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Add KGD net #23

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Jun 14, 2022
Merged

Add KGD net #23

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42 changes: 37 additions & 5 deletions pycofbuilder/building_block.py
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ def __init__(self, name=None, lib='bb_lib', verbosity=False):
self.get_BB()

def get_BB(self):
'''Automatically read or creats a buiding block based on its name'''
'''Automatically read or create a buiding block based on its name'''
simm_check, nucleo_check, conector_check, radicals_check = self.check_existence()

if simm_check and nucleo_check and conector_check and radicals_check:
Expand All @@ -58,6 +58,9 @@ def get_BB(self):
if simmetry == 'C4':
self.create_C4_BB(nucleo, conector, radicals[0], radicals[1], radicals[2], radicals[3], radicals[4], radicals[5])
self.save()
if simmetry == 'C6':
self.create_C6_BB(nucleo, conector, radicals[0], radicals[1], radicals[2], radicals[3], radicals[4], radicals[5])
self.save()

def n_atoms(self):
''' Returns the number of atoms in the unitary cell'''
Expand Down Expand Up @@ -366,6 +369,29 @@ def create_C4_BB(self, nucleo_name='BENZ', conector='CHO', R1='H', R2='H', R3='H
self.connectivity = len([i for i in self.atom_labels if 'X' in i])
self.align_to()
self.calculate_size()

def create_C6_BB(self, nucleo_name='BENZ', conector='CHO', R1='H', R2='H', R3='H', R4='H', R5='H', R6='H', R7='H', R8='H', R9='H'):
'''Create a building block with C4 simmetry'''

self.name = f'C6_{nucleo_name}_{conector}'

self.atom_labels, self.atom_pos = Tools.read_gjf_file(os.path.join(self.main_path, 'nucleo', 'C6'), nucleo_name)

self.centralize_molecule()

self.add_connection_group(conector)

R_list_names = [R1, R2, R3, R4, R5, R6, R7, R8, R9]
R_list_labels = ['R1', 'R2', 'R3', 'R4', 'R5', 'R6', 'R7', 'R8', 'R9']

for i in range(len(R_list_names)):
if R_list_labels[i] in self.atom_labels:
self.add_R_group(R_list_names[i], R_list_labels[i])
self.name += f'_{R_list_names[i]}'

self.connectivity = len([i for i in self.atom_labels if 'X' in i])
self.align_to()
self.calculate_size()

def save(self, extension='xyz'):

Expand All @@ -388,8 +414,9 @@ def get_available_nucleo(self):
C2_list = [i.rstrip('.gjf') for i in os.listdir(os.path.join(self.main_path, 'nucleo', 'C2')) if '.gjf' in i]
C3_list = [i.rstrip('.gjf') for i in os.listdir(os.path.join(self.main_path, 'nucleo', 'C3')) if '.gjf' in i]
C4_list = [i.rstrip('.gjf') for i in os.listdir(os.path.join(self.main_path, 'nucleo', 'C4')) if '.gjf' in i]
C6_list = [i.rstrip('.gjf') for i in os.listdir(os.path.join(self.main_path, 'nucleo', 'C6')) if '.gjf' in i]

return C2_list, C3_list, C4_list
return C2_list, C3_list, C4_list, C6_list

def get_available_R(self):

Expand Down Expand Up @@ -417,8 +444,8 @@ def check_existence(self):
conector = name[2]
radicals = name[3:]

if simm not in ['C2', 'C3', 'C4']:
print('ERROR!: Building Block simmetry must be C2, C3 or C4.')
if simm not in ['C2', 'C3', 'C4', 'C6']:
print('ERROR!: Building Block simmetry must be C2, C3, C4, or C6.')
simm_check = False

if simm == 'C2':
Expand All @@ -436,6 +463,11 @@ def check_existence(self):
if nucleo not in list:
print(f'ERROR!: {nucleo} not available! Available nucleos with C4 simmetry is {list}')
nucleo_check = False
if simm == 'C6':
list = self.get_available_nucleo()[3]
if nucleo not in list:
print(f'ERROR!: {nucleo} not available! Available nucleos with C6 simmetry is {list}')
nucleo_check = False

if conector not in self.get_available_conector():
print(f'ERROR! {conector} is not a available conector. Available list: {self.get_available_conector()}')
Expand Down Expand Up @@ -519,4 +551,4 @@ def get_tetrapodal_squared_NH2(self):

files_list = os.listdir(self.lib_path)

return [i.rstrip('.xyz') for i in files_list if 'C4' == i.split('_')[0] and 'NH2' in i.split('_')[2]]
return [i.rstrip('.xyz') for i in files_list if 'C4' == i.split('_')[0] and 'NH2' in i.split('_')[2]]
77 changes: 77 additions & 0 deletions pycofbuilder/data/nucleo/C6/HEXB.gjf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,77 @@
# pbepbe/3-21g/auto geom

Title Card Required

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