本文整理汇总了Python中utils.Atom_utils._calculate_distance方法的典型用法代码示例。如果您正苦于以下问题：Python Atom_utils._calculate_distance方法的具体用法？Python Atom_utils._calculate_distance怎么用？Python Atom_utils._calculate_distance使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类utils.Atom_utils的用法示例。
在下文中一共展示了Atom_utils._calculate_distance方法的5个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: _test_non_bonded_shifts
# 需要导入模块: from utils import Atom_utils [as 别名]
# 或者: from utils.Atom_utils import _calculate_distance [as 别名]
def _test_non_bonded_shifts(self, non_bonded_potential, non_bonded_shifts):
non_bonded_potential.update_non_bonded_list()
target_components = non_bonded_potential._get_component_list('ATOM')
remote_components = non_bonded_potential._get_component_list('NBRM')
for i, component in enumerate( non_bonded_potential._get_all_components('NBLT')):
target_component_index, remote_component_index = component[1:3]
target_atom_id = target_components[target_component_index][0]
remote_atom_id = remote_components[remote_component_index][0]
expected_shift = 0.0
key_good = False
for j, exponent in enumerate((1,-3)):
target_atom_key = Atom_utils._get_atom_info_from_index(target_atom_id)
remote_atom_key = Atom_utils._get_atom_info_from_index(remote_atom_id)
expected_shift_key = target_atom_key, remote_atom_key, int(exponent)
if expected_shift_key in non_bonded_shifts:
expected_shift += non_bonded_shifts[expected_shift_key]
key_good=True
elif j == 0:
distance = Atom_utils._calculate_distance(target_atom_id, remote_atom_id)
self.assertTrue(distance >= 5.0, expected_shift_key)
if key_good:
calculated_shift = non_bonded_potential._calc_component_shift(i)
self.assertAlmostEqual(expected_shift, calculated_shift, self.DEFAULT_DECIMAL_PLACES, expected_shift_key)示例2: _test_non_bonded_forces
# 需要导入模块: from utils import Atom_utils [as 别名]
# 或者: from utils.Atom_utils import _calculate_distance [as 别名]
def _test_non_bonded_forces(self, non_bonded_potential, non_bonded_forces, active_shifts, factors):
components = dict(non_bonded_potential._get_components())
nb_interaction_list = components['NBLT']
active_array = allocate_array(1,'i')
components['ACTI'] = active_array
#TODO: make this less invasive of the potentials encapsulation
components['OFFS'] = 0
non_bonded_potential._force_calculator._set_components(components)
for i, component in enumerate(nb_interaction_list):
zero_array(active_array)
active_array[0] = i
target_atom_id = non_bonded_potential._get_component_list('ATOM')[component[1]][0]
remote_atom_id = non_bonded_potential._get_component_list('NBRM')[component[2]][0]
target_atom_key = Atom_utils._get_atom_info_from_index(target_atom_id)
remote_atom_key = Atom_utils._get_atom_info_from_index(remote_atom_id)
if active_shifts[target_atom_key] == 0:
continue
#
distance = Atom_utils._calculate_distance(target_atom_id, remote_atom_id)
if distance < 5.0:
for exponent_index, exponent in enumerate((1,-3)):
expected_key = target_atom_key, remote_atom_key, int(exponent)
factor = factors[target_atom_key]
non_bonded_potential._force_calculator._build_component(i,exponent_index)
factor = factors[target_atom_key]
out_array = self.make_out_array()
non_bonded_potential._force_calculator._calc_single_force_set(0, factor,out_array)
forces = out_array.add_forces_to_result()
target_force_triplet = forces[target_atom_id]
remote_force_triplet = forces[remote_atom_id]
expected_target_forces = non_bonded_forces[expected_key]
expected_remote_forces = [-elem for elem in expected_target_forces]
#TODO: check change from 7 to 5 dp is ok also improve assertSequenceAlmostEqual ro take a places argument
self.assertSequenceAlmostEqual(target_force_triplet, expected_target_forces,delta= 1e-1**self.DEFAULT_DECIMAL_PLACES)
self.assertSequenceAlmostEqual(remote_force_triplet, expected_remote_forces,delta= 1e-1**self.DEFAULT_DECIMAL_PLACES)
atom_ids = [target_atom_id,remote_atom_id]
atom_ids.sort(reverse=True)
for atom_id in atom_ids:
del forces[atom_id]
forces = self.remove_almost_zero_force_elems_from_list(forces)
self.assertEmpty(forces)
del non_bonded_forces[expected_key]
self.assertEmpty(non_bonded_forces)示例3: test_non_bonded_component_shifts
# 需要导入模块: from utils import Atom_utils [as 别名]
# 或者: from utils.Atom_utils import _calculate_distance [as 别名]
def test_non_bonded_component_shifts(self):
xcamshift = self._get_xcamshift()
sub_potential = xcamshift.get_named_sub_potential(NON_BONDED)
sub_potential.update_non_bonded_list()
components = sub_potential._get_component_list('NBLT')
target_atom_ids = [component[0] for component in components]
xcamshift._prepare(TARGET_ATOM_IDS_CHANGED,target_atom_ids)
xcamshift._prepare(ROUND_CHANGED,None)
non_bonded_components = dict(gb3.gb3_component_shifts_non_bonded)
target_components = sub_potential._get_component_list('ATOM')
remote_components = sub_potential._get_component_list('NBRM')
for i,(target_atom_id, target_index, remote_index, component_index) in enumerate(components):
target_atom_id = target_components[target_index][0]
target_atom_key = Atom_utils._get_atom_info_from_index(target_atom_id)
remote_atom_id = remote_components[remote_index][0]
remote_atom_key = Atom_utils._get_atom_info_from_index(remote_atom_id)
if target_atom_key[2]== 'HA1':
target_atom_key = list(target_atom_key)
target_atom_key[2]= 'HA'
target_atom_key = tuple(target_atom_key)
if Atom_utils._calculate_distance(target_atom_id, remote_atom_id) > 5.0:
continue
shift = sub_potential._calc_component_shift(i)
expected_shift = 0.0
seen_keys = []
for exponent_key in 0,1:
non_bonded_component_key = (target_atom_key, remote_atom_key, exponent_key)
seen_keys.append(non_bonded_component_key)
expected_shift += non_bonded_components[non_bonded_component_key]
self.assertAlmostEqual(shift,expected_shift,self.DEFAULT_DECIMAL_PLACES-2,`i` + ' ' + `non_bonded_component_key`)
for seen_key in seen_keys:
del non_bonded_components[seen_key]
self.assertEmpty(non_bonded_components)示例4: test_non_bonded_components
# 需要导入模块: from utils import Atom_utils [as 别名]
# 或者: from utils.Atom_utils import _calculate_distance [as 别名]
def test_non_bonded_components(self):
#TODO: add common loading method for xcamshift
print 'WARNING using zero shifts with test_non_bonded_components as a hack to get _active_target_atom_ids correct!'
xcamshift = self._setup_xcamshift_with_shifts_table(gb3.gb3_zero_shifts)
sub_potential = xcamshift.get_named_sub_potential(NON_BONDED)
xcamshift._prepare(TARGET_ATOM_IDS_CHANGED,None)
xcamshift._prepare(ROUND_CHANGED,None)
components = sub_potential._get_component_list('NBLT')
non_bonded_components = dict(gb3.gb3_component_shifts_non_bonded)
target_components = sub_potential._get_component_list('ATOM')
remote_components = sub_potential._get_component_list('NBRM')
for target_atom_id, target_index, remote_index, component_index in components:
target_atom_id = target_components[target_index][0]
target_atom_key = Atom_utils._get_atom_info_from_index(target_atom_id)
remote_atom_id = remote_components[remote_index][0]
remote_atom_key = Atom_utils._get_atom_info_from_index(remote_atom_id)
if target_atom_key[2]== 'HA1':
target_atom_key = list(target_atom_key)
target_atom_key[2]= 'HA'
target_atom_key = tuple(target_atom_key)
if Atom_utils._calculate_distance(target_atom_id, remote_atom_id) > 5.0:
continue
for exponent_key in 0,1:
non_bonded_component_key = (target_atom_key, remote_atom_key, exponent_key)
self.assertIn(non_bonded_component_key, non_bonded_components, `non_bonded_component_key`)
del non_bonded_components[non_bonded_component_key]
self.assertEmpty(non_bonded_components)示例5: _test_non_bonded_force_factors
# 需要导入模块: from utils import Atom_utils [as 别名]
# 或者: from utils.Atom_utils import _calculate_distance [as 别名]
def _test_non_bonded_force_factors(self, non_bonded_potential, non_bonded_force_factors, active_shifts, factors):
components = dict(non_bonded_potential._get_components())
nb_interaction_list = components['NBLT']
active_array = allocate_array(1,'i')
components['ACTI'] = active_array
components['OFFS'] = 0
non_bonded_potential._force_calculator._set_components(components)
for i, component in enumerate(nb_interaction_list):
zero_array(active_array)
active_array[0] = i
target_atom_id = non_bonded_potential._get_component_list('ATOM')[component[1]][0]
remote_atom_id = non_bonded_potential._get_component_list('NBRM')[component[2]][0]
target_atom_key = Atom_utils._get_atom_info_from_index(target_atom_id)
remote_atom_key = Atom_utils._get_atom_info_from_index(remote_atom_id)
if active_shifts[target_atom_key] == 0:
continue
#
distance = Atom_utils._calculate_distance(target_atom_id, remote_atom_id)
if distance < 5.0:
for exponent_index, exponent in enumerate((1,-3)):
expected_key = target_atom_key, remote_atom_key, int(exponent)
factor = factors[target_atom_key]
non_bonded_potential._force_calculator._build_component(i,exponent_index)
force_factor = non_bonded_potential._force_calculator._calc_single_force_factor(0, factor)
#TODO: check change from 7 to 5 dp is ok
self.assertAlmostEqual(force_factor, non_bonded_force_factors[expected_key],places=self.DEFAULT_DECIMAL_PLACES)
del non_bonded_force_factors[expected_key]
self.assertEmpty(non_bonded_force_factors)