmd.set("ray_shadow","off")
#cmd.bg_color("white")
sele = "chain A and resi 131 and not name H*"
cmd.show("sticks",sele)
cmd.util.cnc(sele)
#cmd.center("chain A")
cmd.deselect()
### cut below here and paste into script ###
cmd.set_view ([\
0.185403526, -0.784912288, -0.591205537,\
-0.726189077, 0.295874894, -0.620551527,\
0.662004888, 0.544381559, -0.515144050,\
-0.001714554, -0.001769811, -125.023078918,\
30.330446243, 78.181671143, 146.038742065,\
98.763908386, 151.776306152, -20.000000000] )
outfile = "{}cluster{}-{}.png".format(outfolder, cut, freq)
if args.ray:
cmd.save(outfile)
### cut above here and paste into script ###
# Show clusters
if shw is None:
show_cluster(clusters)
else:
shw = [int(c) for c in shw.split(',')]
for c in shw:
show_cluster(clusters[c - 1])
cmd.save(outfile)
cmd.quit()
def testSpace(self):
cmd.space('pymol', 0.5)
cmd.space('cmyk', 0.7)
cmd.space('rgb')
# workspace settings
cmd.bg_color("white")
cmd.set("ray_opaque_background", "off")
cmd.set("orthoscopic", 0)
cmd.set("transparency", 0.5)
cmd.set("dash_gap", 0)
cmd.set("ray_trace_mode", 1)
cmd.set("ray_texture", 2)
cmd.set("antialias", 3)
cmd.set("ambient", 0.5)
cmd.set("spec_count", 5)
cmd.set("shininess", 50)
cmd.set("specular", 1)
cmd.set("reflect", .1)
cmd.space("cmyk")
@cmd.extend
def BallnStick():
cmd.color("gray30", "elem C")
cmd.set("dash_gap", 0.01)
cmd.set("dash_radius", 0.035)
cmd.set("surface_quality", 2)
cmd.set("surface_type", 4)
#cmd.set("spec_reflect", 0)
cmd.set("depth_cue", "off")
preset.ball_and_stick(mode=1)
# From https://github.com/rmera/ncipy/blob/master/nci.py
def testSpace(self):
cmd.space('pymol', 0.5)
cmd.space('cmyk', 0.7)
cmd.space('rgb')
cmd.disable("surface")
cmd.disable("protein")
cmd.show("cartoon")
cmd.set("cartoon_fancy_helices", 1)
cmd.spectrum("count", selection="(protein)&e. c")
#preset.publication("protein")
cmd.show("spheres", "surface")
cmd.clip("atoms", 5, "all")
cmd.select("prot_int", "protein w. 5 of surface")
cmd.disable('prot_int')
cmd.select("surf_int", "surface w. 5 of protein")
cmd.disable('surf_int')
cmd.hide("everything", "surface")
cmd.show("spheres", "surf_int")
cmd.show("sticks", "((byres (prot_int))&(!(n;c,o,h|(n. n&!r. pro))))")
cmd.space('cmyk')
cmd.bg_color('black')
cmd.select("BackBone", "name c+ca+o+n")
cmd.select("SC_Carbon", "elem c and not BackBone")
cmd.color("grey60", "SC_Carbon")
cmd.disable('SC_Carbon')
############## OSTEOCALCIN STUFF ###############
cmd.color("red", "name OE11")
cmd.color("red", "name OE12")
cmd.color("red", "name OE21")
cmd.color("red", "name OE22")
cmd.remove("resn cys and name hg")
cmd.show("sticks", "resn cys and not BackBone")
cmd.show("sticks", "resn cys and name CA+HA")
###########################################
cmd.create("ProtObj", "protein")