def testPretty(self):
cmd.load(self.datafile('1oky.pdb.gz'))
preset.pretty('all')
self._assertPrettyReps()
self.assertFalse(
cmd.get_setting_boolean('cartoon_smooth_loops', '1oky'))
self.assertFalse(
cmd.get_setting_boolean('cartoon_fancy_helices', '1oky'))
def wait_for(name, state=0, quiet=1):
'''
DESCRIPTION
Wait for "name" to be available as selectable object.
'''
if cmd.count_atoms('?' + name, 1, state) == 0:
s = cmd.get_setting_boolean('suspend_updates')
if s: cmd.set('suspend_updates', 0)
cmd.refresh()
if s: cmd.set('suspend_updates')
def wait_for(name, state=0, quiet=1):
'''
DESCRIPTION
Wait for "name" to be available as selectable object.
'''
if cmd.count_atoms('?' + name, 1, state) == 0:
s = cmd.get_setting_boolean('suspend_updates')
if s: cmd.set('suspend_updates', 0)
cmd.refresh()
if s: cmd.set('suspend_updates')
def save_pdb_without_ter(filename, selection, *args, **kwargs):
'''
DESCRIPTION
Save PDB file without TER records. External applications like TMalign and
DynDom stop reading PDB files at TER records, which might be undesired in
case of missing loops.
'''
v = cmd.get_setting_boolean('pdb_use_ter_records')
if v: cmd.set('pdb_use_ter_records', 0)
cmd.save(filename, selection, *args, **kwargs)
if v: cmd.set('pdb_use_ter_records')
def save_pdb_without_ter(filename, selection, **kwargs):
'''
DESCRIPTION
Save PDB file without TER records. External applications like TMalign and
DynDom stop reading PDB files at TER records, which might be undesired in
case of missing loops.
'''
v = cmd.get_setting_boolean('pdb_use_ter_records')
if v: cmd.unset('pdb_use_ter_records')
cmd.save(filename, selection, **kwargs)
if v: cmd.set('pdb_use_ter_records')
def get_object_state(name):
'''
DESCRIPTION
Returns the effective object state.
'''
states = cmd.count_states(name)
if states < 2 and cmd.get_setting_boolean('static_singletons'):
return 1
state = cmd.get_setting_int('state', name)
if state > states:
print(' Error: Invalid state %d for object %s' % (state, name))
raise CmdException
return state
def get_object_state(name):
'''
DESCRIPTION
Returns the effective object state.
'''
states = cmd.count_states(name)
if states < 2 and cmd.get_setting_boolean('static_singletons'):
return 1
state = cmd.get_setting_int('state', name)
if state > states:
print(' Error: Invalid state %d for object %s' % (state, name))
raise CmdException
return state
def save_movie_mpeg1(filename,
mode='',
first=0,
last=0,
preserve=0,
fps=25,
twopass=1,
vbitrate=16000,
quiet=1,
exe='mencoder'):
'''
DESCRIPTION
Save movie as MPEG1
This will not be the best quality possible for the file size, but
we were successfull to play those movies in PowerPoint.
Requires mencoder executable from http://mplayerhq.hu
ARGUMENTS
filename = string: Filename, should end on '.mpeg'
mode = normal | draw | ray
first, last = integer: first and last frame number
preserve = 0 or 1: delete temporary images if 0 {default: 0}
fps = integer: frames per second {default: 25}
twopass = 0 or 1: two pass mode encoding (improves quality) {default: 1}
vbitrate = integer: average video bitrate {default: 16000}
WARNING: 4-16000 (in kbit), 16001-24000000 (in bit)
SEE ALSO
cmd.movie.produce, http://www.freemol.org
'''
import os, subprocess, tempfile
first, last, quiet = int(first), int(last), int(quiet)
fps, twopass, vbitrate = int(fps), int(twopass), int(vbitrate)
if cmd.is_string(mode):
if mode == '':
if cmd.pymol.invocation.options.no_gui \
or cmd.get_setting_boolean('ray_trace_frames'):
mode = 'ray'
else:
mode = 'draw'
mode = produce_mode_sc.auto_err(mode, 'mode')
mode = produce_mode_dict[mode]
mode = int(mode)
try:
subprocess.call([exe])
except OSError:
print(' Error: Cannot execute "%s"' % (exe))
raise CmdException
if not quiet:
print(' save_movie: Rendering frames...')
tmp_path = tempfile.mkdtemp()
prefix = os.path.join(tmp_path, 'frame')
cmd.mpng(prefix, first, last, preserve, mode=mode)
mpeg1line = '-mf type=png:fps=%d -ovc lavc -forceidx -noskip -of rawvideo' \
+ ' -mpegopts format=mpeg1 -lavcopts vcodec=mpeg1video:vbitrate=%d' \
+ ':vhq:trell:keyint=25'
mpeg1line = mpeg1line % (fps, vbitrate)
cmdline = exe + ' -quiet mf://' + prefix + '* ' + mpeg1line
if not quiet:
print(' save_movie: Running mencoder...')
if twopass:
if not quiet:
print(' save_movie: First pass...')
cmdline1 = cmdline + ':vpass=1'
subprocess.call(cmdline1.split() + ['-o', os.devnull])
if not quiet:
print(' save_movie: Second pass...')
cmdline = cmdline + ':vpass=2'
subprocess.call(cmdline.split() + ['-o', filename])
if not preserve:
import shutil
shutil.rmtree(tmp_path)
elif not quiet:
print(' save_movie: Not deleting temporary directory: ' + tmp_path)
if not quiet:
print(' save_movie: Done')
def testGetSettingBoolean(self):
for v_ref in (0, 1):
cmd.set('orthoscopic', v_ref)
v = cmd.get_setting_boolean('orthoscopic')
self.assertTrue(isinstance(v, int))
self.assertEqual(v, v_ref)
def testPretty(self):
cmd.load(self.datafile('1oky.pdb.gz'))
preset.pretty('all')
self._assertPrettyReps()
self.assertFalse(cmd.get_setting_boolean('cartoon_smooth_loops', '1oky'))
self.assertFalse(cmd.get_setting_boolean('cartoon_fancy_helices', '1oky'))
def peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1):
'''
DESCRIPTION
Rebuild the peptide from selection. All atoms which are present in
selection will be kept fixed, while atoms missing in selection are
placed by sculpting.
USAGE
peptide_rebuild name [, selection [, cycles [, state ]]]
SEE ALSO
stub2ala, add_missing_atoms, peptide_rebuild_modeller
'''
from chempy import fragments, feedback, models
cycles, state, quiet = int(cycles), int(state), int(quiet)
# suppress feedback for model merging
feedback['actions'] = False
# work with named selection
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
identifiers = []
cmd.iterate(namedsele + ' and polymer and guide and alt +A',
'identifiers.append([segi,chain,resi,resv,resn])', space=locals())
model = models.Indexed()
for (segi,chain,resi,resv,resn) in identifiers:
try:
fname = resn.lower() if resn != 'MSE' else 'met'
frag = fragments.get(fname)
except IOError:
print(' Warning: unknown residue: ' + resn)
continue
for a in frag.atom:
a.segi = segi
a.chain = chain
a.resi = resi
a.resi_number = resv
a.resn = resn
model.merge(frag)
if not quiet:
print(' Loading model...')
cmd.load_model(model, name, 1, zoom=0)
if cmd.get_setting_boolean('auto_remove_hydrogens'):
cmd.remove(name + ' and hydro')
cmd.protect(name + ' in ' + namedsele)
cmd.sculpt_activate(name)
cmd.update(name, namedsele, 1, state)
cmd.delete(namedsele)
if not quiet:
print(' Sculpting...')
cmd.set('sculpt_field_mask', 0x003, name) # bonds and angles only
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x09F, name) # local + torsions
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x0FF, name) # ... + vdw
cmd.sculpt_iterate(name, 1, int(cycles / 2))
cmd.sculpt_deactivate(name)
cmd.deprotect(name)
cmd.unset('sculpt_field_mask', name)
if not quiet:
print(' Connecting peptide...')
pairs = cmd.find_pairs(name + ' and name C', name + ' and name N', 1, 1, 2.0)
for pair in pairs:
cmd.bond(*pair)
cmd.h_fix(name)
if not quiet:
print(' peptide_rebuild: done')
parser.add_argument('--xml', action='store_true')
parser.add_argument('filenames', nargs='*', default=[])
parser.add_argument('--out', default=sys.stdout)
parser.add_argument('--offline', action='store_true')
parser.add_argument('--no-mmlibs', action='store_true')
parser.add_argument('--no-undo', action='store_true')
parser.add_argument('--verbosity', type=int, default=2)
have_dash_dash = __file__.startswith(sys.argv[0]) or '--run' in sys.argv
cliargs = parser.parse_known_args(None if have_dash_dash else [])[0]
run_all = False
max_threads = int(cmd.get('max_threads'))
cmd.set('use_shaders')
use_shaders = cmd.get_setting_boolean('use_shaders')
pymol_test_dir = os.path.abspath(os.path.dirname(__file__))
deferred_unlink = []
deferred_rmtree = []
class requires_version(object):
'''
Decorator for restricting to PyMOL version
'''
def __init__(self, version):
self.version = version
def _tupleize(self, strversion):
r = []
def peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1):
'''
DESCRIPTION
Rebuild the peptide from selection. All atoms which are present in
selection will be kept fixed, while atoms missing in selection are
placed by sculpting.
USAGE
peptide_rebuild name [, selection [, cycles [, state ]]]
SEE ALSO
stub2ala, add_missing_atoms, peptide_rebuild_modeller
'''
from chempy import fragments, feedback, models
cycles, state, quiet = int(cycles), int(state), int(quiet)
# suppress feedback for model merging
feedback['actions'] = False
# work with named selection
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
identifiers = []
cmd.iterate(namedsele + ' and polymer and guide and alt +A',
'identifiers.append([segi,chain,resi,resv,resn])', space=locals())
model = models.Indexed()
for (segi,chain,resi,resv,resn) in identifiers:
try:
fname = resn.lower() if resn != 'MSE' else 'met'
frag = fragments.get(fname)
except IOError:
print(' Warning: unknown residue:', resn)
continue
for a in frag.atom:
a.segi = segi
a.chain = chain
a.resi = resi
a.resi_number = resv
a.resn = resn
model.merge(frag)
if not quiet:
print(' Loading model...')
cmd.load_model(model, name, 1, zoom=0)
if cmd.get_setting_boolean('auto_remove_hydrogens'):
cmd.remove(name + ' and hydro')
cmd.protect(name + ' in ' + namedsele)
cmd.sculpt_activate(name)
cmd.update(name, namedsele, 1, state)
cmd.delete(namedsele)
if not quiet:
print(' Sculpting...')
cmd.set('sculpt_field_mask', 0x003, name) # bonds and angles only
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x09F, name) # local + torsions
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x0FF, name) # ... + vdw
cmd.sculpt_iterate(name, 1, int(cycles / 2))
cmd.sculpt_deactivate(name)
cmd.deprotect(name)
cmd.unset('sculpt_field_mask', name)
if not quiet:
print(' Connecting peptide...')
pairs = cmd.find_pairs(name + ' and name C', name + ' and name N', 1, 1, 2.0)
for pair in pairs:
cmd.bond(*pair)
cmd.h_fix(name)
if not quiet:
print(' peptide_rebuild: done')
def fetchdialog():
app = plugins.get_pmgapp()
root = plugins.get_tk_root()
self = Tkinter.Toplevel(root)
self.title('PDB Loader Service')
self.minsize(250, 0)
self.resizable(0, 0)
outer = self
pad = 4
type_options = [
"cif (mmCIF)",
"pdb (Asymmetric Unit)",
"pdb1 (Biological Unit)",
"2fofc (Density)",
"fofc (Difference Density)",
"cid (PubChem Compound)",
"sid (PubChem Substance)",
"emd (EMDB Density)",
"cc (Chemical Component)",
]
var_code = Tkinter.StringVar(self)
var_chain = Tkinter.StringVar(self)
var_assembly = Tkinter.StringVar(self, cmd.get('assembly'))
var_name = Tkinter.StringVar(self)
var_type = Tkinter.StringVar(self, type_options[0])
var_keep = Tkinter.BooleanVar(
self, not cmd.get_setting_boolean('autoclose_dialogs'))
def callback(*args):
code = var_code.get()
type = get_trunc(var_type)
if type in ('pdb', 'cif'):
code += var_chain.get()
if type == 'cif':
cmd.set('assembly', var_assembly.get())
try:
result = cmd.fetch(code, var_name.get(), type=type)
if result == -1:
raise CmdException('You entered an invalid pdb code: ' + code)
except CmdException as e:
tkMessageBox.showerror('Error', str(e), parent=self)
return
cmd.log('fetch %s, type=%s, async=0\n' % (code, type))
if not var_keep.get():
self.destroy()
def callback_type(*args):
v = get_trunc(var_type)
if v.startswith('pdb') or v.endswith('fofc') or v.startswith('cif'):
but_code.configure(width=4)
else:
but_code.configure(width=20)
if v in ('pdb', 'cif'):
frame_pdb.pack(side=LEFT)
else:
frame_pdb.pack_forget()
if v == 'cif':
frame_assembly.pack(side=LEFT)
else:
frame_assembly.pack_forget()
def makerow(label=None, parent=None, **kwargs):
master = Tkinter.Frame(parent or outer)
master.pack(fill=Tkinter.X, **kwargs)
if label:
Tkinter.Label(master, text=label).pack(side=LEFT)
return master
padkw = {'padx': pad, 'pady': (pad, 0)}
master = makerow("Type:", **padkw)
but_type = Tkinter.OptionMenu(master,
var_type,
*type_options,
command=callback_type).pack(side=LEFT)
master = makerow("Code:", **padkw)
but_code = Tkinter.Entry(master, textvariable=var_code, width=4)
but_code.bind("<Return>", callback)
but_code.pack(side=LEFT)
frame_pdb = makerow("Chain:", master, side=LEFT, padx=8)
but_chain = Tkinter.Entry(frame_pdb, textvariable=var_chain, width=4)
but_chain.bind("<Return>", callback)
but_chain.pack(side=LEFT)
frame_assembly = makerow("Assembly:", master, side=LEFT, padx=8)
but_assembly = Tkinter.Entry(frame_assembly,
textvariable=var_assembly,
width=4)
but_assembly.bind("<Return>", callback)
but_assembly.pack(side=LEFT)
frame_name = makerow("Name of new object:", **padkw)
but_name = Tkinter.Entry(frame_name, textvariable=var_name, width=8)
but_name.bind("<Return>", callback)
but_name.pack(side=LEFT)
master = makerow(padx=pad, pady=(2 * pad, 0))
but_ok = Tkinter.Button(master, width=10, text="OK", command=callback)
but_cancel = Tkinter.Button(master,
width=10,
text="Cancel",
command=self.destroy)
but_cancel.pack(side=RIGHT, fill=Tkinter.X)
but_ok.pack(side=RIGHT, fill=Tkinter.X)
master = makerow(padx=pad, pady=(2, pad))
but_keep = Tkinter.Checkbutton(master,
text="Keep dialog open",
variable=var_keep)
but_keep.pack(side=RIGHT)
but_code.focus_set()
def save_movie_mpeg1(filename, mode='', first=0, last=0, preserve=0,
fps=25, twopass=1, vbitrate=16000, quiet=1, exe='mencoder'):
'''
DESCRIPTION
Save movie as MPEG1
This will not be the best quality possible for the file size, but
we were successfull to play those movies in PowerPoint.
Requires mencoder executable from http://mplayerhq.hu
ARGUMENTS
filename = string: Filename, should end on '.mpeg'
mode = normal | draw | ray
first, last = integer: first and last frame number
preserve = 0 or 1: delete temporary images if 0 {default: 0}
fps = integer: frames per second {default: 25}
twopass = 0 or 1: two pass mode encoding (improves quality) {default: 1}
vbitrate = integer: average video bitrate {default: 16000}
WARNING: 4-16000 (in kbit), 16001-24000000 (in bit)
SEE ALSO
cmd.movie.produce, http://www.freemol.org
'''
import os, subprocess, tempfile
first, last, quiet = int(first), int(last), int(quiet)
fps, twopass, vbitrate = int(fps), int(twopass), int(vbitrate)
if cmd.is_string(mode):
if mode == '':
if cmd.pymol.invocation.options.no_gui \
or cmd.get_setting_boolean('ray_trace_frames'):
mode = 'ray'
else:
mode = 'draw'
mode = produce_mode_sc.auto_err(mode, 'mode')
mode = produce_mode_dict[mode]
mode = int(mode)
try:
subprocess.call([exe])
except OSError:
print ' Error: Cannot execute "%s"' % (exe)
raise CmdException
if not quiet:
print ' save_movie: Rendering frames...'
tmp_path = tempfile.mkdtemp()
prefix = os.path.join(tmp_path, 'frame')
cmd.mpng(prefix, first, last, preserve, mode=mode)
mpeg1line = '-mf type=png:fps=%d -ovc lavc -forceidx -noskip -of rawvideo' \
+ ' -mpegopts format=mpeg1 -lavcopts vcodec=mpeg1video:vbitrate=%d' \
+ ':vhq:trell:keyint=25'
mpeg1line = mpeg1line % (fps, vbitrate)
cmdline = exe + ' -quiet mf://' + prefix + '* ' + mpeg1line
if not quiet:
print ' save_movie: Running mencoder...'
if twopass:
if not quiet:
print ' save_movie: First pass...'
cmdline1 = cmdline + ':vpass=1'
subprocess.call(cmdline1.split() + ['-o', os.devnull])
if not quiet:
print ' save_movie: Second pass...'
cmdline = cmdline + ':vpass=2'
subprocess.call(cmdline.split() + ['-o', filename])
if not preserve:
import shutil
shutil.rmtree(tmp_path)
elif not quiet:
print ' save_movie: Not deleting temporary directory:', tmp_path
if not quiet:
print ' save_movie: Done'
from pymol import cmd
from pymol.invocation import options
usage = 'pymol [pymol options] %s [test options]' % (os.path.basename(__file__))
parser = argparse.ArgumentParser(usage=usage)
parser.add_argument('--run', dest='filenames', nargs='*', default=[])
parser.add_argument('--out', default=sys.stdout)
parser.add_argument('--offline', action='store_true')
parser.add_argument('--verbosity', type=int, default=2)
cliargs = parser.parse_known_args()[0]
run_all = False
max_threads = int(cmd.get('max_threads'))
cmd.set('use_shaders')
use_shaders = cmd.get_setting_boolean('use_shaders')
pymol_test_dir = os.path.abspath(os.path.dirname(__file__))
deferred_unlink = []
class requires(object):
'''
Decorator for test methods which only should be executed
under certain conditions.
Example:
>>> @requires('gui')
>>> def testSomething(self):
>>> do_something()
def fetchdialog():
from Tkinter import LEFT, RIGHT, TOP, BOTTOM
app = plugins.get_pmgapp()
root = plugins.get_tk_root()
self = Tkinter.Toplevel(root)
self.title('PDB Loader Service')
self.minsize(250, 0)
self.resizable(0,0)
outer = self
pad = 4
type_options = [
"pdb (Asymmetric Unit)",
"pdb1 (Biological Unit)",
"2fofc (Density)",
"fofc (Difference Density)",
"cid (PubChem Compound)",
"sid (PubChem Substance)",
"emd (EMDB Density)",
]
var_code = Tkinter.StringVar(self)
var_chain = Tkinter.StringVar(self)
var_type = Tkinter.StringVar(self, type_options[0])
var_keep = Tkinter.BooleanVar(self,
not cmd.get_setting_boolean('autoclose_dialogs'))
def callback(*args):
code = var_code.get()
type = get_trunc(var_type)
if type == 'pdb':
code += var_chain.get()
try:
result = cmd.fetch(code, type=type)
if result == -1:
raise CmdException('You entered an invalid pdb code: ' + code)
except CmdException as e:
import tkMessageBox
tkMessageBox.showerror('Error', str(e), parent=self)
return
cmd.log('fetch %s, type=%s, async=0\n' % (code, type))
if not var_keep.get():
self.destroy()
def callback_type(*args):
v = get_trunc(var_type)
if v.startswith('pdb') or v.endswith('fofc'):
but_code.configure(width=4)
else:
but_code.configure(width=20)
if v == 'pdb':
frame_pdb.pack(side=LEFT)
else:
frame_pdb.pack_forget()
def makerow(label=None, parent=None, **kwargs):
master = Tkinter.Frame(parent or outer)
master.pack(fill=Tkinter.X, **kwargs)
if label:
Tkinter.Label(master, text=label).pack(side=LEFT)
return master
padkw = {'padx': pad, 'pady': (pad, 0)}
master = makerow("Type:", **padkw)
but_type = Tkinter.OptionMenu(master, var_type, *type_options,
command=callback_type).pack(side=LEFT)
master = makerow("Code:", **padkw)
but_code = Tkinter.Entry(master, textvariable=var_code, width=4)
but_code.bind("<Return>", callback)
but_code.pack(side=LEFT)
frame_pdb = makerow("Chain:", master, side=LEFT, padx=8)
but_chain = Tkinter.Entry(frame_pdb, textvariable=var_chain, width=4)
but_chain.bind("<Return>", callback)
but_chain.pack(side=LEFT)
master = makerow(padx=pad, pady=(2*pad,0))
but_ok = Tkinter.Button(master, width=10, text="OK",
command=callback)
but_cancel = Tkinter.Button(master, width=10, text="Cancel",
command=self.destroy)
but_cancel.pack(side=RIGHT, fill=Tkinter.X)
but_ok.pack(side=RIGHT, fill=Tkinter.X)
master = makerow(padx=pad, pady=(2,pad))
but_keep = Tkinter.Checkbutton(master, text="Keep dialog open", variable=var_keep)
but_keep.pack(side=RIGHT)
but_code.focus_set()
