def test_color_deep(self):
cmd.viewport(100, 70)
self.ambientOnly()
cmd.fragment('trp', 'm1')
cmd.orient('m1')
cmd.show_as('sticks')
cmd.show('spheres', 'name C')
cmd.set('stick_color', 'blue', 'm1')
cmd.set('stick_color', 'red', 'name CH2+CZ3+CE3+CD2')
cmd.set('sphere_color', 'yellow', 'name C')
cmd.color('green')
img = self.get_imagearray()
self.assertImageHasColor('blue', img)
self.assertImageHasColor('red', img)
self.assertImageHasColor('yellow', img)
self.assertImageHasNotColor('green', img)
cmd.color_deep('green')
img = self.get_imagearray()
self.assertImageHasNotColor('blue', img)
self.assertImageHasNotColor('red', img)
self.assertImageHasNotColor('yellow', img)
self.assertImageHasColor('green', img)
def show_ligand_interactions(recsel="not hetatm", ligsel="hetatm", cutoff=5):
"""
DESCRIPTION
Visualize interactions between receptor and ligand.
ARGUMENTS
recsel = string: atom selection of the receptor {default: "not hetatm"}
ligsel = string: atom selections of the ligand {default: "hetatm"}
cutoff = float: show as sticks all receptor residues within this distance from the ligand {default: 5.0}
"""
cmd.select('ligand', ligsel)
cmd.select('receptor', recsel)
cmd.bg_color('white')
cmd.show_as('cartoon')
cmd.show_as('sticks', 'hetatm')
cmd.set('cartoon_transparency', 0.2)
cmd.spectrum(selection=recsel+" or "+ligsel,byres=1)
util.cbag('not elem C')
cmd.set('cartoon_fancy_helices', 1);
cmd.show("sticks", "(hydro)");
cmd.select("pocket", "byres (receptor within %s of ligand)" % cutoff);
cmd.show("sticks", "pocket")
cmd.hide('(h. and (e. c extend 1))')
cmd.set('h_bond_max_angle', 30)
cmd.set('h_bond_cutoff_center', 3.6)
cmd.set('h_bond_cutoff_edge', 3.2)
cmd.dist('ligand_Hbonds', 'ligand', 'receptor', 3.5, mode=2)
cmd.set('dash_radius', 0.15)
# now set the label options
cmd.set('label_size', 20)
cmd.set('label_position', [0,0,10])
def load():
try:
r = 0
list = glob(ent_dir)
list.sort()
# list = [ "pdb/vq" ]
for dir in list:
sys.__stdout__.write("\n"+dir)
sys.__stdout__.flush()
for file in glob(dir+"/pdb*"):
name = os.path.split(file)[-1]
name = string.split(name,'.')[0]
cmd.disable()
cmd.load(file,name)
cmd.show_as("cartoon",name)
cmd.refresh()
cmd.dss(name)
cmd.refresh()
time.sleep(0.1)
sys.__stdout__.write(".")
sys.__stdout__.flush()
sys.__stdout__.write("("+str(cmd.count_atoms())+")")
sys.__stdout__.flush()
cmd.dss()
cmd.delete('all')
except:
traceback.print_exc()
def normalmodes_prody(selection, cutoff=15, first=7, last=10, guide=1,
prefix='prody', states=7, factor=-1, quiet=1):
'''
DESCRIPTION
Anisotropic Network Model (ANM) analysis with ProDy.
Based on:
http://www.csb.pitt.edu/prody/examples/dynamics/enm/anm.html
'''
try:
import prody
except ImportError:
print('Failed to import prody, please add to PYTHONPATH')
raise CmdException
first, last, guide = int(first), int(last), int(guide)
states, factor, quiet = int(states), float(factor), int(quiet)
assert first > 6
if guide:
selection = '(%s) and guide and alt A+' % (selection)
tmpsele = cmd.get_unused_name('_')
cmd.select(tmpsele, selection)
f = StringIO(cmd.get_pdbstr(tmpsele))
conf = prody.parsePDBStream(f)
modes = prody.ANM()
modes.buildHessian(conf, float(cutoff))
modes.calcModes(last - first + 1)
if factor < 0:
from math import log
natoms = modes.numAtoms()
factor = log(natoms) * 10
if not quiet:
print(' set factor to %.2f' % (factor))
for mode in range(first, last + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d' % (name, mode))
for state in range(1, states+1):
xyz_it = iter(modes[mode-7].getArrayNx3() * (factor *
((state-1.0)/(states-1.0) - 0.5)))
cmd.create(name, tmpsele, 1, state, zoom=0)
cmd.alter_state(state, name, '(x,y,z) = xyz_it.next() + (x,y,z)',
space=locals())
cmd.delete(tmpsele)
if guide:
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
def q5():
'''
DESCRIPTION
Question 5: How many axial stacks of helices does
the ribozyme have?
The following commands created the scene for "q5":
delete all;fetch 3zp8, hammer, async=0;show cartoon, hammer;set_view (-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);rock;
To reuse of parts or all of the above commands, copy and paste the commands
onto the command line or into a plain text file.
These commands are sufficient for most editing tasks:
To edit code, positon cursor on command line with left mouse button.
Control-e moves the cursor to the end of the line, even when it is out of view.
Control-a moves the cursor to the beginning of the line, even when it is out of view.
Up arrow key recalls last line of commands for editing.
These commands may not be available on all systems:
Shift-control-a selects everything from the right of the cursor to the end of the line.
Shift-control-e selects everything to the left of the cursor to the end of the line.
Command-f moves the cursor to the end of the current word.
Command-b moves the cursor to the begining of the current word.
Control-f moves the cursor to the right by one character.
Control-b moves the cursor to the left by one character.
'''
cmd.reinitialize()
cmd.fetch('3zp8', type='pdb', name= 'hammer', async='0')
cmd.show_as('cartoon','hammer')
cmd.rock()
cmd.set_view('(-0.5,0.18,-0.85,-0.17,-0.98,-0.11,-0.85,0.09,0.52,0.0,0.0,-167.2,-18.45,10.92,-12.11,126.37,208.02,-20.0);')
print('Enter "q5" to make the scene for question 5.')
print('Enter "help q5" to see question 5 and the commands to make the scene.')
def testStickBall(self, use_shader):
'''
Test some stick_ball* settings
'''
cmd.viewport(100, 100)
cmd.set('use_shaders', use_shader)
self.ambientOnly()
cmd.set('stick_ball')
cmd.set('stick_ball_ratio', 2.0)
cmd.set('stick_ball_color', 'blue')
cmd.set('stick_color', 'red')
cmd.fragment('gly')
cmd.orient()
cmd.color('green')
cmd.show_as('sticks')
img = self.get_imagearray()
self.assertImageHasColor('blue', img)
self.assertImageHasColor('red', img)
self.assertImageHasNotColor('green', img)
def testStickBall(self, use_shader):
'''
Test some stick_ball* settings
'''
cmd.viewport(100, 100)
cmd.set('use_shaders', use_shader)
self.ambientOnly()
cmd.set('stick_ball')
cmd.set('stick_ball_ratio', 2.0)
cmd.set('stick_ball_color', 'blue')
cmd.set('stick_color', 'red')
cmd.fragment('gly')
cmd.orient()
cmd.color('green')
cmd.show_as('sticks')
img = self.get_imagearray()
self.assertImageHasColor('blue', img)
self.assertImageHasColor('red', img)
self.assertImageHasNotColor('green', img)
def testTrilines(self, trilines):
cmd.viewport(100, 100)
cmd.set('use_shaders', True)
self.ambientOnly()
cmd.set('dynamic_width', 0)
cmd.set('line_width', 5)
cmd.set('line_smooth', 0)
cmd.fragment('ethylene')
cmd.show_as('lines')
cmd.color('white')
cmd.orient()
cmd.set('trilines', trilines)
# check percentage of covered pixels
img = self.get_imagearray()
npixels = img.shape[0] * img.shape[1]
covered = numpy.count_nonzero(img[..., :3])
ratio = covered / float(npixels)
msg = "covered=%d npixels=%d ratio=%f" % (covered, npixels, ratio)
self.assertTrue(0.14 < ratio < 0.165, msg)
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.set_title('pdb',1,os.path.split(file)[-1])
cmd.rewind()
cmd.orient('pdb')
cmd.refresh()
cmd.show_as("ribbon")
cmd.refresh()
cmd.show_as("sticks")
cmd.refresh()
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
if n>1:
cmd.rewind()
sys.__stderr__.write(file+"\n")
sys.__stderr__.flush()
for a in range(1,n+1):
cmd.forward()
cmd.refresh()
except:
traceback.print_exc()
def testTrilines(self, trilines):
cmd.viewport(100, 100)
cmd.set('use_shaders', True)
self.ambientOnly()
cmd.set('dynamic_width', 0)
cmd.set('line_width', 5)
cmd.set('line_smooth', 0)
cmd.fragment('ethylene')
cmd.show_as('lines')
cmd.color('white')
cmd.orient()
cmd.set('trilines', trilines)
# check percentage of covered pixels
img = self.get_imagearray()
npixels = img.shape[0] * img.shape[1]
covered = numpy.count_nonzero(img[...,:3])
ratio = covered / float(npixels)
msg = "covered=%d npixels=%d ratio=%f" % (covered, npixels, ratio)
self.assertTrue(0.14 < ratio < 0.165, msg)
def testMMTF(self):
'''Styled MMTF export/import'''
S = 0b10 # 1 << 1 spheres
D = 0b1000000000 # 1 << 9 dots
B = 2 # blue
R = 4 # red
cmd.fragment('gly')
cmd.color(B)
cmd.color(R, 'elem C')
cmd.show_as('spheres')
cmd.show_as('dots', 'elem C')
with testing.mktemp('.mmtf') as filename:
cmd.save(filename)
cmd.delete('*')
cmd.load(filename)
color_list = []
reps_list = []
cmd.iterate('*', 'color_list.append(color)', space=locals())
cmd.iterate('*', 'reps_list.append(reps)', space=locals())
self.assertEqual(color_list, [B, R, R, B, B, B, B])
self.assertEqual(reps_list, [S, D, D, S, S, S, S])
def example():
cmd.fetch('1d7q', async=0)
cmd.show_as('sticks')
with timing():
rmsf('all')
with timing():
spectrumproperty('rmsf', 'blue white red')
def paint_vars_f_Bin(vars_a, vars_b):
cmd.set_view("""0.147443876, -0.624960124, -0.766605735, \
0.453299403, -0.646183312, 0.613975227, \
-0.879078567, -0.438027859, 0.188018516, \
0.000000000, 0.000000000, -252.833984375, \
30.680297852, 182.966445923, 30.680259705, \
199.336242676, 306.331726074, -20.000000000""")
cmd.show_as("cartoon", "all")
color_sel("grey", "all")
cmd.select("epi", "resi 62-69+196-212")
cmd.select("F2", "resi 22-109")
cmd.select("F1", "resi 160-516")
with open(vars_a, "r") as _:
vars_a = _.readline().strip().split()
freq_a = _.readline().strip().split()
with open(vars_b, "r") as _:
vars_b = _.readline().strip().split()
freq_b = _.readline().strip().split()
vars_sel = "resi " + "+".join(vars_a + vars_b)
cmd.select("vars", vars_sel)
cmd.show_as("spheres", "vars")
vars_a_sel = "resi " + "+".join(vars_a)
vars_b_sel = "resi " + "+".join(vars_b)
color_sel("orange", "F1 and " + vars_a_sel)
color_sel("green", "F1 and " + vars_b_sel)
color_sel("yellow", "F2 and " + vars_a_sel)
color_sel("cyan", "F2 and " + vars_b_sel)
color_sel("red", "epi")
set_labels()
cmd.label("vars and name cb", "'%s'%(resi,)")
def testMMTF(self):
'''Styled MMTF export/import'''
S = 0b10 # 1 << 1 spheres
D = 0b1000000000 # 1 << 9 dots
B = 2 # blue
R = 4 # red
cmd.fragment('gly')
cmd.color(B)
cmd.color(R, 'elem C')
cmd.show_as('spheres')
cmd.show_as('dots', 'elem C')
with testing.mktemp('.mmtf') as filename:
cmd.save(filename)
cmd.delete('*')
cmd.load(filename)
color_list = []
reps_list = []
cmd.iterate('*', 'color_list.append(color)', space=locals())
cmd.iterate('*', 'reps_list.append(reps)', space=locals())
self.assertEqual(color_list, [B, R, R, B, B, B, B])
self.assertEqual(reps_list, [S, D, D, S, S, S, S])
def findSurfaceResidues(objSel="(all)",
cutoff=2.5,
doShow=False,
verbose=False):
tmpObj = "__tmp"
cmd.create(tmpObj, objSel + " and polymer")
if verbose != False:
print("WARNING: I'm setting dot_solvent. You may not care for this.")
cmd.set("dot_solvent")
cmd.get_area(selection=tmpObj, load_b=1)
cmd.remove(tmpObj + " and b < " + str(cutoff))
stored.tmp_dict = {}
cmd.iterate(tmpObj, "stored.tmp_dict[(chain,resv)]=1")
exposed = stored.tmp_dict.keys()
exposed.sort()
randstr = str(random.randint(0, 10000))
selName = "exposed_atm_" + randstr
if verbose != False:
print("Exposed residues are selected in: " + selName)
cmd.select(selName, objSel + " in " + tmpObj)
selNameRes = "exposed_res_" + randstr
cmd.select(selNameRes, "byres " + selName)
if doShow != False:
cmd.show_as("spheres", objSel + " and poly")
cmd.color("white", objSel)
cmd.color("red", selName)
cmd.delete(tmpObj)
return exposed
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
cmd.delete('pdb')
cmd.load(file, 'pdb')
cmd.set_title('pdb', 1, os.path.split(file)[-1])
cmd.rewind()
cmd.orient('pdb')
cmd.refresh()
cmd.show_as("ribbon")
cmd.refresh()
cmd.show_as("sticks")
cmd.refresh()
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
if n > 1:
cmd.rewind()
sys.__stderr__.write(file + "\n")
sys.__stderr__.flush()
for a in range(1, n + 1):
cmd.forward()
cmd.refresh()
except:
traceback.print_exc()
def testAA(self):
'''
Make a black/white image and check if gray pixels are found with
antialias_shader=1/2
'''
cmd.viewport(100, 100)
cmd.set('use_shaders', True)
self.ambientOnly()
cmd.fragment('gly')
cmd.show_as('spheres')
cmd.color('white')
cmd.zoom()
# b/w image, we expect only two color values
img = self.get_imagearray()
self.assertTrue(len(numpy.unique(img[...,:3])) == 2)
for aa in (1, 2):
cmd.set('antialias_shader', aa)
# smoothed edges, we expect more than two color values
img = self.get_imagearray()
self.assertTrue(len(numpy.unique(img[...,:3])) > 2)
def plot(self, outfile):
ctrl_id, case_id, snp_df_sub = self.score_on_var()
df = pd.merge(snp_df_sub, self.snps2aa, on='id')
#pymol.finish_launching()
cmd.reinitialize()
cmd.fetch(self.pdb)
cmd.alter(self.pdb, 'b = 0.5')
cmd.show_as('cartoon', self.pdb)
cmd.color('white', self.pdb)
for i, row in df.iterrows():
resi = row['structure_position']
chain = row['chain']
pheno = row['es']
selec = 'snp%s' % i
selec_atom = 'snp_atom%s' % i
cmd.select(selec,
'name ca and resi %s and chain %s' % (resi, chain))
cmd.create(selec_atom, selec)
cmd.set("sphere_scale", 0.8)
cmd.show('sphere', selec_atom)
cmd.alter(selec_atom, 'b=%s' % pheno)
cmd.spectrum("b",
"blue_white_red",
selec_atom,
maximum=1.0,
minimum=0.0)
cmd.bg_color("white")
cmd.zoom()
cmd.orient()
cmd.save('%s.pse' % outfile)
cmd.png('%s.png' % outfile, width=2400, height=2400, dpi=300, ray=1)
def testRepsExist(self):
cmd.viewport(200, 150)
cmd.load(self.datafile('1oky-frag.pdb'), 'm1')
# make some nonbonded
cmd.unbond('resi 115-', 'resi 115-')
# labels
cmd.label('all', 'name')
# measurements
cmd.distance('measure1', 'index 1', 'index 10')
cmd.angle('measure1', 'index 1', 'index 10', 'index 20')
cmd.dihedral('measure1', 'index 1', 'index 10', 'index 20', 'index 30')
# color test setup
cmd.color('white', '*')
cmd.set('ambient', 1)
cmd.set('depth_cue', 0)
cmd.set('antialias', 0)
cmd.set('line_smooth', 0)
cmd.orient()
# test most reps
for rep in REPS:
cmd.show_as(rep)
self.assertImageHasColor('white', msg='rep missing: ' + rep)
# test cartoon
cmd.show_as('cartoon')
for cart in CARTOONS:
cmd.cartoon(cart)
self.assertImageHasColor('white', msg='cartoon missing: ' + cart)
def testAA(self):
'''
Make a black/white image and check if gray pixels are found with
antialias_shader=1/2
'''
cmd.viewport(100, 100)
cmd.set('use_shaders', True)
self.ambientOnly()
cmd.fragment('gly')
cmd.show_as('spheres')
cmd.color('white')
cmd.zoom()
# b/w image, we expect only two color values
img = self.get_imagearray()
self.assertNumColorsEqual(img, 2)
for aa in (1, 2):
cmd.set('antialias_shader', aa)
# smoothed edges, we expect more than two color values
img = self.get_imagearray()
self.assertTrue(len(numpy.unique(img[..., :3])) > 2)
def test(self):
cmd.set('suspend_updates')
cmd.set('depth_cue', 0)
cmd.set('ambient', 1)
cmd.set('specular', 0)
cmd.set('stereo_angle', 10)
cmd.pseudoatom()
cmd.show_as('sphere')
cmd.zoom()
cmd.stereo('anaglyph')
cmd.set('suspend_updates', 0)
wh = (40, 40)
cmd.draw(*wh, antialias=0)
cmd.sync()
img = self.get_imagearray(prior=1)
self.assertEqual(wh, img.shape[:2])
# ray tracing and shaders in PyMOL 1.7.6+:
# 0xe50000
# 0x00e5e5
# -> delta=26 (0x1a)
self.assertImageHasColor('0xff0000', img, delta=0x1a)
self.assertImageHasColor('0x00ffff', img, delta=0x1a)
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
(x, y, z) = (0, 0, 0)
start = time.time()
count = 1
scale = 100.0
for file in list:
cmd.load(file, str(count), quiet=1)
cmd.translate([x * scale, y * scale, z * scale], object=str(count))
# cmd.disable(str(count))
atoms = cmd.count_atoms()
passed = time.time() - start
print "%3d structures/%5.1f sec = %8.1f atom/sec over %6d atoms" % (
count, passed, atoms / passed, atoms)
count = count + 1
if count > 100: break
x = x + 1
if x > 7:
x = 0
y = y + 1
if y > 7:
y = 0
z = z + 1
if z > 9:
y = 0
z = z + 1
cmd.zoom()
cmd.set("sphere_mode", 1)
cmd.show_as("spheres")
cmd.rebuild()
cmd.set("hash_max", 250)
def normalmodes_prody(selection, cutoff=15, first=7, last=10, guide=1,
prefix='prody', states=7, factor=-1, quiet=1):
'''
DESCRIPTION
Anisotropic Network Model (ANM) analysis with ProDy.
Based on:
http://www.csb.pitt.edu/prody/examples/dynamics/enm/anm.html
'''
try:
import prody
except ImportError:
print('Failed to import prody, please add to PYTHONPATH')
raise CmdException
first, last, guide = int(first), int(last), int(guide)
states, factor, quiet = int(states), float(factor), int(quiet)
assert first > 6
if guide:
selection = '(%s) and guide and alt A+' % (selection)
tmpsele = cmd.get_unused_name('_')
cmd.select(tmpsele, selection)
f = StringIO(cmd.get_pdbstr(tmpsele))
conf = prody.parsePDBStream(f)
modes = prody.ANM()
modes.buildHessian(conf, float(cutoff))
modes.calcModes(last - first + 1)
if factor < 0:
from math import log
natoms = modes.numAtoms()
factor = log(natoms) * 10
if not quiet:
print(' set factor to %.2f' % (factor))
for mode in range(first, last + 1):
name = prefix + '%d' % mode
cmd.delete(name)
if not quiet:
print(' normalmodes: object "%s" for mode %d' % (name, mode))
for state in range(1, states+1):
xyz_it = iter(modes[mode-7].getArrayNx3() * (factor *
((state-1.0)/(states-1.0) - 0.5)))
cmd.create(name, tmpsele, 1, state, zoom=0)
cmd.alter_state(state, name, '(x,y,z) = next(xyz_it) + (x,y,z)',
space={'xyz_it': xyz_it, 'next': next})
cmd.delete(tmpsele)
if guide:
cmd.set('ribbon_trace_atoms', 1, prefix + '*')
cmd.show_as('ribbon', prefix + '*')
else:
cmd.show_as('lines', prefix + '*')
def loadFitnessFactors (mol,startaa=1,source="/Users/student/Box Sync/PUBS/Pymol-practice.txt", visual="Y"):
# adapted from http://www.pymolwiki.org/index.php/Load_new_B-factors
"""
Replaces B-factors with a list of fitness factor values contained in a plain txt file
usage: loadFitnessFactors mol, [startaa, [source, [visual]]]
mol = any object selection (within one single object though)
startaa = number of first amino acid in 'new Fitness-factors' file (default=1)
source = name of the file containing new Fitness-factor values (default=newFitnessFactors.txt)
visual = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)
example: loadFitnessFactors 1LVM and chain A
"""
obj=cmd.get_object_list(mol)[0]
cmd.alter(mol,"b=-1.0")
inFile = open(source, 'r')
counter=int(startaa)
fitnessFacts=[]
for line in inFile.readlines():
fitnessFact=float(line)
fitnessFacts.append(fitnessFact)
cmd.alter("%s and resi %s and n. CA"%(mol,counter), "b=%s"%fitnessFact)
counter=counter+1
if visual=="Y":
cmd.show_as("cartoon",mol)
cmd.cartoon("putty", mol)
# cmd.set("cartoon_putty_scale_min", min(fitnessFacts),obj)
# cmd.set("cartoon_putty_scale_max", max(fitnessFacts),obj)
cmd.set("cartoon_putty_transform", 0,obj)
cmd.set("cartoon_putty_radius", 0.2,obj)
cmd.spectrum("b","red_white_blue", "%s and n. CA " %mol)
cmd.ramp_new("count", obj, [min(fitnessFacts), (min(fitnessFacts)+max(fitnessFacts))/2, max(fitnessFacts)], color = ["blue", "white", "red"])
cmd.recolor()
def loadBfacts (mol,startaa=1,source="/Users/student/Box Sync/PUBS/Pymol-practice.txt", visual="Y"):
"""
Replaces B-factors with a list of values contained in a plain txt file
usage: loadBfacts mol, [startaa, [source, [visual]]]
mol = any object selection (within one single object though)
startaa = number of first amino acid in 'new B-factors' file (default=1)
source = name of the file containing new B-factor values (default=newBfactors.txt)
visual = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)
example: loadBfacts 1LVM and chain A
"""
obj=cmd.get_object_list(mol)[0]
cmd.alter(mol,"b=-1.0")
inFile = open(source, 'r')
counter=int(startaa)
bfacts=[]
for line in inFile.readlines():
bfact=float(line)
bfacts.append(bfact)
cmd.alter("%s and resi %s and n. CA"%(mol,counter), "b=%s"%bfact)
counter=counter+1
if visual=="Y":
cmd.show_as("cartoon",mol)
cmd.cartoon("putty", mol)
cmd.set("cartoon_putty_scale_min", min(bfacts),obj)
cmd.set("cartoon_putty_scale_max", max(bfacts),obj)
cmd.set("cartoon_putty_transform", 0,obj)
cmd.set("cartoon_putty_radius", 0.2,obj)
cmd.spectrum("b","rainbow", "%s and n. CA " %mol)
cmd.ramp_new("count", obj, [min(bfacts), max(bfacts)], "rainbow")
cmd.recolor()
def test(self):
cmd.set('suspend_updates')
cmd.set('depth_cue', 0)
cmd.set('ambient', 1)
cmd.set('specular', 0)
cmd.set('stereo_angle', 10)
cmd.pseudoatom()
cmd.show_as('sphere')
cmd.zoom()
cmd.stereo('anaglyph')
cmd.set('suspend_updates', 0)
wh = (40, 40)
cmd.draw(*wh, antialias=0)
cmd.sync()
img = self.get_imagearray(prior=1)
self.assertEqual(wh, img.shape[:2])
# ray tracing and shaders in PyMOL 1.7.6+:
# 0xe50000
# 0x00e5e5
# -> delta=26 (0x1a)
self.assertImageHasColor('0xff0000', img, delta=0x1a)
self.assertImageHasColor('0x00ffff', img, delta=0x1a)
def option2():
vinacomd = str(checkutilities())
A = inputdata2()
global proteinfile, ligandfile
import addwater
addwater.main(ligandfile)
waterfile()
#Writes the water.pdbqt file
import dockcheck
dockcheck.main(proteinfile, ligandfile, vinacomd)
os.remove('waterdetails.txt')
os.remove('placedwaters.pdb')
os.remove('water.pdbqt')
cmd.set("retain_order", 1)
cmd.set("pdb_use_ter_records", 0)
cmd.load(proteinfile, 'pro')
cmd.show_as('cartoon', 'pro')
cmd.color('blue','pro')
cmd.load('predictedwaters.pdb','wats')
cmd.color('red','wats')
cmd.load(ligandfile,'lig')
cmd.show_as('sticks','lig')
cmd.center('lig')
def preProcessPDB(fname):
stored.residues = []
stored.chains = []
cmd.iterate('(name ca)', 'stored.residues.append(resi)')
cmd.iterate('(name ca)', 'stored.chains.append(chain)')
cmd.show_as("cartoon", '(all)')
cmd.color("white", '(all)')
def loadBfacts(mol, startaa=1, source="newBfactors.txt", visual="Y"):
"""
Replaces B-factors with a list of values contained in a plain txt file
usage: loadBfacts mol, [startaa, [source, [visual]]]
mol = any object selection (within one single object though)
startaa = number of first amino acid in 'new B-factors' file (default=1)
source = name of the file containing new B-factor values (default=newBfactors.txt)
visual = redraws structure as cartoon_putty and displays bar with min/max values (default=Y)
example: loadBfacts 1LVM and chain A
"""
obj = cmd.get_object_list(mol)[0]
cmd.alter(mol, "b=-1.0")
inFile = open(source, 'r')
counter = int(startaa)
bfacts = []
for line in inFile.readlines():
bfact = float(line)
bfacts.append(bfact)
cmd.alter("%s and resi %s and n. CA" % (mol, counter), "b=%s" % bfact)
counter = counter + 1
if visual == "Y":
cmd.show_as("cartoon", mol)
cmd.cartoon("putty", mol)
cmd.set("cartoon_putty_scale_min", min(bfacts), obj)
cmd.set("cartoon_putty_scale_max", max(bfacts), obj)
cmd.set("cartoon_putty_transform", 0, obj)
cmd.set("cartoon_putty_radius", 0.2, obj)
cmd.spectrum("b", "rainbow", "%s and n. CA " % mol)
cmd.ramp_new("count", obj, [min(bfacts), max(bfacts)], "rainbow")
cmd.recolor()
def option2():
vinacomd = str(checkutilities())
A = inputdata2()
global proteinfile, ligandfile
import addwater
addwater.main(ligandfile)
waterfile()
#Writes the water.pdbqt file
import dockcheck
dockcheck.main(proteinfile, ligandfile, vinacomd)
os.remove('waterdetails.txt')
os.remove('placedwaters.pdb')
os.remove('water.pdbqt')
cmd.set("retain_order", 1)
cmd.set("pdb_use_ter_records", 0)
cmd.load(proteinfile, 'pro')
cmd.show_as('cartoon', 'pro')
cmd.color('blue', 'pro')
cmd.load('predictedwaters.pdb', 'wats')
cmd.color('red', 'wats')
cmd.load(ligandfile, 'lig')
cmd.show_as('sticks', 'lig')
cmd.center('lig')
def testRepsExist(self):
cmd.viewport(200, 150)
cmd.load(self.datafile('1oky-frag.pdb'), 'm1')
# make some nonbonded
cmd.unbond('resi 115-', 'resi 115-')
# labels
cmd.label('all', 'name')
# measurements
cmd.distance('measure1', 'index 1', 'index 10')
cmd.angle('measure1', 'index 1', 'index 10', 'index 20')
cmd.dihedral('measure1', 'index 1', 'index 10', 'index 20', 'index 30')
# color test setup
cmd.color('white', '*')
cmd.set('ambient', 1)
cmd.set('depth_cue', 0)
cmd.set('antialias', 0)
cmd.set('line_smooth', 0)
cmd.orient()
# test most reps
for rep in REPS:
cmd.show_as(rep)
self.assertImageHasColor('white', msg='rep missing: ' + rep)
# test cartoon
cmd.show_as('cartoon')
for cart in CARTOONS:
cmd.cartoon(cart)
self.assertImageHasColor('white', msg='cartoon missing: ' + cart)
def findSurfaceResidues(objSel="(all)", cutoff=2.5, doShow=False, verbose=True):
"""
findSurfaceResidues
finds those residues on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
PARAMS
objSel (string)
the object or selection in which to find
exposed residues
DEFAULT: (all)
cutoff (float)
your cutoff of what is exposed or not.
DEFAULT: 2.5 Ang**2
asSel (boolean)
make a selection out of the residues found
RETURNS
(list: (chain, resv ) )
A Python list of residue numbers corresponding
to those residues w/more exposure than the cutoff.
"""
tmpObj="__tmp"
cmd.create( tmpObj, objSel + " and polymer");
if verbose!=False:
print "WARNING: I'm setting dot_solvent. You may not care for this."
cmd.set("dot_solvent");
cmd.get_area(selection=tmpObj, load_b=1)
# threshold on what one considers an "exposed" atom (in A**2):
cmd.remove( tmpObj + " and b < " + str(cutoff) )
stored.tmp_dict = {}
cmd.iterate(tmpObj, "stored.tmp_dict[(chain,resv)]=1")
exposed = stored.tmp_dict.keys()
exposed.sort()
randstr = str(random.randint(0,10000))
selName = "exposed_atm_" + randstr
if verbose!=False:
print "Exposed residues are selected in: " + selName
cmd.select(selName, objSel + " in " + tmpObj )
selNameRes = "exposed_res_" + randstr
cmd.select(selNameRes, "byres " + selName )
if doShow!=False:
cmd.show_as("spheres", objSel + " and poly")
cmd.color("white", objSel)
cmd.color("red", selName)
cmd.delete(tmpObj)
print exposed
return exposed
def findSurfaceResidues(objSel="(all)",
cutoff=2.5,
doShow=False,
verbose=False):
"""
findSurfaceResidues
finds those residues on the surface of a protein
that have at least 'cutoff' exposed A**2 surface area.
PARAMS
objSel (string)
the object or selection in which to find
exposed residues
DEFAULT: (all)
cutoff (float)
your cutoff of what is exposed or not.
DEFAULT: 2.5 Ang**2
asSel (boolean)
make a selection out of the residues found
RETURNS
(list: (chain, resv ) )
A Python list of residue numbers corresponding
to those residues w/more exposure than the cutoff.
"""
tmpObj = "__tmp"
cmd.create(tmpObj, objSel + " and polymer")
if verbose != False:
print "WARNING: I'm setting dot_solvent. You may not care for this."
cmd.set("dot_solvent")
cmd.get_area(selection=tmpObj, load_b=1)
# threshold on what one considers an "exposed" atom (in A**2):
cmd.remove(tmpObj + " and b < " + str(cutoff))
stored.tmp_dict = {}
cmd.iterate(tmpObj, "stored.tmp_dict[(chain,resv)]=1")
exposed = stored.tmp_dict.keys()
exposed.sort()
randstr = str(random.randint(0, 10000))
selName = "exposed_atm_" + randstr
if verbose != False:
print "Exposed residues are selected in: " + selName
cmd.select(selName, objSel + " in " + tmpObj)
selNameRes = "exposed_res_" + randstr
cmd.select(selNameRes, "byres " + selName)
if doShow != False:
cmd.show_as("spheres", objSel + " and poly")
cmd.color("white", objSel)
cmd.color("red", selName)
cmd.delete(tmpObj)
return exposed
def _testSpectrum_setup(self):
cmd.pseudoatom('m1', pos=(-2, 0, 0))
cmd.pseudoatom('m2', pos=(0, 0, 0))
cmd.pseudoatom('m3', pos=(2, 0, 0))
cmd.show_as('spheres')
self.ambientOnly()
cmd.viewport(40, 20)
cmd.zoom()
def photo_pdb(pdb_file, out_file):
pymol.finish_launching(['pymol', '-qc'])
cmd.reinitialize()
cmd.load(pdb_file)
cmd.show_as('cartoon', 'all')
cmd.util.cbc()
cmd.png(filename=out_file, width=350, height=350, ray=0, dpi=300)
cmd.quit()
def testCOLLADA(self):
cmd.fragment('gly')
for rep in ['spheres', 'sticks', 'surface']:
cmd.show_as(rep)
with testing.mktemp('.dae') as filename:
cmd.save(filename)
contents = file_get_contents(filename)
self.assertTrue('<COLLADA' in contents)
def testVRML(self):
cmd.fragment('gly')
for rep in ['spheres', 'sticks', 'surface']:
cmd.show_as(rep)
with testing.mktemp('.wrl') as filename:
cmd.save(filename)
contents = file_get_contents(filename)
self.assertTrue(contents.startswith('#VRML V2'))
def testGetPovray(self):
cmd.fragment('gly')
cmd.show_as('sticks')
pov = cmd.get_povray()
self.assertTrue(isinstance(pov, tuple))
self.assertEqual(len(pov), 2)
self.assertTrue(pov[0].startswith('camera {direction<0.0,0.0'))
self.assertTrue(pov[1].startswith('cylinder{<'))
def show_as(show, selection):
'''`as` is a reserved word as of python 2.6
pymol used cmd.as before this and
had to change to cmd.show_as'''
try:
cmd.show_as(show, selection)
except AttributeError:
getattr(cmd, 'as')(show, selection)
def _testSpectrum_setup(self):
cmd.pseudoatom('m1', pos=(-2,0,0))
cmd.pseudoatom('m2', pos=(0,0,0))
cmd.pseudoatom('m3', pos=(2,0,0))
cmd.show_as('spheres')
self.ambientOnly()
cmd.viewport(40,20)
cmd.zoom()
def dehydron(selection='all', angle_range=40, max_distance=3.5, desolv=6.5, min_wrappers=19, quiet=0):
'''
DESCRIPTION
dehydron calculator
USAGE
dehydron [ selection [, angle_range [, max_distance [, desolv [, min_wrappers ]]]]]
'''
angle, max_distance = float(angle_range), float(max_distance)
desolv, min_wrappers = float(desolv), int(min_wrappers)
quiet = int(quiet)
name = cmd.get_legal_name('DH_%s' % selection)
cmd.delete(name)
selection_hb = '((%s) and polymer)' % (selection)
hb = cmd.find_pairs("((byres "+selection_hb+") and n. n)","((byres "+selection_hb+") and n. o)",mode=1,cutoff=max_distance,angle=angle_range)
if not quiet:
hb.sort(lambda x,y:(cmp(x[0][1],y[0][1])))
print "--------------------------------------------------------------------"
print "--------------------------Dehydron Results--------------------------"
print "--------------------------------------------------------------------"
print " Donor | Aceptor |"
print " Object Chain Residue | Object Chain Residue | # wrappers"
cmd.select('_nonpolar', '(elem C) and not (solvent or (elem N+O) extend 1)', 0)
try:
cmd.select('_selection', '%s' % selection, 0)
except:
pass
sel = []
for pairs in hb:
wrappers = cmd.count_atoms('((%s and _nonpolar and _selection) within %f of byca (%s`%d %s`%d))' %
((pairs[0][0], desolv) + pairs[0] + pairs[1]))
if wrappers < min_wrappers:
cmd.distance(name, pairs[0], pairs[1])
if not quiet:
cmd.iterate(pairs[0], 'stored.nitro = chain, resi, resn')
cmd.iterate(pairs[1], 'stored.oxy = chain, resi, resn')
print ' %12s%4s%6s%5d | %12s%4s%6s%5d |%7s' % (pairs[0][0], stored.nitro[0], stored.nitro[2], int(stored.nitro[1]), pairs[1][0], stored.oxy[0], stored.oxy[2], int(stored.oxy[1]), wrappers)
sel.append(pairs[0])
sel.append(pairs[1])
cmd.delete('_nonpolar')
cmd.delete('_selection')
if len(sel) > 0:
cmd.show_as('dashes', name)
elif not quiet and len(hb) != 0:
print ' - no dehydrons were found - '
else:
print ' - no hydrogen bonds were found - '
def launchPyMol(self, pdbfile):
"""Open pdb in PyMOL"""
import pymol
# Call the function below before using any PyMOL modules.
pymol.finish_launching()
from pymol import cmd
cmd.load(pdbfile)
cmd.show_as('sticks')
return
def testGetIdtf(self):
cmd.fragment('gly')
cmd.show_as('surface')
r = cmd.get_idtf()
self.assertTrue(isinstance(r, tuple))
self.assertEqual(len(r), 2)
self.assertTrue(r[0].startswith('FILE_FORMAT "IDTF"'))
self.assertTrue('MODEL_POSITION_LIST' in r[1])
self.assertTrue('MODEL_NORMAL_LIST' in r[1])
def launchPyMol(self, pdbfile):
"""Open pdb in PyMOL"""
import pymol
# Call the function below before using any PyMOL modules.
pymol.finish_launching()
from pymol import cmd
cmd.load(pdbfile)
cmd.show_as('sticks')
return
def colour_by_heatmap(colour_data,
structure_path,
molecule_name="protein",
output_path="colour_by_heatmap",
view=None):
'''
DESCRIPTION
Colours PDB structure by colour map data.
output_filepath
>>> colour_by_heatmap(df, structure_filepath="xxxx.pdb", mol_name="protein", out_dir='.')
'''
# if not (isinstance(colour_data, pd.core.series.Series) or isinstance(colour_data, dict)):
# print('''
# Passed data must be either dictionary or Pandas Series object.
# Key = residue number
# Value = PyMOL hex code
# ''')
# return None
cmd.load(structure_path, object=molecule_name)
# Set view
if view == None:
cmd.reset()
cmd.orient()
else:
cmd.set_view(view)
cmd.viewport(width=1200, height=1200)
cmd.zoom(complete=1)
cmd.set('cartoon_discrete_colors', 1)
cmd.set('sphere_scale', 1)
cmd.show_as('cartoon', molecule_name)
cmd.color('white', molecule_name)
# Iterate over the alpha-carbons
# residue_numbers = []
# cmd.iterate('{} and name CA'.format(molecule_name) , 'residue_numbers.append(resi)')
# Colour the structure
for residue_number in colour_data.columns:
# print(colour_data[residue_number].item())
cmd.color(colour_data[residue_number].item(),
'{0} and resi {1}'.format(molecule_name, residue_number))
png_out_path = output_path + ".png"
pse_out_path = output_path + ".pse"
cmd.save(pse_out_path)
cmd.set('ray_opaque_background', 0)
cmd.png(png_out_path, width=1200, height=1200, ray=1, quiet=0)
def Mutagenesis(kinase1, model, template,peptide_instance):
"""superposition the model and template, remove template and leave peptide behind """
"""replace peptide with instance peptide"""
list_name = peptide_instance
with open(input_data_folder+list_name,'r') as f:
instances = f.readlines()
instance = [x.strip() for x in instances]
print "your peptide: ", instance
for pep in instance:
cmd.delete('all')
cmd.fetch(model) # model_candidate, ex.chk1,chk2...
cmd.remove("hetatm") #remove the nonstandard residues
cmd.fetch(template) #mutagenesis template, ex.2phk
peptide_template = cmd.get_fastastr( "/"+template+'//B') #get the peptide from the template and generate another one for mutagenesis
peptide_template = peptide_template + 'G' #peptide of 2phk is 7 amino acid long, when our input peptide is 8 aa, we need to plus one character
for aa in peptide_template[6:].lower(): #creat template_peptide for mutagenesis
cmd._alt(aa)
firstaa = AAcode_1_to_3(peptide_template[6]) #translate template_peptide to 3 letter
low_firstaa = firstaa[0].lower()
cmd.alter(low_firstaa, 'chain = "B"') #select this template_peptide
cmd.show_as("cartoon")
cmd.align(model, template) #superpostion of model and template
cmd.align(low_firstaa,template) #superpostion of template_peptide and template
remove_part = "("+template+" and not resn ATP"+")"
cmd.select("remove_part",remove_part)
cmd.remove("remove_part") #remove the template except for ATP, there are only model and template_peptide
cmd.remove("resn hoh") #remove water
cmd.wizard("mutagenesis")
peptide_position = 0
for i in pep:
#the peptide_position starting point depends the first position of mutagenesis peptide
#pymol's peptide start from 1, not 0
mutagenesis_template = '/'+low_firstaa+ '///' + str(peptide_position + 2) # because of 2phk start at 2nd of peptide
#mutagenesis_template = '/' + template + '//B/' + str(peptide_position + 2)
cmd.get_wizard().do_select(mutagenesis_template) # select peptide position of mutation
replace_aminoacid = AAcode_1_to_3(pep)[peptide_position]
cmd.get_wizard().set_mode(replace_aminoacid) # select which residue want to mutate to
cmd.get_wizard().apply()
peptide_position += 1
filename = kinase1 + '_' + model + 'model_' + template + 'muta_' + pep + '.pdb' #build the canonical name
cmd.save(filename)
ATPchange(filename) #change ATP naming to the format of ATP.params
cmd.wizard(None)
return
def testGetVrml(self):
cmd.fragment('gly')
cmd.show_as('sticks')
s = cmd.get_vrml()
self.assertTrue(s.startswith('#VRML V'))
self.assertTrue('geometry Cylinder' in s)
cmd.show_as('spheres')
s = cmd.get_vrml()
self.assertFalse('geometry Cylinder' in s)
self.assertTrue('geometry Sphere' in s)
def testSTL(self):
cmd.fragment('gly')
for rep in ['spheres', 'sticks', 'surface']:
cmd.show_as(rep)
with testing.mktemp('.stl') as filename:
cmd.save(filename)
contents = file_get_contents(filename, 'rb')
# 80 bytes header
# 4 bytes (uint32) number of triangles
self.assertTrue(len(contents) > 84)
def createAtomObj(self, number):
view = cmd.get_view()
cmd.create(self.indexes_list[number], self.object_prefix + str(number))
cmd.set_view(view)
cmd.set("sphere_scale", '0.3', self.indexes_list[number])
cmd.show_as('spheres', self.indexes_list[number])
if number < 3:
cmd.color("red", self.indexes_list[number])
else:
cmd.color("green", self.indexes_list[number])
def _testSpectrum_setup(self):
cmd.pseudoatom('m1', pos=(-2,0,0))
cmd.pseudoatom('m2', pos=(0,0,0))
cmd.pseudoatom('m3', pos=(2,0,0))
cmd.show_as('spheres')
cmd.set('ambient', 1)
cmd.set('specular', 0)
cmd.set('reflect', 0)
cmd.set('direct', 0)
cmd.viewport(40,20)
cmd.zoom()
def testSpheresForSpheroidTrajectory(self, use_shader):
pdbfile = self.datafile("sampletrajectory.pdb")
dcdfile = self.datafile("sampletrajectory.dcd")
cmd.load(pdbfile)
cmd.load_traj(dcdfile)
cmd.set('use_shaders', use_shader)
cmd.spheroid("sampletrajectory", 3)
self.ambientOnly()
cmd.color('blue')
cmd.show_as('spheres')
self.assertImageHasColor('blue')
def _load_example(self):
# object in hidden group
cmd.fragment('ile', 'm1')
cmd.fragment('his', 'm2')
cmd.group('g1', 'm1')
cmd.disable('g1')
# testable styling
self.ambientOnly()
cmd.orient()
cmd.color('red', 'm1')
cmd.color('blue', 'm2')
cmd.show_as('spheres')
def InitPymol():
'''
setup pymol so that it works right and plays nice with this program
'''
import pymol
pymol.pymol_argv = ['pymol', '-q'] #c=command line (no gui), q=quiet (no messages)
pymol.finish_launching()
from pymol import cmd
for switchon in ['retain_order','pdb_no_end_record','cartoon_cylindrical_helices']: #'pdb_retain_ids',
cmd.set(switchon, 1)
for switchoff in ['pdb_use_ter_records']:
cmd.set(switchoff, 0)
cmd.show_as('cartoon')
def test(self, ribbon_as_cylinders):
cmd.set('ribbon_as_cylinders', ribbon_as_cylinders)
cmd.set('ribbon_width', 8)
cmd.fab('AG')
cmd.color('red', 'resn ALA')
cmd.color('blue', 'resn GLY')
cmd.show_as('ribbon')
cmd.orient()
self.ambientOnly()
cmd.viewport(100, 100)
cmd.draw(100, 100)
img = self.get_imagearray()
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
def testAsyncBuilds(self, rep, async_builds):
target = "1aon"
if async_builds:
msg = '%s cpus' % max_threads
else:
msg = '1 cpu'
cmd.set("async_builds", async_builds)
cmd.load(self.datafile('1aon.pdb.gz'), target)
for x in cmd.get_chains():
cmd.create("Chain_%s" % x, target + " & c. " + x)
cmd.delete(target)
with self.timing('%s' % msg):
cmd.show_as(rep)
cmd.draw()
def disp_ball_stick( selection='all' , hydrogens=0, only=False):
'''
DESCRIPTION
Formats the passed object into ball and stick
USEAGE
disp_ball_stick [ selection [, hydrogens [, only ]]]
EXAMPLE
fetch 1hpv, async=0
disp_ball_stick
util.cbaw
PARAMETERS
NAME=DEFAULT TYPE FUNCTION
selection='all' <str> input selection
hydrogens <int> -1: remove; 1: add; else: as is
only=False <bool> if True will use show_as; else show
'''
try:
selection='('+selection+')'
hydrogens=int(hydrogens)
only=bool(str(only)!='False')
except:
print "Input error"
return False
if hydrogens==1:
cmd.h_add('%s' %selection)
if hydrogens==-1:
cmd.remove('%s and elem H' %selection)
for p in cmd.get_object_list(selection):
cmd.set('valence', 'on', p)
cmd.set('stick_ball', 'on', p)
cmd.set('stick_ball_ratio', 3, p)
cmd.set('stick_radius', 0.12, p)
if only:
cmd.show_as('sticks', '%s' %(selection))
else:
cmd.show('sticks', '%s' %(selection))