def assign_torsion_types(cgmodel, torsion_list):
"""Internal function for assigning torsion types"""
torsion_types = [] # List of torsion types for each torsion in torsion_list
torsion_array = np.zeros((len(torsion_list),4))
# Relevant torsion types are added to a dictionary as they are discovered
torsion_dict = {}
# Create an inverse dictionary for getting torsion string name from integer type
inv_torsion_dict = {}
# Counter for number of torsion types found:
i_torsion_type = 0
for i in range(len(torsion_list)):
torsion_array[i,0] = torsion_list[i][0]
torsion_array[i,1] = torsion_list[i][1]
torsion_array[i,2] = torsion_list[i][2]
torsion_array[i,3] = torsion_list[i][3]
particle_types = [
CGModel.get_particle_type_name(cgmodel,torsion_list[i][0]),
CGModel.get_particle_type_name(cgmodel,torsion_list[i][1]),
CGModel.get_particle_type_name(cgmodel,torsion_list[i][2]),
CGModel.get_particle_type_name(cgmodel,torsion_list[i][3])
]
string_name = ""
reverse_string_name = ""
for particle in particle_types:
string_name += f"{particle}_"
string_name = string_name[:-1]
for particle in reversed(particle_types):
reverse_string_name += f"{particle}_"
reverse_string_name = reverse_string_name[:-1]
if (string_name in torsion_dict.keys()) == False:
# New torsion type found, add to torsion dictionary
i_torsion_type += 1
torsion_dict[string_name] = i_torsion_type
torsion_dict[reverse_string_name] = i_torsion_type
# For inverse dict we will use only the forward name based on first encounter
inv_torsion_dict[str(i_torsion_type)] = string_name
# print(f"adding new torsion type {i_torsion_type}: {string_name} to dictionary")
# print(f"adding reverse version {i_torsion_type}: {reverse_string_name} to dictionary")
torsion_types.append(torsion_dict[string_name])
# Sort torsions by type into separate sub arrays for mdtraj compute_dihedrals
torsion_sub_arrays = {}
for i in range(i_torsion_type):
torsion_sub_arrays[str(i+1)] = np.zeros((torsion_types.count(i+1),4))
# Counter vector for all angle types
n_i = np.zeros((i_torsion_type,1), dtype=int)
for i in range(len(torsion_list)):
torsion_sub_arrays[str(torsion_types[i])][n_i[torsion_types[i]-1],:] = torsion_array[i,:]
n_i[torsion_types[i]-1] += 1
return torsion_types, torsion_array, torsion_sub_arrays, n_i, i_torsion_type, torsion_dict, inv_torsion_dict
def assign_bond_types(cgmodel, bond_list):
"""Internal function for assigning bond types"""
bond_types = []
bond_array = np.zeros((len(bond_list), 2))
# Relevant bond types are added to a dictionary as they are discovered
bond_dict = {}
# Create an inverse dictionary for getting bond string name from integer type
inv_bond_dict = {}
# Counter for number of bond types found:
i_bond_type = 0
# Assign bond types:
for i in range(len(bond_list)):
bond_array[i, 0] = bond_list[i][0]
bond_array[i, 1] = bond_list[i][1]
particle_types = [
CGModel.get_particle_type_name(cgmodel, bond_list[i][0]),
CGModel.get_particle_type_name(cgmodel, bond_list[i][1])
]
string_name = ""
reverse_string_name = ""
for particle in particle_types:
string_name += f"{particle}_"
string_name = string_name[:-1]
for particle in reversed(particle_types):
reverse_string_name += f"{particle}_"
reverse_string_name = reverse_string_name[:-1]
if (string_name in bond_dict.keys()) == False:
# New bond type found, add to bond dictionary
i_bond_type += 1
bond_dict[string_name] = i_bond_type
bond_dict[reverse_string_name] = i_bond_type
# For inverse dict we will use only the forward name based on first encounter
inv_bond_dict[str(i_bond_type)] = string_name
# print(f"adding new bond type {i_bond_type}: {string_name} to dictionary")
# print(f"adding reverse version {i_bond_type}: {reverse_string_name} to dictionary")
bond_types.append(bond_dict[string_name])
# Sort bonds by type into separate sub arrays for mdtraj compute_distances
bond_sub_arrays = {}
for i in range(i_bond_type):
bond_sub_arrays[str(i + 1)] = np.zeros((bond_types.count(i + 1), 2))
# Counter vector for all bond types
n_i = np.zeros((i_bond_type, 1), dtype=int)
for i in range(len(bond_list)):
bond_sub_arrays[str(bond_types[i])][n_i[bond_types[i] -
1], :] = bond_array[i, :]
n_i[bond_types[i] - 1] += 1
return bond_types, bond_array, bond_sub_arrays, n_i, i_bond_type, bond_dict, inv_bond_dict
