def setWorkingDirectory(self):
newWorkDir = tkFileDialog.askdirectory(
title='Set working directory', initialdir='',
parent=self.parent)
cmd.cd(newWorkDir)
cwd.set(newWorkDir)
message("Working directory changed to: " + newWorkDir);
return
def setWorkingDirectory(self):
newWorkDir = tkFileDialog.askdirectory(title='Set working directory',
initialdir='',
parent=self.parent)
cmd.cd(newWorkDir)
self.cwd.set(newWorkDir)
message("Working directory changed to: " + newWorkDir)
return
def testCdLsPwd(self):
with testing.mkdtemp() as path:
cmd.cd(path)
self.assertEqual(os.getcwd(),
os.path.realpath(path))
touch('foo1.txt')
touch('foo2.txt')
touch('foo3.bin')
cmd.feedback("disable", "python", "output")
cmd.pwd()
# no test of output possible
cmd.ls('*.txt')
# Count
counts = pd.Series(0, index=RADS)
for a, b in product(internal_coords, all_coords):
es = euclid_step(a, b)
if es is not None:
counts.loc[es] += 1
counts = counts.cumsum()
# Mean per center atom
meancounts = counts / N
# Normalize to density
volumina = pd.Series(4 / 3.0 * sp.pi * (RADS ** 3), index=RADS)
density = meancounts / volumina
# Correct for center
density -= 1 / (4/3 * sp.pi * RADS ** 3)
# Results
counts.index = ["{}_correctcount".format(i) for i in counts.index]
density.index = ["{}_density".format(i) for i in density.index]
return pd.concat(([counts, density]))
cmd.cd(PATH)
result = []
pdbs = []
for pdb in os.listdir("."):
if not pdb.endswith(".pdb"):
continue
pdbs.append(pdb)
result.append(slowpacking(pdb))
#break
result = pd.DataFrame(result, index=pdbs)
result.to_csv("packing.csv")
def pymol_chdir(outdir):
cmd.cd(outdir)
from pymol import cmd
from chempy.models import Indexed
from chempy import Bond, Atom
from pymol import cmd
if not os.path.exists("../data/clusters"):
cmd.cd("$pymol_scripts")
filename = './modules/rgb.py'
exec(compile(open(filename, "rb").read(), filename, 'exec'))
def create_bond(model, a1, a2): # one-based atom serial numbers
b = Bond()
b.index = [a1 - 1, a2 - 1] # zero-based indices!
model.bond.append(b)
def create_spheres(name, spheres, links, frame):
cmd.delete(name)
model = Indexed()
for i in (range(len(spheres) / 4)):
ai = i * 4
r = spheres[ai + 3]
cluster = int(name[7:10])
if r <> 0.5:
a=Atom()
a.name = "X" + str(i)
a.resi = str(cluster)
a.vdw = spheres[ai + 3]
a.coord = [spheres[ai], spheres[ai + 1], spheres[ai + 2]]
model.atom.append(a)
from pymol import cmd
if not os.path.exists("../data/clusters_timeless"):
cmd.cd("$pymol_scripts")
cmd.cd("modules")
import caver
cmd.cd("..")
filename = './modules/rgb.py'
exec(compile(open(filename, "rb").read(), filename, 'exec'))
color = 1
list = os.listdir("../data/clusters_timeless")
list.sort()
name = ''
for fn in list:
old_name = name
name = fn
if color < 1000 and caver.new_cluster(old_name, name):
color += 1
cmd.load('../data/clusters_timeless/' + fn, name)
cmd.color('caver' + str(color), name)
cmd.alter(name, 'vdw=b')
cmd.do('set all_states,1')
cmd.set('two_sided_lighting', 'on')
cmd.set('transparency', '0.2')
# [proposed] use CNS to do simulated annealing on models and tidy them up (like in Morph)
# <minimize powell> is the command (from morph_dist.inp)
##
# Tell PyMOL to launch quiet (-q), and with no GUI (-c)
# Make sure PyMOL has finished to launch before using any PyMOL modules.
# Beware - many of the numbers here may have to be tweaked for your application
# for example, Cys max accessible area is 30 ang^2
# would be different for other residues
# different structures may require other convergence parameters
__main__.pymol_argv = [ 'pymol', '-qc' ]
pymol.finish_launching()
wd = os.path.expanduser('~') #working directory == home directory. Messy.
cmd.cd(wd)
#prepare logfile for results only
logfile = "log_" + datetime.now().strftime("%y%m%d-%H%M%S") + ".txt"
header = "PDB_file, probe, C666SG_dist, C666_access, C666_clashes, all_clashes, fract_COM, BD_L2, AC_L2, del_dimer_COM\n".replace(", ","\t")
l = open(logfile, 'w+')
l.write(header)
l.close()
#fixed parameters
source = "LBD_tet"
residue_bury = 666
perp_axis = [0, 1, 0] #y??
para_axis = [1, 0, 0] #x??
dimer_one_subs = ["A", "D"]
dimer_two_subs = ["C", "B"]
from pymol import cmd
from pymol import preset
from pymol import util
from glob import glob
import sys
import os
path = ""
params = []
basepath = os.getcwd()
try:
path = sys.argv[len(sys.argv) - 1]
print path
cmd.cd(path)
#index = sys.argv.index("--")
#params = sys.argv[index:]
#if(len(params) == 2):
#path = params[1]
#cmd.cd(path)
#else:
#print "No Path specified"
except ValueError:
print "No Path specified"
for file in glob("*.pdb"):
print "file: ", file
listname = file.split(".")
name = listname[0]
cmd.load(file, name)
from pymol import cmd
from pymol import preset
from pymol import util
from glob import glob
import sys
import os
path = ""
params = []
basepath = os.getcwd()
try:
path = sys.argv[len(sys.argv) - 1]
print path
cmd.cd(path)
#index = sys.argv.index("--")
#params = sys.argv[index:]
#if(len(params) == 2):
#path = params[1]
#cmd.cd(path)
#else:
#print "No Path specified"
except ValueError:
print "No Path specified"
for file in glob("*.pdb"):
print "file: ", file
listname = file.split(".")
name = listname[0];
cmd.load(file, name)
