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Changes to Globally Forbidden Structures to account for N chemistry #120

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Changes to Globally Forbidden Structures to account for N chemistry #120

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e1fdf34
Ethylamine library
alongd Aug 9, 2016
d15d2a1
changed Globally Forbidden Structure file to account for N chemistry,…
alongd Aug 9, 2016
b317b8e
Added a comment to forbiddenStructures.py
alongd Aug 12, 2016
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75 changes: 2 additions & 73 deletions input/forbiddenStructures.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
#!/usr/bin/env python
# encoding: utf-8

# IMPORTANT REQUEST: If you add a globally forbidden group, please comment why it is forbidden and give example\s.

name = ""
shortDesc = u""
longDesc = u"""
Expand Down Expand Up @@ -35,37 +37,6 @@
""",
)

entry(
label = "N_monorad_3singleBonds",
group =
"""
1 N u1 p0 {2,S} {3,S} {4,S}
2 R ux {1,S}
3 R ux {1,S}
4 R ux {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""

""",
)

entry(
label = "N_birad_singlet_2singleBonds",
group =
"""
1 N u0 p1 {2,S} {3,S}
2 R ux {1,S}
3 R ux {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""

""",
)

entry(
label = "N_birad_triplet_2singleBonds",
group =
Expand Down Expand Up @@ -168,34 +139,6 @@
""",
)

entry(
label = "Carbene_D_triplet",
group =
"""
1 C u2 p0 {2,D}
2 C u0 {1,D}
""",
shortDesc = u"""""",
longDesc =
u"""

""",
)

entry(
label = "Carbene_D_singlet",
group =
"""
1 C u0 p1 {2,D}
2 C u0 {1,D}
""",
shortDesc = u"""""",
longDesc =
u"""

""",
)

entry(
label = "Carbene_S_triplet",
group =
Expand All @@ -210,20 +153,6 @@
""",
)

entry(
label = "Carbene_S_singlet",
group =
"""
1 C u0 p1 {2,S}
2 R!H u0 {1,S}
""",
shortDesc = u"""""",
longDesc =
u"""

""",
)

entry(
label = "O3",
group =
Expand Down
193 changes: 193 additions & 0 deletions input/kinetics/libraries/Ethylamine/dictionary.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,193 @@
NCC
1 N u0 p1 c0 {2,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {3,S} {6,S} {7,S}
3 C u0 p0 c0 {2,S} {8,S} {9,S} {10,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {2,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}

CH2CH2NH2
multiplicity 2
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,S} {6,S} {7,S}
5 N u0 p1 c0 {4,S} {8,S} {9,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {4,S}
8 H u0 p0 c0 {5,S}
9 H u0 p0 c0 {5,S}

CH3CHNH2
multiplicity 2
1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S}
2 C u1 p0 c0 {1,S} {3,S} {4,S}
3 H u0 p0 c0 {2,S}
4 N u0 p1 c0 {2,S} {8,S} {9,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {4,S}
9 H u0 p0 c0 {4,S}

CH3CH2NH
multiplicity 2
1 C u0 p0 c0 {2,S} {5,S} {6,S} {7,S}
2 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
3 N u1 p1 c0 {2,S} {4,S}
4 H u0 p0 c0 {3,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {2,S}

H
multiplicity 2
1 H u1 p0 c0

H2
1 H u0 p0 c0 {2,S}
2 H u0 p0 c0 {1,S}

CH3
multiplicity 2
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}

CH4
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}

NH2
multiplicity 2
1 N u1 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}

NH3
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}

C2H4
1 C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u0 p0 c0 {1,D} {5,S} {6,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}

CH2CHNH2
1 C u0 p0 c0 {2,S} {3,S} {4,D}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,D} {5,S} {6,S}
5 N u0 p1 c0 {4,S} {7,S} {8,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {5,S}
8 H u0 p0 c0 {5,S}

CH2NH
1 C u0 p0 c0 {2,S} {3,S} {4,D}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 N u0 p1 c0 {1,D} {5,S}
5 H u0 p0 c0 {4,S}

CH2NH2
multiplicity 2
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 N u0 p1 c0 {1,S} {5,S} {6,S}
5 H u0 p0 c0 {4,S}
6 H u0 p0 c0 {4,S}

N2H4
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 N u0 p1 c0 {1,S} {5,S} {6,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {2,S}

N2H3
multiplicity 2
1 N u0 p1 c0 {2,S} {4,S} {5,S}
2 N u1 p1 c0 {1,S} {3,S}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}

CH2CHNH
multiplicity 2
1 C u1 p0 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,D} {6,S}
5 N u0 p1 c0 {4,D} {7,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {5,S}

CH3CHN
multiplicity 2
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,D} {7,S}
3 N u1 p1 c0 {2,D}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}

CH2CNH
1 C u0 p0 c0 {2,D} {4,S} {5,S}
2 C u0 p0 c0 {1,D} {3,D}
3 N u0 p1 c0 {2,D} {6,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {3,S}

CH3CHNH
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,D} {7,S}
3 N u0 p1 c0 {2,D} {8,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {3,S}

HCN
1 C u0 p0 c0 {2,S} {3,T}
2 H u0 p0 c0 {1,S}
3 N u0 p1 c0 {1,T}

CH3CN
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,T}
3 N u0 p1 c0 {2,T}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}

OH
multiplicity 2
1 O u1 p2 c0 {2,S}
2 H u0 p0 c0 {1,S}

H2O
1 O u0 p2 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}

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