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Add more terminal groups #36

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Oct 16, 2023
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
__pycache__/
*.py[cod]
*$py.class
.DS_Store

# C extensions
*.so
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@
from .methyl import Methyl
from .toluene import Toluene
from .trifluoromethyl import Trifluoromethyl
from .aniline import Aniline
39 changes: 39 additions & 0 deletions surface_coatings/monomers/mnbdac/terminal_groups/aniline.mol2
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
@<TRIPOS>MOLECULE
RES
14 14 1 0 1
SMALL
NO_CHARGES
@<TRIPOS>CRYSIN
10.8923 9.1115 6.7245 90.0000 90.0000 90.0000 1 1
@<TRIPOS>ATOM
1 N 2.3241 -0.1626 -0.0120 N 1 RES
2 C 0.8976 -0.0628 -0.0046 C 1 RES
3 C 0.1177 -1.1233 0.4813 C 1 RES
4 C -1.2775 -1.0242 0.4879 C 1 RES
5 C -1.8996 0.1329 0.0098 C 1 RES
6 C -1.1273 1.1924 -0.4755 C 1 RES
7 C 0.2681 1.0963 -0.4833 C 1 RES
8 H 2.8017 -1.0213 0.3422 H 1 RES
9 H 2.9130 0.6214 -0.3717 H 1 RES
10 H 0.5901 -2.0236 0.8537 H 1 RES
11 H -1.8761 -1.8440 0.8634 H 1 RES
12 H -2.9793 0.2085 0.0153 H 1 RES
13 H -1.6098 2.0879 -0.8454 H 1 RES
14 H 0.8574 1.9224 -0.8612 H 1 RES
@<TRIPOS>BOND
1 1 2 1
2 1 8 1
3 1 9 1
4 2 3 1
5 2 7 1
6 3 4 1
7 3 10 1
8 4 5 1
9 4 11 1
10 5 6 1
11 5 12 1
12 6 7 1
13 6 13 1
14 7 14 1
@<TRIPOS>SUBSTRUCTURE
1 RES 1 RESIDUE 0 **** ROOT 0
19 changes: 19 additions & 0 deletions surface_coatings/monomers/mnbdac/terminal_groups/aniline.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
"""Toluene terminal group class."""
import mbuild as mb


class Aniline(mb.Compound):
"""Aniline terminal group class."""

def __init__(self):
super().__init__()
mb.load(
"aniline.mol2",
compound=self,
backend="gmso",
relative_to_module=self.__module__,
infer_hierarchy=False,
)

self.remove(self[11])
self.labels["terminal"] = self["Compound[0]"].labels.pop("port[1]")
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