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- # Copyright 2021 Huawei Technologies Co., Ltd
- #
- # Licensed under the Apache License, Version 2.0 (the "License");
- # you may not use this file except in compliance with the License.
- # You may obtain a copy of the License at
- #
- # http://www.apache.org/licenses/LICENSE-2.0
- #
- # Unless required by applicable law or agreed to in writing, software
- # distributed under the License is distributed on an "AS IS" BASIS,
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- # See the License for the specific language governing permissions and
- # limitations under the License.
- # ============================================================================
- '''NON BOND'''
- class NON_BOND_14:
- '''NON BOND'''
- def __init__(self, controller, dihedral, atom_numbers):
- self.dihedral_with_hydrogen = dihedral.dihedral_with_hydrogen
- self.dihedral_numbers = dihedral.dihedral_numbers
- self.dihedral_type_numbers = dihedral.dihedral_type_numbers
- self.atom_numbers = atom_numbers
-
- if controller.amber_parm is not None:
- file_path = controller.amber_parm
- self.read_information_from_amberfile(file_path)
- self.h_atom_a = self.h_atom_a[:self.nb14_numbers]
- self.h_atom_b = self.h_atom_b[:self.nb14_numbers]
- self.h_lj_scale_factor = self.h_lj_scale_factor[:self.nb14_numbers]
- self.h_cf_scale_factor = self.h_cf_scale_factor[:self.nb14_numbers]
-
- def read_information_from_amberfile(self, file_path):
- '''read amber file'''
- file = open(file_path, 'r')
- context = file.readlines()
- file.close()
-
- self.cf_scale_type = [0] * self.dihedral_type_numbers
- self.lj_scale_type = [0] * self.dihedral_type_numbers
-
- for idx, val in enumerate(context):
- if "%FLAG SCEE_SCALE_FACTOR" 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.cf_scale_type = information[:self.dihedral_type_numbers]
- break
-
- for idx, val in enumerate(context):
- if "%FLAG SCNB_SCALE_FACTOR" 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.lj_scale_type = information[:self.dihedral_type_numbers]
- break
- self.processor(context)
-
- def processor(self, context):
- '''processor'''
- self.h_atom_a = [0] * self.dihedral_numbers
- self.h_atom_b = [0] * self.dihedral_numbers
- self.h_lj_scale_factor = [0] * self.dihedral_numbers
- self.h_cf_scale_factor = [0] * self.dihedral_numbers
- nb14_numbers = 0
- 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):
- tempa = information[i * 5 + 0]
- tempi = information[i * 5 + 1]
- tempi2 = information[i * 5 + 2]
- tempb = information[i * 5 + 3]
- tempi = information[i * 5 + 4]
-
- tempi -= 1
- if tempi2 > 0:
- self.h_atom_a[nb14_numbers] = tempa / 3
- self.h_atom_b[nb14_numbers] = abs(tempb / 3)
- self.h_lj_scale_factor[nb14_numbers] = self.lj_scale_type[tempi]
- if self.h_lj_scale_factor[nb14_numbers] != 0:
- self.h_lj_scale_factor[nb14_numbers] = 1.0 / self.h_lj_scale_factor[nb14_numbers]
- self.h_cf_scale_factor[nb14_numbers] = self.cf_scale_type[tempi]
- if self.h_cf_scale_factor[nb14_numbers] != 0:
- self.h_cf_scale_factor[nb14_numbers] = 1.0 / self.h_cf_scale_factor[nb14_numbers]
- nb14_numbers += 1
- 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):
- tempa = information[(i - self.dihedral_with_hydrogen) * 5 + 0]
- tempi = information[(i - self.dihedral_with_hydrogen) * 5 + 1]
- tempi2 = information[(i - self.dihedral_with_hydrogen) * 5 + 2]
- tempb = information[(i - self.dihedral_with_hydrogen) * 5 + 3]
- tempi = information[(i - self.dihedral_with_hydrogen) * 5 + 4]
-
- tempi -= 1
- if tempi2 > 0:
- self.h_atom_a[nb14_numbers] = tempa / 3
- self.h_atom_b[nb14_numbers] = abs(tempb / 3)
- self.h_lj_scale_factor[nb14_numbers] = self.lj_scale_type[tempi]
- if self.h_lj_scale_factor[nb14_numbers] != 0:
- self.h_lj_scale_factor[nb14_numbers] = 1.0 / self.h_lj_scale_factor[nb14_numbers]
- self.h_cf_scale_factor[nb14_numbers] = self.cf_scale_type[tempi]
- if self.h_cf_scale_factor[nb14_numbers] != 0:
- self.h_cf_scale_factor[nb14_numbers] = 1.0 / self.h_cf_scale_factor[nb14_numbers]
- nb14_numbers += 1
- break
-
- self.nb14_numbers = nb14_numbers
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