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Merged
nyee merged 16 commits into from
Jul 27, 2016
Merged

Add evaluateKinetics.py script to testing folder #117

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9fd81a5
Add the evaluateKinetics.py script to the testing folder
connie Jul 22, 2016
7adbe25
Gitignore kinetics evaluation folder
connie Jul 22, 2016
878c4ef
Get rid of try/except blocks top see what is goin on
connie Jul 22, 2016
2984803
Deleted missingGroups attribute. Updated such that this works on cur…
connie Jul 22, 2016
c47a198
Fix compareNIST function
connie Jul 22, 2016
498113d
Fix the obtainKineticsFamilyStatistics
connie Jul 22, 2016
f255c7f
Change node description to rate rule because that's what it is
connie Jul 22, 2016
f0db6ff
Fix leaveOneOut test and add some time stamping for the leaveOneTest
connie Jul 22, 2016
e90692c
Improve print statements and change script to test all families by de…
connie Jul 22, 2016
797bece
Fix NIST reactions
connie Jul 23, 2016
53d7907
More comment fixing in script
connie Jul 26, 2016
cb2f649
Add argument for performing leaveOneOutTest without averaging
connie Jul 26, 2016
20c2ee9
Remove the cutoff argument for in analyzeForParity
connie Jul 27, 2016
9edd391
Add an argument `pruneForExact` in compareNIST to return only exact R…
connie Jul 27, 2016
8f0c922
Safer re.escape for finding depository using its label
connie Jul 27, 2016
78e42c5
Some fixed docstrings and lengthier explanations
connie Jul 27, 2016
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5 changes: 4 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -12,4 +12,7 @@
# C-Compiled scripts
*.pyc

*.ipynb_checkpoints
*.ipynb_checkpoints

# evaluate kinetics folder stuff
testing/eval/*
4 changes: 2 additions & 2 deletions input/kinetics/families/Intra_R_Add_Endocyclic/NIST/dictionary.txt
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
C6H11-2
multiplicity 2
1 *4 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
2 *6 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
3 *1 C u0 p0 c0 {1,S} {5,S} {11,S} {12,S}
4 *5 C u0 p0 c0 {2,S} {6,S} {13,S} {14,S}
5 *3 C u0 p0 c0 {3,S} {6,S} {15,S} {16,S}
Expand Down Expand Up @@ -140,7 +140,7 @@ multiplicity 2

C6H11
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 *5 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
3 *4 C u0 p0 c0 {1,S} {5,S} {11,S} {12,S}
4 *2 C u0 p0 c0 {2,S} {6,D} {13,S}
Expand Down
2 changes: 1 addition & 1 deletion input/kinetics/families/R_Addition_MultipleBond/NIST/reactions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4333,7 +4333,7 @@
Ea = (100.6, 'kJ/mol'),
T0 = (1, 'K'),
Tmin = (400, 'K'),
Tmax = (400, 'K'),
Tmax = (2000, 'K'),
),
reference = Article(
authors = ["Hoyermann, K.", "Olzmann, M.", "Seeba, J.", "Viskolcz, B."],
Expand Down
64 changes: 32 additions & 32 deletions input/kinetics/families/intra_H_migration/NIST/dictionary.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ multiplicity 2
C5H11O2-2
multiplicity 2
1 *4 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {6,S} {8,S} {9,S}
2 *6 C u0 p0 c0 {1,S} {6,S} {8,S} {9,S}
3 C u0 p0 c0 {1,S} {10,S} {11,S} {12,S}
4 C u0 p0 c0 {1,S} {13,S} {14,S} {15,S}
5 *1 C u1 p0 c0 {1,S} {16,S} {17,S}
Expand All @@ -46,7 +46,7 @@ multiplicity 2
C4H9O
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
2 *6 C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
3 *2 C u0 p0 c0 {1,S} {10,S} {11,S} {12,S}
4 *4 C u0 p0 c0 {2,S} {9,S} {13,S} {14,S}
5 H u0 p0 c0 {1,S}
Expand All @@ -64,7 +64,7 @@ C7H15O
multiplicity 2
1 *2 C u0 p0 c0 {2,S} {5,S} {6,S} {8,S}
2 *5 C u0 p0 c0 {1,S} {3,S} {10,S} {11,S}
3 C u0 p0 c0 {2,S} {4,S} {12,S} {13,S}
3 *6 C u0 p0 c0 {2,S} {4,S} {12,S} {13,S}
4 *4 C u0 p0 c0 {3,S} {7,S} {9,S} {14,S}
5 C u0 p0 c0 {1,S} {15,S} {16,S} {17,S}
6 C u0 p0 c0 {1,S} {18,S} {19,S} {20,S}
Expand Down Expand Up @@ -205,7 +205,7 @@ multiplicity 2

C4H9O-2
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {6,S} {7,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {6,S} {7,S}
2 *4 C u0 p0 c0 {1,S} {4,S} {8,S} {9,S}
3 *5 C u0 p0 c0 {1,S} {5,S} {10,S} {11,S}
4 *1 C u1 p0 c0 {2,S} {12,S} {13,S}
Expand All @@ -223,7 +223,7 @@ multiplicity 2
C6H13O-10
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
2 *6 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
3 C u0 p0 c0 {1,S} {5,S} {11,S} {12,S}
4 *4 C u0 p0 c0 {2,S} {6,S} {13,S} {14,S}
5 C u0 p0 c0 {3,S} {15,S} {16,S} {17,S}
Expand Down Expand Up @@ -276,7 +276,7 @@ multiplicity 2

C6H11O2-4
multiplicity 2
1 C u0 p0 c0 {2,S} {4,S} {7,S} {9,S}
1 *6 C u0 p0 c0 {2,S} {4,S} {7,S} {9,S}
2 C u0 p0 c0 {1,S} {3,S} {10,S} {11,S}
3 C u0 p0 c0 {2,S} {5,S} {12,S} {13,S}
4 *4 C u0 p0 c0 {1,S} {6,S} {14,S} {15,S}
Expand Down Expand Up @@ -320,8 +320,8 @@ multiplicity 2

C6H11O2-2
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {7,S} {9,S}
2 C u0 p0 c0 {1,S} {4,S} {10,S} {11,S}
1 *7 C u0 p0 c0 {2,S} {3,S} {7,S} {9,S}
2 *6 C u0 p0 c0 {1,S} {4,S} {10,S} {11,S}
3 C u0 p0 c0 {1,S} {5,S} {12,S} {13,S}
4 *4 C u0 p0 c0 {2,S} {6,S} {14,S} {15,S}
5 C u0 p0 c0 {3,S} {6,S} {16,S} {17,S}
Expand All @@ -342,7 +342,7 @@ multiplicity 2

C6H11O2-3
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 *5 C u0 p0 c0 {1,S} {5,S} {10,S} {11,S}
3 C u0 p0 c0 {1,S} {6,S} {12,S} {13,S}
4 C u0 p0 c0 {5,S} {6,S} {14,S} {15,S}
Expand Down Expand Up @@ -387,7 +387,7 @@ multiplicity 2
C5H11O-6
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {4,S} {6,S} {7,S}
2 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
2 *6 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
3 *4 C u0 p0 c0 {2,S} {5,S} {10,S} {11,S}
4 C u0 p0 c0 {1,S} {12,S} {13,S} {14,S}
5 *1 C u1 p0 c0 {3,S} {15,S} {16,S}
Expand All @@ -406,7 +406,7 @@ multiplicity 2

C5H11O-4
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {4,S} {7,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {4,S} {7,S}
2 *4 C u0 p0 c0 {1,S} {5,S} {8,S} {9,S}
3 *5 C u0 p0 c0 {1,S} {6,S} {10,S} {11,S}
4 C u0 p0 c0 {1,S} {12,S} {13,S} {14,S}
Expand All @@ -426,7 +426,7 @@ multiplicity 2

C5H11O-5
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 *5 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
3 *4 C u0 p0 c0 {1,S} {5,S} {6,S} {11,S}
4 *2 C u0 p0 c0 {2,S} {12,S} {13,S} {14,S}
Expand All @@ -446,7 +446,7 @@ multiplicity 2

C5H11O-2
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 *4 C u0 p0 c0 {1,S} {5,S} {9,S} {10,S}
3 *5 C u0 p0 c0 {1,S} {6,S} {11,S} {12,S}
4 C u0 p0 c0 {5,S} {13,S} {14,S} {15,S}
Expand Down Expand Up @@ -519,7 +519,7 @@ multiplicity 2
C6H13O-8
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {4,S} {5,S} {7,S}
2 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
2 *6 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
3 *4 C u0 p0 c0 {2,S} {6,S} {10,S} {11,S}
4 C u0 p0 c0 {1,S} {12,S} {13,S} {14,S}
5 C u0 p0 c0 {1,S} {15,S} {16,S} {17,S}
Expand Down Expand Up @@ -607,7 +607,7 @@ multiplicity 2
1 *2 C u0 p0 c0 {3,S} {5,S} {6,S} {10,S}
2 *4 C u0 p0 c0 {4,S} {7,S} {8,S} {9,S}
3 *5 C u0 p0 c0 {1,S} {4,S} {11,S} {12,S}
4 C u0 p0 c0 {2,S} {3,S} {13,S} {14,S}
4 *6 C u0 p0 c0 {2,S} {3,S} {13,S} {14,S}
5 C u0 p0 c0 {1,S} {15,S} {16,S} {17,S}
6 C u0 p0 c0 {1,S} {18,S} {19,S} {20,S}
7 C u0 p0 c0 {2,S} {21,S} {22,S} {23,S}
Expand Down Expand Up @@ -665,8 +665,8 @@ multiplicity 2

C6H11O2
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 C u0 p0 c0 {1,S} {5,S} {10,S} {11,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 *7 C u0 p0 c0 {1,S} {5,S} {10,S} {11,S}
3 C u0 p0 c0 {1,S} {6,S} {12,S} {13,S}
4 *2 C u0 p0 c0 {5,S} {6,S} {9,S} {14,S}
5 *5 C u0 p0 c0 {2,S} {4,S} {15,S} {16,S}
Expand Down Expand Up @@ -783,7 +783,7 @@ multiplicity 2
C7H15O-4
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {4,S} {5,S} {8,S}
2 C u0 p0 c0 {1,S} {3,S} {9,S} {10,S}
2 *6 C u0 p0 c0 {1,S} {3,S} {9,S} {10,S}
3 *4 C u0 p0 c0 {2,S} {7,S} {11,S} {12,S}
4 C u0 p0 c0 {1,S} {13,S} {14,S} {15,S}
5 C u0 p0 c0 {1,S} {16,S} {17,S} {18,S}
Expand Down Expand Up @@ -828,7 +828,7 @@ multiplicity 2

C6H11-2
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 *5 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
3 *4 C u0 p0 c0 {1,S} {6,S} {11,S} {12,S}
4 *2 C u0 p0 c0 {2,S} {13,S} {14,S} {15,S}
Expand All @@ -851,7 +851,7 @@ multiplicity 2
1 *2 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 *5 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
3 C u0 p0 c0 {1,S} {5,S} {11,S} {12,S}
4 C u0 p0 c0 {2,S} {6,S} {13,S} {14,S}
4 *6 C u0 p0 c0 {2,S} {6,S} {13,S} {14,S}
5 C u0 p0 c0 {3,S} {16,S} {17,S} {18,S}
6 *4 C u0 p0 c0 {4,S} {15,S} {19,S} {20,S}
7 *3 H u0 p0 c0 {1,S}
Expand All @@ -872,7 +872,7 @@ multiplicity 2
C8H17O-2
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {4,S} {5,S} {9,S}
2 C u0 p0 c0 {1,S} {3,S} {10,S} {11,S}
2 *6 C u0 p0 c0 {1,S} {3,S} {10,S} {11,S}
3 *4 C u0 p0 c0 {2,S} {8,S} {12,S} {13,S}
4 C u0 p0 c0 {1,S} {14,S} {15,S} {16,S}
5 C u0 p0 c0 {1,S} {17,S} {18,S} {19,S}
Expand Down Expand Up @@ -929,7 +929,7 @@ multiplicity 2
C6H13O-7
multiplicity 2
1 *4 C u0 p0 c0 {2,S} {4,S} {5,S} {7,S}
2 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
2 *6 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
3 *5 C u0 p0 c0 {2,S} {6,S} {10,S} {11,S}
4 C u0 p0 c0 {1,S} {13,S} {14,S} {15,S}
5 C u0 p0 c0 {1,S} {16,S} {17,S} {18,S}
Expand All @@ -952,7 +952,7 @@ multiplicity 2
C5H11O2
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
2 *6 C u0 p0 c0 {1,S} {6,S} {7,S} {8,S}
3 *2 C u0 p0 c0 {1,S} {9,S} {10,S} {11,S}
4 C u0 p0 c0 {1,S} {12,S} {13,S} {14,S}
5 C u0 p0 c0 {1,S} {15,S} {16,S} {17,S}
Expand Down Expand Up @@ -990,7 +990,7 @@ multiplicity 2

C6H13O-6
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {8,S} {9,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {8,S} {9,S}
2 *4 C u0 p0 c0 {1,S} {6,S} {10,S} {11,S}
3 *5 C u0 p0 c0 {1,S} {7,S} {12,S} {13,S}
4 C u0 p0 c0 {6,S} {14,S} {15,S} {16,S}
Expand All @@ -1013,7 +1013,7 @@ multiplicity 2

C6H13O-9
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {8,S} {9,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {8,S} {9,S}
2 *4 C u0 p0 c0 {1,S} {4,S} {7,S} {10,S}
3 *5 C u0 p0 c0 {1,S} {5,S} {11,S} {12,S}
4 C u0 p0 c0 {2,S} {6,S} {13,S} {14,S}
Expand Down Expand Up @@ -1058,7 +1058,7 @@ C6H13O-5
multiplicity 2
1 *2 C u0 p0 c0 {2,S} {4,S} {5,S} {7,S}
2 *5 C u0 p0 c0 {1,S} {3,S} {8,S} {9,S}
3 C u0 p0 c0 {2,S} {6,S} {10,S} {11,S}
3 *6 C u0 p0 c0 {2,S} {6,S} {10,S} {11,S}
4 C u0 p0 c0 {1,S} {13,S} {14,S} {15,S}
5 C u0 p0 c0 {1,S} {16,S} {17,S} {18,S}
6 *4 C u0 p0 c0 {3,S} {12,S} {19,S} {20,S}
Expand Down Expand Up @@ -1098,7 +1098,7 @@ multiplicity 2
C6H13O-3
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {3,S} {9,S} {10,S}
2 C u0 p0 c0 {1,S} {4,S} {11,S} {12,S}
2 *6 C u0 p0 c0 {1,S} {4,S} {11,S} {12,S}
3 *2 C u0 p0 c0 {1,S} {5,S} {8,S} {13,S}
4 *4 C u0 p0 c0 {2,S} {6,S} {7,S} {14,S}
5 C u0 p0 c0 {3,S} {15,S} {16,S} {17,S}
Expand All @@ -1120,7 +1120,7 @@ multiplicity 2

C6H13O-2
multiplicity 2
1 C u0 p0 c0 {2,S} {4,S} {8,S} {9,S}
1 *6 C u0 p0 c0 {2,S} {4,S} {8,S} {9,S}
2 *4 C u0 p0 c0 {1,S} {6,S} {10,S} {11,S}
3 C u0 p0 c0 {5,S} {6,S} {12,S} {13,S}
4 *5 C u0 p0 c0 {1,S} {7,S} {14,S} {15,S}
Expand All @@ -1144,7 +1144,7 @@ multiplicity 2
C7H15O-2
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {4,S} {8,S} {9,S}
2 C u0 p0 c0 {1,S} {3,S} {10,S} {11,S}
2 *6 C u0 p0 c0 {1,S} {3,S} {10,S} {11,S}
3 *4 C u0 p0 c0 {2,S} {7,S} {12,S} {13,S}
4 C u0 p0 c0 {1,S} {14,S} {15,S} {16,S}
5 C u0 p0 c0 {7,S} {17,S} {18,S} {19,S}
Expand All @@ -1170,7 +1170,7 @@ multiplicity 2
C7H15O-3
multiplicity 2
1 *4 C u0 p0 c0 {2,S} {5,S} {6,S} {8,S}
2 C u0 p0 c0 {1,S} {3,S} {10,S} {11,S}
2 *6 C u0 p0 c0 {1,S} {3,S} {10,S} {11,S}
3 *5 C u0 p0 c0 {2,S} {4,S} {12,S} {13,S}
4 *2 C u0 p0 c0 {3,S} {7,S} {9,S} {14,S}
5 C u0 p0 c0 {1,S} {15,S} {16,S} {17,S}
Expand Down Expand Up @@ -1235,7 +1235,7 @@ multiplicity 2

C6H11
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
1 *6 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S}
2 *5 C u0 p0 c0 {1,S} {4,S} {9,S} {10,S}
3 *4 C u0 p0 c0 {1,S} {5,S} {11,S} {12,S}
4 *2 C u0 p0 c0 {2,S} {6,D} {13,S}
Expand All @@ -1256,7 +1256,7 @@ multiplicity 2
C6H13O-4
multiplicity 2
1 *5 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S}
2 C u0 p0 c0 {1,S} {3,S} {9,S} {10,S}
2 *6 C u0 p0 c0 {1,S} {3,S} {9,S} {10,S}
3 *4 C u0 p0 c0 {2,S} {6,S} {11,S} {12,S}
4 C u0 p0 c0 {1,S} {13,S} {14,S} {15,S}
5 C u0 p0 c0 {6,S} {16,S} {17,S} {18,S}
Expand Down
Empty file added input/kinetics/families/ketoenol/NIST/dictionary.txt
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Empty file.
8 changes: 8 additions & 0 deletions input/kinetics/families/ketoenol/NIST/reactions.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
#!/usr/bin/env python
# encoding: utf-8

name = "ketoenol/NIST"
shortDesc = u""
longDesc = u"""

"""
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