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Merge pull request #92 from ReactionMechanismGenerator/ipsoDatabase
Cyclic database improvements
2 parents 42b7ccc + 3c5c4cd commit eeb8c98

15 files changed

Lines changed: 7899 additions & 578 deletions

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‎input/kinetics/families/Diels_alder_addition/groups.py‎

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""",
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)
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forbidden(
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label= 'benzyl_isomer1',
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group=
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"""
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1 C 0 {2,D}
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2 C 0 {1,D} {3,S} {7,S}
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3 C 0 {2,S} {4,D}
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4 C 0 {3,D} {5,S}
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5 C 1 {4,S} {6,S}
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6 C 0 {5,S} {7,D}
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7 C 0 {2,S} {6,D}
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"""
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)
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forbidden(
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label= 'benzyl_isomer2',
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group=
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"""
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1 C 0 {2,D}
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2 C 0 {1,D} {3,S} {7,S}
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3 C 1 {2,S} {4,S}
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4 C 0 {3,S} {5,D}
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5 C 0 {4,D} {6,S}
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6 C 0 {5,S} {7,D}
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7 C 0 {2,S} {6,D}
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"""
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)

‎input/kinetics/families/H_shift_cyclopentadiene/training/dictionary.txt‎

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C9H8-2
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1 *2 C u0 p0 c0 {2,S} {4,S} {10,S} {11,S}
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2 *1 C u0 p0 c0 {1,S} {3,D} {5,S}
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3 *5 C u0 p0 c0 {2,D} {6,S} {7,S}
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4 *3 C u0 p0 c0 {1,S} {6,D} {12,S}
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5 C u0 p0 c0 {2,S} {8,D} {13,S}
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6 *4 C u0 p0 c0 {3,S} {4,D} {14,S}
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7 C u0 p0 c0 {3,S} {9,D} {15,S}
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8 C u0 p0 c0 {5,D} {9,S} {17,S}
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9 C u0 p0 c0 {7,D} {8,S} {16,S}
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10 *6 H u0 p0 c0 {1,S}
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11 H u0 p0 c0 {1,S}
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12 H u0 p0 c0 {4,S}
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13 H u0 p0 c0 {5,S}
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14 H u0 p0 c0 {6,S}
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15 H u0 p0 c0 {7,S}
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16 H u0 p0 c0 {9,S}
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17 H u0 p0 c0 {8,S}
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C7H9
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multiplicity 2
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1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {8,S}
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2 C u0 p0 c0 {1,S} {7,S} {9,S} {10,S}
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3 *2 C u0 p0 c0 {1,S} {5,D} {11,S}
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4 *5 C u0 p0 c0 {1,S} {6,D} {12,S}
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5 *3 C u0 p0 c0 {3,D} {6,S} {13,S}
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6 *4 C u0 p0 c0 {4,D} {5,S} {14,S}
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7 C u1 p0 c0 {2,S} {15,S} {16,S}
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8 *6 H u0 p0 c0 {1,S}
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9 H u0 p0 c0 {2,S}
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10 H u0 p0 c0 {2,S}
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11 H u0 p0 c0 {3,S}
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12 H u0 p0 c0 {4,S}
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13 H u0 p0 c0 {5,S}
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14 H u0 p0 c0 {6,S}
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15 H u0 p0 c0 {7,S}
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16 H u0 p0 c0 {7,S}
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C7H9-4
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multiplicity 2
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1 C u0 p0 c0 {3,S} {7,S} {9,S} {10,S}
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2 *2 C u0 p0 c0 {4,S} {5,S} {8,S} {11,S}
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3 *5 C u0 p0 c0 {1,S} {4,D} {6,S}
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4 *1 C u0 p0 c0 {2,S} {3,D} {12,S}
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5 *3 C u0 p0 c0 {2,S} {6,D} {13,S}
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6 *4 C u0 p0 c0 {3,S} {5,D} {14,S}
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7 C u1 p0 c0 {1,S} {15,S} {16,S}
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8 *6 H u0 p0 c0 {2,S}
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9 H u0 p0 c0 {1,S}
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10 H u0 p0 c0 {1,S}
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11 H u0 p0 c0 {2,S}
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12 H u0 p0 c0 {4,S}
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13 H u0 p0 c0 {5,S}
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14 H u0 p0 c0 {6,S}
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15 H u0 p0 c0 {7,S}
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16 H u0 p0 c0 {7,S}
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C9H8
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1 *1 C u0 p0 c0 {2,S} {3,S} {4,S} {10,S}
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2 *5 C u0 p0 c0 {1,S} {5,D} {6,S}
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3 *2 C u0 p0 c0 {1,S} {7,D} {11,S}
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4 C u0 p0 c0 {1,S} {8,D} {12,S}
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5 *4 C u0 p0 c0 {2,D} {7,S} {13,S}
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6 C u0 p0 c0 {2,S} {9,D} {15,S}
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7 *3 C u0 p0 c0 {3,D} {5,S} {14,S}
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8 C u0 p0 c0 {4,D} {9,S} {17,S}
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9 C u0 p0 c0 {6,D} {8,S} {16,S}
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10 *6 H u0 p0 c0 {1,S}
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11 H u0 p0 c0 {3,S}
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12 H u0 p0 c0 {4,S}
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13 H u0 p0 c0 {5,S}
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14 H u0 p0 c0 {7,S}
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15 H u0 p0 c0 {6,S}
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16 H u0 p0 c0 {9,S}
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17 H u0 p0 c0 {8,S}
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C7H9-3
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multiplicity 2
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1 *1 C u0 p0 c0 {3,S} {4,S} {8,S} {9,S}
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2 C u0 p0 c0 {3,S} {7,S} {10,S} {11,S}
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3 *5 C u0 p0 c0 {1,S} {2,S} {5,D}
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4 *2 C u0 p0 c0 {1,S} {6,D} {12,S}
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5 *4 C u0 p0 c0 {3,D} {6,S} {13,S}
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6 *3 C u0 p0 c0 {4,D} {5,S} {14,S}
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7 C u1 p0 c0 {2,S} {15,S} {16,S}
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8 *6 H u0 p0 c0 {1,S}
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9 H u0 p0 c0 {1,S}
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10 H u0 p0 c0 {2,S}
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11 H u0 p0 c0 {2,S}
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12 H u0 p0 c0 {4,S}
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13 H u0 p0 c0 {5,S}
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14 H u0 p0 c0 {6,S}
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15 H u0 p0 c0 {7,S}
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16 H u0 p0 c0 {7,S}
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C7H9-2
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multiplicity 2
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1 *2 C u0 p0 c0 {3,S} {4,S} {8,S} {11,S}
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2 C u0 p0 c0 {3,S} {7,S} {9,S} {10,S}
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3 *1 C u0 p0 c0 {1,S} {2,S} {5,D}
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4 *3 C u0 p0 c0 {1,S} {6,D} {12,S}
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5 *5 C u0 p0 c0 {3,D} {6,S} {13,S}
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6 *4 C u0 p0 c0 {4,D} {5,S} {14,S}
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7 C u1 p0 c0 {2,S} {15,S} {16,S}
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8 *6 H u0 p0 c0 {1,S}
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9 H u0 p0 c0 {2,S}
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10 H u0 p0 c0 {2,S}
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11 H u0 p0 c0 {1,S}
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12 H u0 p0 c0 {4,S}
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13 H u0 p0 c0 {5,S}
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14 H u0 p0 c0 {6,S}
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15 H u0 p0 c0 {7,S}
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16 H u0 p0 c0 {7,S}
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‎input/kinetics/families/H_shift_cyclopentadiene/training/reactions.py‎

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Put kinetic parameters for reactions to use as a training set for fitting
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group additivity values in this file.
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"""
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entry(
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index = 1,
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label = "C7H9 <=> C7H9-2",
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degeneracy = 1,
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kinetics = Arrhenius(A=(4.39e+07, 's^-1'), n=1.58, Ea=(21.7, 'kcal/mol'), T0=(1, 'K')),
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rank = 3,
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shortDesc = u"""Training reaction from kinetics library: vinylCPD_H""",
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longDesc =
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u"""
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Taken from entry: addB <=> product21
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""",
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)
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entry(
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index = 2,
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label = "C7H9-3 <=> C7H9-4",
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degeneracy = 1,
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kinetics = Arrhenius(A=(5.06e+07, 's^-1'), n=1.74, Ea=(24.3, 'kcal/mol'), T0=(1, 'K')),
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rank = 3,
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shortDesc = u"""Training reaction from kinetics library: vinylCPD_H""",
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longDesc =
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u"""
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Taken from entry: product21 <=> product22
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""",
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)
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entry(
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index = 3,
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label = "C9H8 <=> C9H8-2",
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degeneracy = 1,
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kinetics = Arrhenius(A=(5.2e+09, 's^-1'), n=0.96, Ea=(6.8, 'kcal/mol'), T0=(1, 'K')),
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rank = 3,
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shortDesc = u"""Training reaction from kinetics library: C10H11""",
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longDesc =
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u"""
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Taken from entry: pdt22 <=> INDENE
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""",
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)
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