class Dihedral(nn.Cell):
"""dihedral class"""
def __init__(self, controller):
super(Dihedral, self).__init__()
self.CONSTANT_Pi = 3.1415926535897932
if controller.amber_parm is not None:
file_path = controller.amber_parm
self.read_information_from_amberfile(file_path)
self.atom_a = Tensor(np.asarray(self.h_atom_a, np.int32), mstype.int32)
self.atom_b = Tensor(np.asarray(self.h_atom_b, np.int32), mstype.int32)
self.atom_c = Tensor(np.asarray(self.h_atom_c, np.int32), mstype.int32)
self.atom_d = Tensor(np.asarray(self.h_atom_d, np.int32), mstype.int32)
self.pk = Tensor(np.asarray(self.pk, np.float32), mstype.float32)
self.gamc = Tensor(np.asarray(self.gamc, np.float32), mstype.float32)
self.gams = Tensor(np.asarray(self.gams, np.float32), mstype.float32)
self.pn = Tensor(np.asarray(self.pn, np.float32), mstype.float32)
self.ipn = Tensor(np.asarray(self.ipn, np.int32), mstype.int32)
def process1(self, context):
"""process1: read information from amberfile"""
for idx, val in enumerate(context):
if idx < len(context) - 1:
if "%FLAG POINTERS" in val + context[
idx + 1] and "%FORMAT(10I8)" in val + context[idx + 1]:
start_idx = idx + 2
count = 0
value = list(map(int, context[start_idx].strip().split()))
self.dihedral_with_hydrogen = value[6]
self.dihedral_numbers = value[7]
self.dihedral_numbers += self.dihedral_with_hydrogen
information = []
information.extend(value)
while count < 15:
start_idx += 1
value = list(
map(int, context[start_idx].strip().split()))
information.extend(value)
count += len(value)
self.dihedral_type_numbers = information[17]
print("dihedral type numbers ", self.dihedral_type_numbers)
break
self.phase_type = [0] * self.dihedral_type_numbers
self.pk_type = [0] * self.dihedral_type_numbers
self.pn_type = [0] * self.dihedral_type_numbers
for idx, val in enumerate(context):
if "%FLAG DIHEDRAL_FORCE_CONSTANT" in val:
count = 0
start_idx = idx
information = []
while count < self.dihedral_type_numbers:
start_idx += 1
if "%FORMAT" in context[start_idx]:
continue
else:
value = list(
map(float, context[start_idx].strip().split()))
information.extend(value)
count += len(value)
self.pk_type = information[:self.dihedral_type_numbers]
break
for idx, val in enumerate(context):
if "%FLAG DIHEDRAL_PHASE" in val:
count = 0
start_idx = idx
information = []
while count < self.dihedral_type_numbers:
start_idx += 1
if "%FORMAT" in context[start_idx]:
continue
else:
value = list(
map(float, context[start_idx].strip().split()))
information.extend(value)
count += len(value)
self.phase_type = information[:self.dihedral_type_numbers]
break
for idx, val in enumerate(context):
if "%FLAG DIHEDRAL_PERIODICITY" in val:
count = 0
start_idx = idx
information = []
while count < self.dihedral_type_numbers:
start_idx += 1
if "%FORMAT" in context[start_idx]:
continue
else:
value = list(
map(float, context[start_idx].strip().split()))
information.extend(value)
count += len(value)
self.pn_type = information[:self.dihedral_type_numbers]
break
def read_information_from_amberfile(self, file_path):
"""read information from amberfile"""
file = open(file_path, 'r')
context = file.readlines()
file.close()
self.process1(context)
self.h_atom_a = [0] * self.dihedral_numbers
self.h_atom_b = [0] * self.dihedral_numbers
self.h_atom_c = [0] * self.dihedral_numbers
self.h_atom_d = [0] * self.dihedral_numbers
self.pk = []
self.gamc = []
self.gams = []
self.pn = []
self.ipn = []
for idx, val in enumerate(context):
if "%FLAG DIHEDRALS_INC_HYDROGEN" in val:
count = 0
start_idx = idx
information = []
while count < 5 * self.dihedral_with_hydrogen:
start_idx += 1
if "%FORMAT" in context[start_idx]:
continue
else:
value = list(
map(int, context[start_idx].strip().split()))
information.extend(value)
count += len(value)
for i in range(self.dihedral_with_hydrogen):
self.h_atom_a[i] = information[i * 5 + 0] / 3
self.h_atom_b[i] = information[i * 5 + 1] / 3
self.h_atom_c[i] = information[i * 5 + 2] / 3
self.h_atom_d[i] = abs(information[i * 5 + 3] / 3)
tmpi = information[i * 5 + 4] - 1
self.pk.append(self.pk_type[tmpi])
tmpf = self.phase_type[tmpi]
if abs(tmpf - self.CONSTANT_Pi) <= 0.001:
tmpf = self.CONSTANT_Pi
tmpf2 = math.cos(tmpf)
if abs(tmpf2) < 1e-6:
tmpf2 = 0
self.gamc.append(tmpf2 * self.pk[i])
tmpf2 = math.sin(tmpf)
if abs(tmpf2) < 1e-6:
tmpf2 = 0
self.gams.append(tmpf2 * self.pk[i])
self.pn.append(abs(self.pn_type[tmpi]))
self.ipn.append(int(self.pn[i] + 0.001))
break
for idx, val in enumerate(context):
if "%FLAG DIHEDRALS_WITHOUT_HYDROGEN" in val:
count = 0
start_idx = idx
information = []
while count < 5 * (self.dihedral_numbers -
self.dihedral_with_hydrogen):
start_idx += 1
if "%FORMAT" in context[start_idx]:
continue
else:
value = list(
map(int, context[start_idx].strip().split()))
information.extend(value)
count += len(value)
for i in range(self.dihedral_with_hydrogen,
self.dihedral_numbers):
self.h_atom_a[i] = information[
(i - self.dihedral_with_hydrogen) * 5 + 0] / 3
self.h_atom_b[i] = information[
(i - self.dihedral_with_hydrogen) * 5 + 1] / 3
self.h_atom_c[i] = information[
(i - self.dihedral_with_hydrogen) * 5 + 2] / 3
self.h_atom_d[i] = abs(
information[(i - self.dihedral_with_hydrogen) * 5 + 3]
/ 3)
tmpi = information[(i - self.dihedral_with_hydrogen) * 5 +
4] - 1
self.pk.append(self.pk_type[tmpi])
tmpf = self.phase_type[tmpi]
if abs(tmpf - self.CONSTANT_Pi) <= 0.001:
tmpf = self.CONSTANT_Pi
tmpf2 = math.cos(tmpf)
if abs(tmpf2) < 1e-6:
tmpf2 = 0
self.gamc.append(tmpf2 * self.pk[i])
tmpf2 = math.sin(tmpf)
if abs(tmpf2) < 1e-6:
tmpf2 = 0
self.gams.append(tmpf2 * self.pk[i])
self.pn.append(abs(self.pn_type[tmpi]))
self.ipn.append(int(self.pn[i] + 0.001))
break
for i in range(self.dihedral_numbers):
if self.h_atom_c[i] < 0:
self.h_atom_c[i] *= -1
def Dihedral_Engergy(self, uint_crd, uint_dr_to_dr_cof):
"""compute dihedral energy"""
self.dihedral_energy = P.DihedralEnergy(self.dihedral_numbers)(
uint_crd, uint_dr_to_dr_cof, self.atom_a, self.atom_b, self.atom_c,
self.atom_d, self.ipn, self.pk, self.gamc, self.gams, self.pn)
self.sigma_of_dihedral_ene = P.ReduceSum()(self.dihedral_energy)
return self.sigma_of_dihedral_ene
def Dihedral_Force_With_Atom_Energy(self, uint_crd, scaler):
"""compute dihedral force and atom energy"""
self.dfae = P.DihedralForceWithAtomEnergy(
dihedral_numbers=self.dihedral_numbers)
self.frc, self.ene = self.dfae(uint_crd, scaler, self.atom_a,
self.atom_b, self.atom_c, self.atom_d,
self.ipn, self.pk, self.gamc, self.gams,
self.pn)
return self.frc, self.ene
