def test_solvation_with_additional_ions(self):
""" Test that we can solvate CB6-BUT with additional ions. """
waters = np.random.randint(1000, 10000)
cations = ['LI', 'Na+', 'K+', 'RB', 'CS']
anions = ['F', 'Cl-', 'BR', 'IOD']
n_cations = np.random.randint(1, 10)
n_anions = np.random.randint(1, 10)
random_cation = random.choice(cations)
random_anion = random.choice(anions)
log.debug('Trying {} waters with additional ions...'.format(waters))
solvate(tleapfile='./cb6-but/tleap.in', pdbfile='cb6-but.pdb',
bufferwater=waters, neutralize=0,
addions=[random_cation, n_cations, random_anion, n_anions])
# These should come in the RESIDUE_LABEL region of the prmtop and be before all the water.
cation_number = sp.check_output(["grep -A 99 RESIDUE_LABEL ./cb6-but/solvated.prmtop | " +
"grep -oh '{} ' | wc -w".format(random_cation)],
shell=True)
anion_number = sp.check_output(["grep -A 99 RESIDUE_LABEL ./cb6-but/solvated.prmtop | " +
"grep -oh '{} ' | wc -w".format(random_anion)],
shell=True)
# Have to think about what to do here...
# log.debug('Expecting...')
# log.debug('cation = {}\tn_cations={}'.format(random_cation, n_cations))
# log.debug('anion = {}\t n_anions={}'.format(random_anion, n_anions))
# log.debug('Found...')
# log.debug(' n_cations={}'.format(cation_number))
# log.debug(' n_anions={}'.format(anion_number))
self.assertTrue(int(cation_number) == n_cations and int(anion_number) == n_anions)
def test_solvation_box(self):
""" Test that we can solvate CB6-BUT with an isometric box. """
waters = np.random.randint(1000, 10000)
log.debug('Trying {} waters in an isometric box...'.format(waters))
solvate(tleapfile='./cb6-but/tleap.in', pdbfile='cb6-but.pdb',
bufferwater=waters, pbctype=0)
grepped_waters = sp.check_output(["grep -oh 'WAT' ./cb6-but/solvated.prmtop | wc -w"],
shell=True)
self.assertEqual(int(grepped_waters), waters)
def test_solvation_potassium_control(self):
""" Test there is no potassium by default. A negative control. """
waters = np.random.randint(1000, 10000)
log.debug('Trying {} waters with potassium...'.format(waters))
solvate(tleapfile='./cb6-but/tleap.in', pdbfile='cb6-but.pdb',
bufferwater=waters, counter_cation='K+')
potassium = sp.check_output(["grep -oh 'K+' ./cb6-but/solvated.prmtop | wc -w"],
shell=True)
self.assertEqual(int(potassium), 0)
def test_solvation_simple(self):
""" Test that we can solvate CB6-BUT using default settings. """
waters = np.random.randint(1000, 10000)
log.debug('Trying {} waters with default settings...'.format(waters))
solvate(tleapfile='./cb6-but/tleap.in', pdbfile='cb6-but.pdb',
bufferwater=waters)
grepped_waters = sp.check_output(["grep -oh 'WAT' ./cb6-but/solvated.prmtop | wc -w"],
shell=True)
self.assertEqual(int(grepped_waters), waters)
def test_solvation_spatial_size(self):
""" Test that we can solvate CB6-BUT with an buffer size in Angstroms. """
random_int = np.random.randint(10, 100)
random_size = random_int * np.random.random_sample(1) + random_int
log.debug('Trying buffer size of {} A...'.format(random_size[0]))
solvate(tleapfile='./cb6-but/tleap.in', pdbfile='cb6-but.pdb',
bufferwater='{0:1.4f}A'.format(random_size[0]))
log.warning('I don\'t know the proper test case for this. \
We\'d have to parse the coordinates, perhaps.')
# This is bad, but I'll think of a better way.
self.assertEqual(0, 0)
def test_alignment_workflow(self):
""" Test that we can solvate CB6-BUT after alignment. """
cb6 = pmd.load_file('./cb6-but/vac.pdb')
align(cb6, ':CB6', ':BUT', save=True, filename='./cb6-but/tmp.pdb')
waters = np.random.randint(1000, 10000)
log.debug('Trying {} waters after alignment...'.format(waters))
solvate(tleapfile='./cb6-but/tleap.in', pdbfile='tmp.pdb',
bufferwater=waters)
grepped_waters = sp.check_output(["grep -oh 'WAT' ./cb6-but/solvated.prmtop | wc -w"],
shell=True)
self.assertEqual(int(grepped_waters), waters)
def test_solvation_by_molality(self):
""" Test that we can solvate CB6-BUT through molarity. """
log.debug('Trying 2000 water buffer with 150 mmol/kg NaCl...')
solvate(tleapfile='./cb6-but/tleap.in', pdbfile='cb6-but.pdb',
bufferwater=2000, neutralize=0, pbctype=1,
addions=['Na+', '0.150m', 'Cl-', '0.150m'])
cation_number = sp.check_output(["grep -A 99 RESIDUE_LABEL ./cb6-but/solvated.prmtop | " +
"grep -oh 'Na+ ' | wc -w"], shell=True)
anion_number = sp.check_output(["grep -A 99 RESIDUE_LABEL ./cb6-but/solvated.prmtop | " +
"grep -oh 'Cl- ' | wc -w"], shell=True)
n_cations = np.ceil(0.150 * 2000 * 0.018)
n_anions = np.ceil(0.150 * 2000 * 0.018)
self.assertTrue(int(cation_number) == n_cations and int(anion_number) == n_anions)
def test_solvation_by_molarity(self):
""" Test that we can solvate CB6-BUT through molarity. """
log.debug('Trying 10 A buffer with 150 mM NaCl...')
solvate(tleapfile='./cb6-but/tleap.in', pdbfile='cb6-but.pdb',
bufferwater='10A', neutralize=0, pbctype=1,
addions=['Na+', '0.150M', 'Cl-', '0.150M'])
cation_number = sp.check_output(["grep -A 99 RESIDUE_LABEL ./cb6-but/solvated.prmtop | " +
"grep -oh 'Na+ ' | wc -w"], shell=True)
anion_number = sp.check_output(["grep -A 99 RESIDUE_LABEL ./cb6-but/solvated.prmtop | " +
"grep -oh 'Cl- ' | wc -w"], shell=True)
# Approximate volume of the solvated system in liters
volume_in_liters = 4.6766 * 10**-23
n_cations = np.ceil((6.022 * 10**23) * (0.150) * volume_in_liters)
n_anions = np.ceil((6.022 * 10**23) * (0.150) * volume_in_liters)
self.assertTrue(int(cation_number) == n_cations and int(anion_number) == n_anions)
