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 na():
cmd.view('v', 'store')
object = cmd.get_names()[0]
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na", "%s and chain %s" % (object, "B"))
cmd.select("native_na", "%s and chain %s" % (pdbid, chainid))
cmd.select("other_na", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("design_na", "native_na")
cmd.select("none")
cmd.orient(object)
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
def zoom_tetramer_1a8y(object_name):
# Get a neutral, symmetric view of the molecule(s)
# cmd.viewport(viewport_width_tetramer(), viewport_height_tetramer())
cmd.orient(object_name)
cmd.rotate("y", 180)
cmd.zoom("center", 45)
return
def load():
r = 0
rep = [
"simple", "technical", "ligands", "ligand_sites", "ligand_sites_trans",
"ligand_sites_mesh", "pretty", "publication"
]
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
print file
cmd.delete('pdb')
cmd.load(file, 'pdb')
cmd.orient('pdb')
cur_rep = rep.pop(0)
rep = rep + [cur_rep]
getattr(pymol.preset, cur_rep)('pdb')
cmd.refresh()
# give PyMOL a chance
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
cmd.refresh()
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
while (pymol.run == 0):
time.sleep(0.1)
def orient(self): if self.toggle['view']: cmd.set_view(self.toggle['view']) self.toggle['view'] = None else: self.toggle['view'] = cmd.get_view() cmd.orient(self.d.obj+" or pnt*")
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 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.zoom('center',16)
cmd.label("polymer and (name ca or elem P)","'//%s/%s/%s`%s/%s'%(segi,chain,resn,resi,name)")
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 scene_photo(rec, xtal, covalentized, photo_name):
pymol.finish_launching()
cmd.delete('all')
for file_name in [rec, xtal, covalentized]:
cmd.load(file_name)
cmd.select('lig', 'org')
if cmd.count_atoms('lig') == 0:
return 0
cmd.set('valence', 0)
cmd.color('cyan', xtal.split('.')[0])
cmd.select('cov', covalentized.split('.')[0])
cmd.select('cysteine', 'br. ' + covalentized.split('.')[0] + ' around 2 and resn CYS')
cmd.select('cys_cov', 'cysteine or cov')
cmd.save('tmp.pdb', 'cys_cov')
cmd.load('tmp.pdb')
cmd.hide('(hydro)')
cmd.delete('cov')
cmd.select('cov', 'tmp and org')
cmd.select('cysteine', 'tmp and resn cys')
cmd.color('white', 'cysteine')
cmd.color('magenta', 'cov')
cmd.color('green', rec.split('.')[0])
cmd.util.cnc('all')
cmd.select('all_mols', 'tmp or ' + xtal.split('.')[0])
cmd.orient('all_mols')
pnghack('./tmp.png')
os.rename('tmp0001.png', photo_name)
os.remove('tmp.pdb')
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 na():
cmd.view('v', 'store')
object = cmd.get_names()[0]
if object[0] == 'd':
pdbid = object[1:5]
chainid = object[5:6]
else:
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na", "%s and chain %s and not hydro" % (object, "B"))
cmd.select("native_na", "%s and chain %s and not hydro" % (pdbid, chainid))
cmd.select("other_na", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("native_na", "design_na")
cmd.hide("lines", "all")
cmd.show("sticks", "native_na")
cmd.show("cartoon", "native_na")
cmd.select("none")
cmd.orient(object)
pdbid = pdbid.lower()
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
def rezoom_tetramer_deo_alignment(target, mobile_pdb):
# cmd.viewport(viewport_width_tetramer_alignment(), viewport_height_tetramer_alignment())
cmd.orient(target)
cmd.zoom("center", 75)
y = tetramer_alignment_centering_y(mobile_pdb)
cmd.translate([0,y,0], "(all)")
return
def load():
r = 0
rep = [ "simple", "technical", "ligands", "ligand_sites","ligand_sites_trans","ligand_sites_mesh","pretty", "publication" ]
list = glob("pdb/*/*")
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
print file
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.orient('pdb')
cur_rep = rep.pop(0)
rep = rep + [cur_rep]
getattr(pymol.preset,cur_rep)('pdb')
cmd.refresh()
# give PyMOL a chance
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
cmd.refresh()
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
time.sleep(0.02)
while(pymol.run==0):
time.sleep(0.1)
def nat(pdbid, chainid):
cmd.view('v', 'store')
object = cmd.get_names()[0]
cmd.fetch(pdbid)
cmd.select("design_nat", "%s and chain %s and not hydro" % (object, "B"))
cmd.select("native_nat",
"%s and chain %s and not hydro" % (pdbid, chainid))
cmd.select("other_nat", "%s and not chain %s" % (pdbid, chainid))
cmd.hide("everything", "other")
cmd.hide('(resn HOH)')
cmd.super("design_nat", "native_nat")
cmd.select("none")
cmd.orient(object)
cmd.hide("lines", "all")
cmd.show("sticks", "native_nat")
cmd.show("cartoon", "native_nat")
cmd.system("rm %s.pdb" % (pdbid))
cmd.view('v', 'recall')
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 _cartoon(selection='all'):
"""
Draw `selection` in a cartoon style.
"""
cmd.show('spheres', selection)
cmd.set('sphere_scale', 0.23, selection)
cmd.hide('sticks', selection)
cmd.show('lines', selection)
cmd.set('line_as_cylinders', 1)
cmd.set('line_radius', 0.08)
cmd.set('line_use_shader', 1)
cmd.set('valence_mode', 0, selection)
cmd.set('valence_size', 0.14, selection)
cmd.set('ray_trace_mode', 3)
cmd.set('ray_trace_color', 'black')
cmd.set_color('lgray', [0.6, 0.6, 0.6])
cmd.color('lgray', 'elem C')
cmd.orient(selection)
cmd.zoom(selection, 3, complete=1)
def load(self):
self.manager.d = self
self.manager.m = None
self.manager.m = None # to also set prevm = None
# cmd.delete(self.manager.prevd.obj)
# cmd.delete(self.manager.prevd.pid)
# print self.manager.d.obj
# print self.manager.prevd.obj
# sys.exit()
cmd.delete("all")
cmd.load(self.getloadname(),self.obj,1)
cmd.remove(self.obj+" and not chain A")
cmd.fetch(self.pid)
cmd.remove("het or hydro")
cmd.color('gray',self.pid+' and elem C')
self.scores['rms'] = cmd.align(self.pid,self.obj+" and chain A")[0]
cmd.hide('ev')
cmd.show('lines')
cmd.show("car")
#cmd.disable(self.pid)
redopent(self.obj)
self.recalc_design_pos()
self.read_data_dir('avg_deg')
self.read_data_dir('ddG')
self.read_data_dir('rot_boltz')
self.read_bup()
self.read_tot_scores()
self.read_res_scores()
cmd.orient(self.obj+" or pnt*")
self.manager.m = self.remembermm
if self.manager.m: self.manager.m.focus()
if self.remembermv: cmd.set_view(self.remembermv)
def zoom_dimer(object_name):
# Get a neutral, symmetric view of the molecule(s)
# cmd.viewport(viewport_width_dimer(), viewport_height_dimer())
cmd.orient(object_name)
cmd.zoom("center", 35)
cmd.translate([0,4,0], "(all)")
return
def zoom_tetramer_any(object_name):
# Get a neutral, symmetric view of the molecule(s)
# No rotations allowed, since this is generic for many tetramers that may or may not be oriented with respect to 1a8y.
# cmd.viewport(viewport_width_tetramer(), viewport_height_tetramer())
cmd.orient(object_name)
cmd.zoom(object_name, 45)
return
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 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 na():
cmd.view('v', 'store');
object = cmd.get_names()[0]
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na","%s and chain %s"%(object,"B"))
cmd.select("native_na","%s and chain %s"%(pdbid,chainid))
cmd.select("other_na","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("design_na","native_na")
cmd.select("none")
cmd.orient(object)
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
def carve(selection='(all)', cut_range="5", view_key=None):
cut_range = cut_range.split(":")
try:
cut_range = [int(n) for n in cut_range]
except ValueError as e:
msg = f"Malformed range {cut_range}"
e.message = msg
raise e
# First align to principal axes
princ_align(selection)
cachedir = Path.home() / "mjtadema_pymol_cache"
if len(cut_range) == 1:
# symmetrically cut with thickness t
t = cut_range[0]
cut_select = f"{selection} and (y > {-t} and y < {t})"
cmd.orient(cut_select)
cmd.clip('slab', t * 2, cut_select)
if view_key is not None:
cmd.view(view_key, 'store')
elif len(cut_range) == 2:
# cut from start to end
raise NotImplementedError("Didn't get to asymmetric cuts yet")
pass
else:
# panic
raise ValueError("range can be at most 2 integers")
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 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 draw_ENM(structure_filepath, script_filepath, structure_name="CAonly", output_dir='.', view=None):
""" Draws elastic network model of a structure and saves image.
"""
cmd.delete('all')
cmd.load(structure_filepath, "CAonly")
cmd.run(script_filepath)
# Set name
if structure_name == "CAonly":
pass
else:
cmd.set_name("CAonly", structure_name)
# Set view
if view == None:
cmd.orient()
else:
cmd.set_view(view)
cmd.viewport(width=1200, height=1200)
cmd.zoom(complete=1)
png_filepath = os.path.join(output_dir, structure_name) + ".png"
pse_filepath = os.path.join(output_dir, structure_name) + ".pse"
cmd.save(pse_filepath)
cmd.set('ray_opaque_background', 0)
cmd.png(png_filepath, width=1200, height=1200, ray=1)
return (pse_filepath, png_filepath)
def na():
cmd.view('v', 'store');
object = cmd.get_names()[0]
if object[0] == 'd':
pdbid = object[1:5]
chainid = object[5:6]
else:
pdbid = object[0:4]
chainid = object[4:5]
cmd.fetch(pdbid)
cmd.select("design_na","%s and chain %s and not hydro"%(object,"B"))
cmd.select("native_na","%s and chain %s and not hydro"%(pdbid,chainid))
cmd.select("other_na","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("native_na","design_na")
cmd.hide("lines","all");
cmd.show("sticks","native_na");
cmd.show("cartoon","native_na");
cmd.select("none")
cmd.orient(object)
pdbid = pdbid.lower()
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
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 nat(pdbid,chainid):
cmd.view('v', 'store');
object = cmd.get_names()[0]
cmd.fetch(pdbid)
cmd.select("design_nat","%s and chain %s and not hydro"%(object,"B"))
cmd.select("native_nat","%s and chain %s and not hydro"%(pdbid,chainid))
cmd.select("other_nat","%s and not chain %s"%(pdbid,chainid))
cmd.hide("everything","other")
cmd.hide('(resn HOH)')
cmd.super("design_nat","native_nat")
cmd.select("none")
cmd.orient(object)
cmd.hide("lines","all");
cmd.show("sticks","native_nat");
cmd.show("cartoon","native_nat");
cmd.system("rm %s.pdb"%(pdbid));
cmd.view('v', 'recall')
def Start(self):
# self.queue.put(lambda: self.top.top.root.withdraw())
cmd.window('hide')
cmd.refresh_wizard()
cmd.orient()
cmd.window('show')
# self.queue.put(lambda: cmd.window('show'))
self.ErrorCode = 1
try:
self.State = cmd.get_state()
self.config_mouse = General_cmd.get_config_mouse()
cmd.config_mouse('three_button_editing')
self.exc = [ self.SphereDisplay ]
General_cmd.mask_Objects(self.exc)
# success
self.ErrorCode = 0
except:
self.queue.put(lambda: self.App.DisplayMessage(" ERROR: Could not start the Sphere wizard", 1))
self.queue.put(lambda: self.App.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
if self.DisplaySphere():
self.queue.put(lambda: self.App.DisplayMessage(" ERROR: Could not display the Sphere", 1))
self.queue.put(lambda: self.App.DisplayMessage(" The wizard will abort prematurely", 1))
self.Quit_Wizard()
return
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 helicize_beta_peptide(helixtype, selection='all'):
"""
DESCRIPTION
Adjust the torsion angles of a beta-peptide to different helical conformations
USAGE
helicize_beta_peptide helixtype [, selection]
ARGUMENTS
helixtype = the type of the helix (either short or IUPAC name),
or a tuple of 3 floats, representing three torsional angles, or
a list of tuples / short names / IUPAC names.
selection = the selection to operate on. Must be a single peptide chain with
unique residue IDs (default: all)
NOTES"""
if isinstance(helixtype, str):
for perczelname, iupacname, angles, theorylevel in helixtypes:
helixtype = helixtype.replace(iupacname, perczelname).replace(
perczelname, '({}, {}, {})'.format(*angles))
helixtype = helixtype.strip()
if not all([h in '0123456789.,()[] -+efg' for h in helixtype]):
raise ValueError(
'Helixtype parameter contains an invalid character (only numbers, parentheses, brackets, space and commas are accepted)'
)
helixtype = eval(helixtype, {}, {})
assert isinstance(helixtype, collections.Iterable)
if all([isinstance(x, numbers.Real)
for x in helixtype]) and len(helixtype) == 3:
helixtype = [helixtype]
print('Helixtypes: {}'.format(helixtype))
space = {'lis': []}
cmd.iterate(selection, 'lis.append(resv)', space=space)
residues = sorted(set(space['lis']))
for r, ht in zip(sorted(residues), itertools.cycle(helixtype)):
if len(ht) != 3 and not all([isinstance(x, numbers.Real) for x in ht]):
raise ValueError('Invalid helixtype: {}'.format(ht))
calpha = '({}) and (name CA) and (resi {})'.format(selection, r)
cbeta = '({}) and (name CB+CB1) and (resi {})'.format(selection, r)
c = '({}) and (name C) and (resi {})'.format(selection, r)
n = '({}) and (name N) and (resi {})'.format(selection, r)
prevc = '(neighbor ({})) and (name C)'.format(n)
nextn = '(neighbor ({})) and (name N)'.format(c)
prevo = '(neighbor ({})) and (name O)'.format(prevc)
hn = '(neighbor ({})) and (name H+HN)'.format(n)
o = '(neighbor ({})) and (name O)'.format(c)
nexthn = '(neighbor ({})) and (name H+HN)'.format(nextn)
set_beta_helix(prevc, n, cbeta, calpha, c, nextn, ht, selection)
for n_, h_, c_, o_ in [(n, hn, prevc, prevo), (nextn, nexthn, c, o)]:
if cmd.count_atoms(n_) + cmd.count_atoms(h_) + cmd.count_atoms(
c_) + cmd.count_atoms(o_) == 4:
cmd.set_dihedral(h_, n_, c_, o_, 180.)
cmd.orient(selection)
def zoom_tetramer_deo(object_name):
# Get a neutral, symmetric view of the molecule(s)
# Note: this is the best view overall, but not the best view for observing the interface.
# cmd.viewport(viewport_width_tetramer(), viewport_height_tetramer())
cmd.orient(object_name)
# cmd.rotate("x", 180)
cmd.rotate("y", 180)
cmd.zoom("center", 45)
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 orient_origin(selection):
shift_to_center(selection)
cmd.orient(selection)
cv = list(cmd.get_view(quiet=1))
#cmd.origin(selection, position=origin1)
cmd.transform_selection(selection,
cv[0:3] + [0.0] + cv[3:6] + [0.0] + cv[6:9] +
[0.0] + cv[12:15] + [1.0],
transpose=1)
cmd.reset()
def zoom_to_ligand(self):
"""Zoom in too ligand and its interactions."""
cmd.center(self.ligname)
cmd.orient(self.ligname)
cmd.turn('x', 110) # If the ligand is aligned with the longest axis, aromatic rings are hidden
if 'AllBSRes' in cmd.get_names("selections"):
cmd.zoom('%s or AllBSRes' % self.ligname, 3)
else:
if self.object_exists(self.ligname):
cmd.zoom(self.ligname, 3)
cmd.origin(self.ligname)
def load():
global last1, last2
list = glob("pdb/*/*")
list = map(lambda x: (random.random(), x), list)
list.sort()
list = map(lambda x: x[1], list)
l = len(list)
c = 0
for file in list:
c = c + 1
try:
cmd.set("suspend_updates", "1")
cmd.delete("pdb")
print file, last1, last2, c, "of", l
last2 = last1
last1 = file
cmd.load(file, "pdb")
cmd.set_title("pdb", 1, os.path.split(file)[-1])
cmd.rewind()
# cmd.refresh()
# cmd.hide()
cmd.show("cartoon")
cmd.color("auto", "ss h")
cmd.color("auto", "ss s")
cmd.orient("pdb")
cmd.color("auto", "organic and elem c")
cmd.show("spheres", "organic")
cmd.move("z", -50.0)
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
finally:
cmd.set("suspend_updates", "0")
if cmd.count_atoms():
start = time.time()
if n > 1:
while (time.time() - start) < cycle_time:
for a in range(1, n + 1):
cmd.refresh()
cmd.frame(a)
cmd.move("z", 2)
cmd.turn("y", 1)
time.sleep(0.025)
sys.__stderr__.write(" %d of %d" % (c, l))
sys.__stderr__.write("\n")
sys.__stderr__.flush()
else:
cmd.refresh()
while (time.time() - start) < cycle_time:
for a in range(1, n + 1):
time.sleep(0.05)
cmd.move("z", 1.0)
cmd.turn("y", 1)
def load():
global last1, last2
list = glob("pdb/*/*")
list = map(lambda x: (random.random(), x), list)
list.sort()
list = map(lambda x: x[1], list)
l = len(list)
c = 0
for file in list:
c = c + 1
try:
cmd.set("suspend_updates", "1")
cmd.delete('pdb')
print file, last1, last2, c, "of", l
last2 = last1
last1 = file
cmd.load(file, 'pdb')
cmd.set_title('pdb', 1, os.path.split(file)[-1])
cmd.rewind()
# cmd.refresh()
# cmd.hide()
cmd.show('cartoon')
cmd.color('auto', 'ss h')
cmd.color('auto', 'ss s')
cmd.orient('pdb')
cmd.color('auto', 'organic and elem c')
cmd.show('spheres', 'organic')
cmd.move('z', -50.0)
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
finally:
cmd.set("suspend_updates", "0")
if cmd.count_atoms():
start = time.time()
if n > 1:
while (time.time() - start) < cycle_time:
for a in range(1, n + 1):
cmd.refresh()
cmd.frame(a)
cmd.move('z', 2)
cmd.turn('y', 1)
time.sleep(0.025)
sys.__stderr__.write(" %d of %d" % (c, l))
sys.__stderr__.write("\n")
sys.__stderr__.flush()
else:
cmd.refresh()
while (time.time() - start) < cycle_time:
for a in range(1, n + 1):
time.sleep(0.05)
cmd.move('z', 1.0)
cmd.turn('y', 1)
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 interface_analyse_multi(dist=10):
cmd.disable('all')
all_objects = cmd.get_object_list()
for obj in all_objects:
print 'analysing', obj
interface_analyser(obj, dist, animate=False)
cmd.disable(obj)
cmd.disable(obj + '_h.bonds')
cmd.do('order *, yes')
cmd.zoom(all_objects[0], animate=-1)
cmd.orient(all_objects[0], animate=-1)
cmd.enable(all_objects[0])
cmd.enable(all_objects[0] + '_h.bonds')
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 interface_analyser(name, dist_cuoff=10, animate=True):
'''
DESCRIPTION
displays the chains in different colors, showas cavity surfaces, and h.bonds with an interface cutoff
of 10 (default)
'''
# cmd.hide("lines")
cmd.select("interface", "none")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain" + letter
cmd.select(
chainname,
"%s and chain %s and not hetatm and not symbol w" % (name, letter))
if cmd.count_atoms("chain%s" % (letter)) > 0:
interfacename = "interface" + letter
cmd.select(
"not_this_chain",
"%s and not hetatm and not symbol w and not %s" %
(name, chainname))
cmd.select(
interfacename,
"%s and byres %s and (not_this_chain around %s)" %
(name, chainname, str(dist_cuoff)))
cmd.select("interface", "interface or %s" % (interfacename))
cmd.delete("not_this_chain")
cmd.delete("interface" + letter)
cmd.delete("chain%s" % (letter))
else:
cmd.delete(chainname)
cmd.hide("lines", name)
cmd.show("lines", "interface")
cmd.show("cartoon")
cmd.dist(
"%s_h.bonds" % name,
"interface",
"interface",
quiet=1,
mode=2,
label=0,
reset=1,
)
cmd.enable("%s_h.bonds" % name)
cmd.show("surface", "all")
cmd.set('surface_cavity_mode', 1)
util.color_chains("(all and elem c)", _self=cmd)
if animate:
cmd.zoom("interface", animate=-1)
cmd.orient("interface", animate=-1)
cmd.delete("interface")
cmd.remove("(all) and hydro")
def edges(selection):
"""Save selection into a file in a temp folder and run rna_draw_edges.py on it and load it into this session"""
f = tempfile.TemporaryDirectory()
tmpf = f.name + os.sep + strip_selection_name(selection) + '.pdb'
outf = f.name + '/output.py'
cmd.save(tmpf, selection)
cmdline = '/Users/magnus/miniconda3/bin/rna_draw_edges.py --name %s %s > %s' % (
strip_selection_name(selection), tmpf, outf)
print(cmdline)
out, err = exe(cmdline)
if err:
print(err)
cmd.load(outf)
cmd.orient()
def interface_analyser_with_surface(name='all',
chain_sur='A',
dist_cutoff=10,
animate=True):
cmd.select("interface", "none")
alphabet = list(('abcdefghijklmnopqrstuvwxyz').upper())
for letter in alphabet:
chainname = "chain" + letter
cmd.select(
chainname,
"%s and chain %s and not hetatm and not symbol w" % (name, letter))
if cmd.count_atoms("chain%s" % (letter)) > 0:
interfacename = "interface" + letter
cmd.select(
"not_this_chain",
"%s and not hetatm and not symbol w and not %s" %
(name, chainname))
cmd.select(
interfacename,
"%s and byres %s and (not_this_chain around %s)" %
(name, chainname, str(dist_cutoff)))
cmd.select("interface", "interface or %s" % (interfacename))
cmd.delete("not_this_chain")
cmd.delete("interface" + letter)
cmd.delete("chain%s" % (letter))
else:
cmd.delete(chainname)
cmd.hide("lines", name)
cmd.show("lines", "interface")
cmd.show("cartoon")
cmd.dist(
"%s_h.bonds" % name,
"interface",
"interface",
quiet=1,
mode=2,
label=0,
reset=1,
)
cmd.enable("%s_h.bonds" % name)
cmd.create("chain%s" % chain_sur,
name + " and chain %s" % chain_sur,
zoom=0)
cmd.show("surface", "chain%s" % chain_sur)
util.color_chains("(all and elem c)", _self=cmd)
if animate:
cmd.zoom("interface", animate=-1)
cmd.orient("interface", animate=-1)
cmd.delete("interface")
cmd.remove("(all) and hydro")
def pymol_z_scale(self):
vol_file, from_selection = self.get_pymol_input()
if not self.packing.vol_file:
self.packing.select_first_message("PyMOL selection or .vol file")
return
self.packing.get_options()
self.packing.options["bfactor"] = "zscore"
cmd.delete(self.obj_name)
# copy options, to create some special selections
diff_options = self.packing.options.copy()
diff_options["discard_buried"] = False
diff_options["discard_surface"] = False
diff_options["discard_hetero_neighbors"] = False
diff_options["discard_cavity_neighbors"] = False
diff_options["discard_non_cavity_neighbors"] = False
# 1) load complete object, if its not there yet
# if not from_selection:
complete_name = self.obj_name
self.load_vol_to_pymol(self.packing.vol_file, complete_name, diff_options)
cmd.color("gray", complete_name)
# else:
# complete_name = self.pymol_sel
# 2) define surface selection
diff_options["discard_buried"] = True
self.load_vol_to_pymol(self.packing.vol_file, complete_name + "_surface", diff_options, complete_name)
# 3) define buried selection
diff_options["discard_buried"] = False
diff_options["discard_surface"] = True
self.load_vol_to_pymol(self.packing.vol_file, complete_name + "_buried", diff_options, complete_name)
# 4) load set of atoms where packing should be displayed
self.load_vol_to_pymol(self.packing.vol_file, self.obj_name, diff_options)
cmd.show("spheres", self.obj_name)
cmd.set("sphere_scale", 0.5, self.obj_name)
cmd.color("gray", self.obj_name)
cmd.show("spheres", self.obj_name)
cmd.set("sphere_scale", 0.5, self.obj_name)
cmd.color("gray", self.obj_name)
self.color_bfactor(self.obj_name, "zscore")
cmd.do("indicate none")
cmd.orient()
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 edot1(event):
delcrea()
try:
if len(nameit.get()) < 1:
showinfo("Error", 'Enter a name for the object')
interior.mainloop()
elif len(pdbname.get()) < 1:
showinfo('Error', "Enter the Map Filename")
interior.mainloop()
else:
cmd.isodot(nameit.get(), pdbname.get(), contour1.get(), ('sele'))
except:
cmd.orient('all')
showinfo("Error", 'No map is present\n Or there is no selection ("sele")')
interior.mainloop()
def pymol_cavnb(self):
vol_file = self.get_pymol_input()
if not self.packing.vol_file:
self.packing.select_first_message("PyMOL selection or .vol file")
return
temp_file = tempfile.mktemp() + ".pdb"
cavnbobject = "cav_neighbors"
cmd.delete(cavnbobject)
cavnbfile = self.packing.write_cavnb(0)
cmd.load(cavnbfile, cavnbobject)
cmd.show("spheres", cavnbobject)
cmd.set("sphere_scale", 0.8, cavnbobject)
cmd.color("slate", cavnbobject)
cmd.orient()
def pymol_cav(self):
vol_file = self.get_pymol_input()
if not self.packing.vol_file:
self.packing.select_first_message("PyMOL selection or .vol file")
return
cavobject = "cavities"
cmd.delete(cavobject)
cavfile = self.packing.write_cav(0)
temp_file = tempfile.mktemp() + ".pdb"
cmd.load(cavfile, cavobject)
cmd.show("spheres", cavobject)
cmd.set("sphere_scale", 1.0, cavobject)
cmd.color("tv_orange", cavobject)
cmd.orient()
def _testAtomCartoonTransparency(self):
self.ambientOnly()
cmd.viewport(100, 100)
cmd.set('opaque_background')
cmd.set('ray_shadow', 0)
cmd.orient()
cmd.color('0xFF0000')
cmd.color('0x0000FF', 'sele')
# all opaque
img = self.get_imagearray()
self.assertImageHasColor('0xFF0000', img)
self.assertImageHasColor('0x0000FF', img)
# object-level transparency
cmd.set('cartoon_transparency', 0.4)
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0x000099', img) # 40%
self.assertImageHasNotColor('0xFF0000', img)
self.assertImageHasNotColor('0x0000FF', img)
# atom-level full-opaque
cmd.set('cartoon_transparency', 0.0, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0x0000FF', img) # 0%
self.assertImageHasNotColor('0xFF0000', img)
self.assertImageHasNotColor('0x000099', img)
# atom-level semi-transparent
cmd.set('cartoon_transparency', 0.6, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0x000066', img, delta=1) # 60%
self.assertImageHasNotColor('0xFF0000', img)
self.assertImageHasNotColor('0x0000FF', img)
self.assertImageHasNotColor('0x000099', img)
# atom-level full-transparent (expect only two color values)
cmd.set('cartoon_transparency', 0.0)
cmd.set('cartoon_transparency', 1.0, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0xFF0000', img)
self.assertTrue(len(numpy.unique(img[...,:3])) == 2)
def test(self, bb_rep, sc_rep, bb_set, n_a_m):
cmd.viewport(100, 100)
# color classes
color = {'cartoon': 'blue', 'ribbon': 'red'}
sc_color = 'white'
op_color = 'green'
p_color = 'yellow'
# lighting setup for color testing
self.ambientOnly()
cmd.set('dynamic_width', 0)
cmd.set('line_width', 4)
cmd.set('ribbon_width', 4)
# settings setup
cmd.set(bb_set + '_side_chain_helper')
cmd.set(bb_set + '_nucleic_acid_mode', n_a_m)
cmd.set('ribbon_color', color['ribbon'])
cmd.set('cartoon_color', color['cartoon'])
# data
cmd.load(self.datafile('1ehz-5.pdb'))
cmd.orient()
# atom colors
cmd.color(sc_color)
cmd.color(op_color, "name OP1+OP2") # not visible with SCH
cmd.color(p_color, "name P+O3'+C5'+O5'") # not visible with SCH and NAM=1
# need to check for OP1 and O1P naming scheme, so alter some atoms
cmd.alter('name OP1 & resi 1-2', 'name="O1P"')
cmd.alter('name OP2 & resi 1-2', 'name="O2P"')
# reps
cmd.show_as(bb_rep)
cmd.show(sc_rep)
# test
img = self.get_imagearray()
self.assertImageHasColor(sc_color, img) # always visible
for bb_test in ['cartoon', 'ribbon']:
self._assertImageHasColor(bb_rep == bb_test, color[bb_test], img, 0, bb_test + ' wrong')
self._assertImageHasColor(not (bb_rep == bb_set), op_color, img, 0, 'OP wrong')
self._assertImageHasColor(not (bb_rep == bb_set and n_a_m == 1), p_color, img, 0, 'NAM=1 wrong')
def esurf1(event):
delcrea()
try:
cmd.isosurface('map1','map', contour1.get(), 'sele')
except:
try:
cmd.set("suspend_updates",1,quiet=1)
cmd.remove("hydro")
cmd.enable('all')
cmd.map_new('map',"gaussian","0.75", 'all')
cmd.isosurface("map1", "map", 9999.0, 'all')
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.isosurface('map1','map', contour1.get(), 'sele')
except:
cmd.orient('all')
showinfo("Error", 'No PDB is present\nOr there is no selection ('"sele"')')
interior.mainloop()
def _testTransparency(self, rep, setting_name):
cmd.fab('GGGG')
cmd.remove('resi 2+3')
cmd.select('sele', 'resi 4', 0)
self.ambientOnly()
cmd.viewport(100, 100)
cmd.set('opaque_background')
cmd.set('ray_shadow', 0)
cmd.orient()
cmd.color('0xFF0000')
cmd.show_as(rep)
# all opaque
img = self.get_imagearray()
self.assertImageHasColor('0xFF0000', img)
# object-level transparency
cmd.set(setting_name, 0.4)
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasNotColor('0xFF0000', img)
# atom-level full-opaque
cmd.set(setting_name, 0.0, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0xFF0000', img) # 0%
# atom-level semi-transparent
cmd.set(setting_name, 0.6, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0x990000', img) # 40%
self.assertImageHasColor('0x660000', img, delta=1) # 60%
self.assertImageHasNotColor('0xFF0000', img)
# atom-level full-transparent (expect only two color values)
cmd.set(setting_name, 0.0)
cmd.set(setting_name, 1.0, 'sele')
img = self.get_imagearray()
self.assertImageHasColor('0xFF0000', img)
self.assertTrue(len(numpy.unique(img[...,:3])) == 2)
def emesh1(event):
delcrea()
try:
cmd.isomesh('map1','map', contour1.get(), 'sele')
except:
try:
cmd.remove("hydro")
cmd.enable('all')
cmd.map_new('map',"gaussian","0.75", 'all')
cmd.isomesh('map1','map', contour1.get(), 'sele')
except:
cmd.orient('all')
showinfo("Error", 'No PDB is present\nOr there is no selection ('"sele"')')
interior.mainloop()
def get_PCA_views(selection):
old_view = cmd.get_view(quiet=1)
cmd.orient(selection)
view = cmd.get_view(quiet=1)
rot = get_rotation_from_view(view)
# now rot resembles view
pc3 = rot.getRow(2)
pc1 = rot.getRow(0)
pc2 = rot.getRow(1)
preferred1 = rot.getRow(2).normalize()
rot2 = rot.rotate(pi, pc1)
preferred2 = rot2.getRow(2).normalize()
return (preferred1, preferred2)
def test(self):
if not (pymol.invocation.options.no_gui or cmd.get_setting_int('use_shaders')):
self.skipTest('no ray or shaders')
self.ambientOnly()
cmd.set('valence', 0)
cmd.viewport(350, 200)
cmd.fragment('ile')
cmd.remove('hydro')
cmd.show_as('sticks')
cmd.orient()
cmd.set('stick_ball', 0)
img1 = self.get_imagearray()
cmd.set('stick_ball', 1)
img2 = self.get_imagearray()
self.assertImageEqual(img1, img2, count=10)
def ray(self,cleanup=0):
if not cleanup:
cmd.set("suspend_updates",1,quiet=1)
cmd.disable()
cmd.delete("ray")
cmd.set("sphere_mode",5)
cmd.set("sphere_scale",1.0)
cmd.load("$PYMOL_DATA/demo/il2.pdb","ray")
cmd.remove("(ray and hydro)")
cmd.hide("lines","ray")
cmd.show("spheres","ray")
cmd.orient("ray")
cmd.turn("x",90)
util.ray_shadows('heavy')
cmd.mstop()
cmd.rock(0)
cmd.set("suspend_updates",0,quiet=1)
cmd.refresh()
cmd.do("ray")
else:
cmd.delete("ray")
def testBumpsPSE(self):
self.ambientOnly()
cmd.viewport(100, 100)
# expect some clashes in this helix
cmd.fab('AAAAA', 'm1', ss=1)
cmd.orient()
cmd.set('sculpt_vdw_vis_mode', 1)
cmd.set('sculpt_field_mask', 0x020) # cSculptVDW
cmd.sculpt_activate('m1')
cmd.sculpt_iterate('m1', cycles=0)
cmd.show_as('cgo')
img = self.get_imagearray()
self.assertImageHasColor('0xFF3333', img)
with testing.mktemp('.pse') as filename:
cmd.save(filename)
cmd.load(filename)
self.assertImageEqual(img)
def test(self):
cmd.viewport(200, 100)
cmd.fragment('ethylene', 'm1')
cmd.remove('hydro')
cmd.pseudoatom('p1', 'index 1')
cmd.disable('p1')
cmd.ramp_new('r1', 'p1', [0.1, 1.2], ['red', 'blue'])
cmd.disable('r1')
cmd.color('r1')
cmd.show_as('sticks', 'm1')
cmd.orient('m1')
cmd.move('z', 11)
self.ambientOnly()
img = self.get_imagearray()
self.assertImageHasColor('red', img)
self.assertImageHasColor('blue', img)
self.assertImageHasColor([.5, .0, .5], img, delta=1)
def load():
r = 0
rep = [ "lines","sticks","spheres","dots","ribbon","cartoon" ]
list = glob("pdb/*/*")
list = map(lambda x:(random.random(),x),list)
list.sort()
list = map(lambda x:x[1],list)
# list = [ "pdb/rb/pdb0rbs.noc" ] + list
# while list[0]!="pdb/f8/pdb1f8u":
# list.pop(0)
for file in list:
try:
print file
cmd.delete('pdb')
cmd.load(file,'pdb')
cmd.orient('pdb')
cmd.color('red','ss h')
cmd.color('yellow','ss s')
cmd.hide()
if cmd.count_atoms()<15000:
cmd.show(rep[r],"all")
elif cmd.count_atoms()<50000:
cmd.show("cartoon","all")
else:
cmd.show("lines","all")
r = r + 1
if r>=len(rep): r=0;
sys.__stderr__.write(".")
sys.__stderr__.flush()
n = cmd.count_states()
cmd.ray(160,120)
cmd.dirty()
time.sleep(0.1)
if n>1:
sys.__stderr__.write("\n")
sys.__stderr__.flush()
except:
traceback.print_exc()
