Generating COF structures from custom Building Blocks
To create a COF structure from custom Building Blocks, you need the desired Building Block in the .xyz, .gjf, or .cjson format, as in the example below:
9
T3 building block
C 0.9828406 0.9992759 0.0000000
C -0.3739780 1.3508029 0.0000000
C -1.3568187 0.3515270 0.0000000
C -0.9828406 -0.9992759 0.0000000
C 0.3739780 -1.3508029 0.0000000
C 1.3568187 -0.3515270 0.0000000
C -1.9996089 -2.0330469 0.0000000
H -1.8107021 -3.1273182 0.0000000
C 2.7604747 -0.7151886 0.0000000
H 3.6136881 -0.0044549 0.0000000
C -0.7608658 2.7482355 0.0000000
H -1.8029860 3.1317731 0.0000000
O 1.9855845 2.0187880 0.0000000
H 1.7077038 3.0013254 0.0000000
O -2.7411139 0.7101726 0.0000000
H -3.4530759 -0.0217478 0.0000000
O 0.7555294 -2.7289606 0.0000000
H 1.7453721 -2.9795776 0.0000000
X 0.0000000 3.7112465 0.0000000
X -3.2140338 -1.8556233 0.0000000
X 3.2140338 -1.8556233 0.0000000
# hf/3-21g T3 building block 0 1 C 0.9828406 0.9992759 0.0000000 C -0.3739780 1.3508029 0.0000000 C -1.3568187 0.3515270 0.0000000 C -0.9828406 -0.9992759 0.0000000 C 0.3739780 -1.3508029 0.0000000 C 1.3568187 -0.3515270 0.0000000 C -1.9996089 -2.0330469 0.0000000 H -1.8107021 -3.1273182 0.0000000 C 2.7604747 -0.7151886 0.0000000 H 3.6136881 -0.0044549 0.0000000 C -0.7608658 2.7482355 0.0000000 H -1.8029860 3.1317731 0.0000000 O 1.9855845 2.0187880 0.0000000 H 1.7077038 3.0013254 0.0000000 O -2.7411139 0.7101726 0.0000000 H -3.4530759 -0.0217478 0.0000000 O 0.7555294 -2.7289606 0.0000000 H 1.7453721 -2.9795776 0.0000000 X 0.0000000 3.7112465 0.0000000 X -3.2140338 -1.8556233 0.0000000 X 3.2140338 -1.8556233 0.0000000
{
"chemical json": 1,
"name": "T3_BENZ_CHO_OH",
"formula": "C9O3H6X3",
"atoms": {
"elements": {
"type": [
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"X",
"H",
"C",
"X",
"H",
"C",
"X",
"H",
"O",
"H",
"O",
"H",
"O",
"H"
],
"number": [
6,
6,
6,
6,
6,
6,
6,
0.0,
1,
6,
0.0,
1,
6,
0.0,
1,
8,
1,
8,
1,
8,
1
]
},
"coords": {
"3d": [
0.9828406,
0.9992759,
0.0,
-0.373978,
1.3508029,
0.0,
-1.3568187,
0.351527,
0.0,
-0.9828406,
-0.9992759,
0.0,
0.373978,
-1.3508029,
0.0,
1.3568187,
-0.351527,
0.0,
-1.9996089,
-2.0330469,
0.0,
-3.2140338,
-1.8556233,
0.0,
-1.8107021,
-3.1273182,
0.0,
2.7604747,
-0.7151886,
0.0,
3.2140338,
-1.8556233,
0.0,
3.6136881,
-0.0044549,
0.0,
-0.7608658,
2.7482355,
0.0,
0.0,
3.7112465,
0.0,
-1.802986,
3.1317731,
0.0,
1.9855845,
2.018788,
0.0,
1.7077038,
3.0013254,
0.0,
-2.7411139,
0.7101726,
0.0,
-3.4530759,
-0.0217478,
0.0,
0.7555294,
-2.7289606,
0.0,
1.7453721,
-2.9795776,
0.0
]
}
},
"partialCharges": {},
"results": [],
"properties": {
"totalCharge": 0,
"spinMultiplicity": 1
}
}
Then, you will need to create a BuildingBlock object from the desired Building Block. Don’t forget to add the X atoms on the structure where the building blocks will be connected to each other.
This method requires the path to the Building Block file and the name of the Building Block file and the type of connector.
The connector atom is the atom that will be used to determine the correct atom to connect the Building Blocks.
The method to create the BuildingBlock object is shown below:
import pycofbuilder as pcb
building_block = pcb.BuildingBlock(
name='BB_T3.xyz',
out_dir='.',
conector='NH2'
)
Then, you can use the from_building_blocks method to generate the COF structure.
The method requires the following parameters: the Building Blocks, the net type and the stacking/interpenetration degree.
The method to create the COF structure is shown below:
import pycofbuilder as pcb
# Create the building blocks
bb_t3 = pcb.BuildingBlock('BB_T3.xyz', out_dir='.', conector='NH2')
bb_l2 = pcb.BuildingBlock('BB_L2.xyz', out_dir='.', conector='CHO')
# Create the structure
cof = pcb.Framework()
cof.from_building_blocks(bb_t3, bb_l2, 'HCB_A', 'AA')