def testGetSettingFloat(self):
for v_ref in (0.0, 1.0):
# bool as float
cmd.set('orthoscopic', v_ref)
v = cmd.get_setting_float('orthoscopic')
self.assertTrue(isinstance(v, float))
self.assertEqual(v, v_ref)
# float with 6 significant digits
cmd.set('sphere_scale', 1.234565)
v = cmd.get_setting_float('sphere_scale')
self.assertEqual(int(v * 1e5), 123456)
def testStereo(self):
for (k, v) in cmd.stereo_dict.items():
if v < 1:
continue
cmd.stereo(k)
self.assertTrue(cmd.get_setting_int('stereo'))
self.assertEqual(cmd.get_setting_int('stereo_mode'), v)
cmd.stereo('off')
self.assertFalse(cmd.get_setting_int('stereo'))
cmd.stereo('on')
self.assertTrue(cmd.get_setting_int('stereo'))
shift = cmd.get_setting_float('stereo_shift')
cmd.stereo('swap')
self.assertAlmostEqual(cmd.get_setting_float('stereo_shift'), -shift)
def testStereo(self):
for (k,v) in cmd.stereo_dict.items():
if v < 1:
continue
cmd.stereo(k)
self.assertTrue(cmd.get_setting_int('stereo'))
self.assertEqual(cmd.get_setting_int('stereo_mode'), v)
cmd.stereo('off')
self.assertFalse(cmd.get_setting_int('stereo'))
cmd.stereo('on')
self.assertTrue(cmd.get_setting_int('stereo'))
shift = cmd.get_setting_float('stereo_shift')
cmd.stereo('swap')
self.assertAlmostEqual(cmd.get_setting_float('stereo_shift'), -shift)
def testExportStyle(self):
cmd.fab('ACDEF', 'm1')
cmd.hide()
cmd.show('cartoon', 'resi 1-3')
cmd.show('lines', 'resn CYS')
cmd.show('sticks', 'resn ASP+PHE')
cmd.show('spheres', 'resn GLU')
cmd.set('stick_ball', 1, 'resn PHE')
cmd.set('stick_ball_ratio', 1.5, 'm1')
testlabel = 'Hello "World"'
cmd.label('name SG', repr(testlabel))
with testing.mktemp('.mae') as filename:
cmd.save(filename)
cmd.delete('*')
cmd.load(filename, 'm2')
g_labels = []
cmd.iterate('name SG', 'g_labels.append(label)', space=locals())
cmd.alter('*', 'b = 1 if s.stick_ball else 0')
self._assertCountEqual('rep cartoon & guide', 'resi 1-3 & guide')
self._assertCountEqual('rep lines', 'resn CYS', delta=1)
self._assertCountEqual('rep sticks', 'resn ASP+PHE')
self._assertCountEqual('rep spheres', 'resn GLU')
self._assertCountEqual('b > 0.5', 'resn PHE')
self.assertTrue(cmd.get_setting_float('stick_ball_ratio', 'm2') > 1.1)
self.assertEqual(g_labels[0], testlabel)
def get_sasa_mmtk(selection, state=-1, hydrogens='auto', quiet=1):
'''
DESCRIPTION
Get solvent accesible surface area using MMTK.MolecularSurface
http://dirac.cnrs-orleans.fr/MMTK/
This command is very picky with missing atoms and wrong atom naming.
SEE ALSO
stub2ala, get_sasa, get_sasa_ball
'''
try:
import MMTK
except ImportError:
print(' ImportError: please install MMTK')
raise CmdException
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import Protein
from MMTK.MolecularSurface import surfaceAndVolume
try:
from cStringIO import StringIO
except ImportError:
from io import StringIO
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
radius = cmd.get_setting_float('solvent_radius')
if hydrogens == 'auto':
if cmd.count_atoms('(%s) and hydro' % selection) > 0:
hydrogens = 'all'
else:
hydrogens = 'no_hydrogens'
elif hydrogens == 'none':
hydrogens = 'no_hydrogens'
conf = PDBConfiguration(StringIO(cmd.get_pdbstr(selection)))
system = Protein(conf.createPeptideChains(hydrogens))
try:
area, volume = surfaceAndVolume(system, radius * 0.1)
except:
print(' Error: MMTK.MolecularSurface.surfaceAndVolume failed')
raise CmdException
if not quiet:
print(' get_sasa_mmtk: %.3f Angstroms^2 (volume: %.3f Angstroms^3).' %
(area * 1e2, volume * 1e3))
return area * 1e2
def get_sasa_mmtk(selection, state=-1, hydrogens='auto', quiet=1):
'''
DESCRIPTION
Get solvent accesible surface area using MMTK.MolecularSurface
http://dirac.cnrs-orleans.fr/MMTK/
This command is very picky with missing atoms and wrong atom naming.
SEE ALSO
stub2ala, get_sasa, get_sasa_ball
'''
try:
import MMTK
except ImportError:
print(' ImportError: please install MMTK')
raise CmdException
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import Protein
from MMTK.MolecularSurface import surfaceAndVolume
try:
from cStringIO import StringIO
except ImportError:
from io import StringIO
selection = selector.process(selection)
state, quiet = int(state), int(quiet)
radius = cmd.get_setting_float('solvent_radius')
if hydrogens == 'auto':
if cmd.count_atoms('(%s) and hydro' % selection) > 0:
hydrogens = 'all'
else:
hydrogens = 'no_hydrogens'
elif hydrogens == 'none':
hydrogens = 'no_hydrogens'
conf = PDBConfiguration(StringIO(cmd.get_pdbstr(selection)))
system = Protein(conf.createPeptideChains(hydrogens))
try:
area, volume = surfaceAndVolume(system, radius * 0.1)
except:
print(' Error: MMTK.MolecularSurface.surfaceAndVolume failed')
raise CmdException
if not quiet:
print(' get_sasa_mmtk: %.3f Angstroms^2 (volume: %.3f Angstroms^3).' % (area * 1e2, volume * 1e3))
return area * 1e2
def get_sasa_ball(selection, state=-1, quiet=1):
'''
DESCRIPTION
Get solvent accesible surface area using BALL.NumericalSAS
http://www.ball-project.org/
'''
try:
import BALL
except ImportError:
print(' ImportError: please install BALL python bindings')
raise CmdException
import tempfile, os
state, quiet = int(state), int(quiet)
radius = cmd.get_setting_float('solvent_radius')
filename = tempfile.mktemp('.pdb')
cmd.save(filename, selection, state, 'pdb')
system = BALL.System()
BALL.PDBFile(filename) >> system
os.remove(filename)
fragment_db = BALL.FragmentDB('')
system.apply(fragment_db.normalize_names)
system.apply(BALL.AssignRadiusProcessor('radii/PARSE.siz'))
sas = BALL.NumericalSAS()
sas_options = BALL.Options()
sas_options.setBool(sas.Option.COMPUTE_AREA, True)
sas_options.setBool(sas.Option.COMPUTE_SURFACE, False)
sas_options.setReal(sas.Option.PROBE_RADIUS, radius)
sas.setOptions(sas_options)
sas(system)
area = sas.getTotalArea()
if not quiet:
print(' get_sasa_ball: %.3f Angstroms^2.' % (area))
return area
def get_sasa_ball(selection, state=-1, quiet=1):
'''
DESCRIPTION
Get solvent accesible surface area using BALL.NumericalSAS
http://www.ball-project.org/
'''
try:
import BALL
except ImportError:
print(' ImportError: please install BALL python bindings')
raise CmdException
import tempfile, os
state, quiet = int(state), int(quiet)
radius = cmd.get_setting_float('solvent_radius')
filename = tempfile.mktemp('.pdb')
cmd.save(filename, selection, state, 'pdb')
system = BALL.System()
BALL.PDBFile(filename) >> system
os.remove(filename)
fragment_db = BALL.FragmentDB('')
system.apply(fragment_db.normalize_names)
system.apply(BALL.AssignRadiusProcessor('radii/PARSE.siz'))
sas = BALL.NumericalSAS()
sas_options = BALL.Options()
sas_options.setBool(sas.Option.COMPUTE_AREA, True)
sas_options.setBool(sas.Option.COMPUTE_SURFACE, False)
sas_options.setReal(sas.Option.PROBE_RADIUS, radius)
sas.setOptions(sas_options)
sas(system)
area = sas.getTotalArea()
if not quiet:
print(' get_sasa_ball: %.3f Angstroms^2.' % (area))
return area
def testGetSettingFloatExact(self):
# PyMOL 2.4 uses pymol::pretty_f2d which rounds 7 significant digits
for v_ref in (1.234567, 1234567.e6, 9999999.0):
cmd.set('sphere_scale', v_ref)
v = cmd.get_setting_float('sphere_scale')
self.assertEqual(v, v_ref)
