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Rewrite AST generation code to be generic over the literal type

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peptides/datasets/ChouZhang1995/README.md 0 → 100644
View file @ 7631e195
# Chou & Zhang (1995)
## Overview
These tables contain the average amino acid composition, and eigendecomposition
of the covariance matrix for the average amino acid composition of a set of
120 proteins, grouped in one of four structural class.
## Reference
Chou, K-C., and C-T. Zhang.
*Prediction of Protein Structural Classes*.
Critical Reviews in Biochemistry and Molecular Biology. Feb 1995;30:275–349. Appendix C.
doi:10.3109/10409239509083488. PMID:7587280.
peptides/datasets/ChouZhang1995/alpha+beta/eigen.txt 0 → 100644
View file @ 7631e195
# eig A C D E F G H I K L M N P Q R S T V W Y
0.0 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22
2.7 0.23 -0.09 -0.15 -0.01 0.39 -0.16 -0.03 0.06 0.08 -0.21 -0.56 -0.19 0.26 -0.25 0.08 0.03 0.25 -0.18 0.20 0.24
6.3 0.03 0.17 0.27 0.04 0.20 -0.06 -0.24 0.04 0.00 -0.03 -0.01 -0.24 0.11 0.20 -0.04 -0.11 -0.01 0.10 -0.74 0.33
18.0 -0.12 0.12 0.18 -0.20 0.21 -0.16 -0.59 -0.13 0.10 -0.10 0.23 0.02 -0.19 -0.20 0.17 -0.16 0.00 0.34 0.36 0.11
21.6 -0.01 0.06 0.09 -0.03 -0.19 -0.29 0.38 0.34 -0.15 -0.11 -0.03 0.24 0.07 -0.40 -0.10 -0.39 0.05 0.39 -0.08 0.15
24.6 0.11 0.02 -0.19 0.12 0.06 0.12 -0.01 0.19 -0.09 -0.14 0.64 -0.29 0.13 -0.48 -0.01 0.11 -0.06 -0.29 -0.05 0.10
31.2 0.07 0.19 -0.32 0.16 0.59 0.08 0.10 0.04 -0.25 -0.09 0.06 0.24 -0.33 0.12 0.07 -0.35 0.02 -0.06 -0.09 -0.25
41.1 0.07 -0.03 -0.24 0.01 -0.27 0.00 -0.09 -0.09 -0.04 0.32 -0.08 0.17 -0.27 -0.23 0.64 0.04 0.22 -0.09 -0.26 0.22
56.0 0.01 0.31 -0.25 -0.22 -0.03 -0.12 0.28 0.10 -0.02 0.19 -0.01 -0.57 -0.39 0.19 -0.06 0.03 -0.06 0.15 0.19 0.27
62.9 -0.18 -0.08 -0.02 -0.33 0.19 0.24 0.23 0.13 0.28 -0.25 -0.07 -0.15 0.00 -0.16 0.36 0.24 -0.16 0.31 -0.23 -0.35
78.8 -0.33 -0.42 -0.38 0.19 0.21 -0.05 0.02 -0.22 -0.03 0.20 0.12 -0.01 0.08 -0.03 -0.26 0.19 0.24 0.43 -0.09 0.14
87.4 0.15 -0.01 -0.43 -0.58 -0.04 0.08 -0.04 -0.07 0.19 0.05 0.18 0.20 0.41 0.22 -0.03 -0.30 -0.05 -0.04 -0.04 0.14
146.4 0.00 -0.03 0.02 0.24 -0.12 -0.24 0.29 -0.49 -0.02 -0.40 0.19 -0.22 0.19 0.23 0.39 -0.21 0.08 0.05 0.07 -0.01
159.1 0.10 -0.20 0.05 0.03 0.16 -0.05 0.21 -0.21 0.17 -0.17 0.00 0.30 -0.26 -0.05 -0.05 0.16 -0.58 -0.09 -0.01 0.48
169.9 -0.05 -0.07 0.36 -0.33 0.14 0.12 0.30 -0.30 0.20 0.06 0.14 0.00 -0.26 -0.17 -0.21 -0.13 0.50 -0.26 -0.08 0.03
266.7 -0.09 0.38 0.08 -0.02 0.20 -0.09 0.14 -0.42 -0.12 0.49 -0.09 -0.03 0.33 -0.33 0.02 0.01 -0.31 0.00 -0.01 -0.14
337.9 -0.36 0.03 -0.02 0.22 -0.10 0.68 -0.01 -0.03 0.05 -0.03 -0.19 -0.13 0.05 -0.08 0.02 -0.42 -0.09 0.01 0.13 0.27
511.0 -0.06 -0.52 0.29 -0.23 0.20 0.00 0.07 0.19 -0.50 0.26 0.07 -0.14 0.09 0.15 0.27 -0.13 -0.13 -0.08 0.13 0.08
743.4 -0.43 -0.09 -0.02 0.19 0.10 -0.39 0.03 0.29 0.54 0.23 0.07 -0.03 0.02 0.07 0.12 -0.23 -0.09 -0.31 0.01 -0.06
968.5 0.60 -0.33 0.03 0.20 -0.03 0.08 -0.05 -0.07 0.31 0.27 0.00 -0.24 -0.11 -0.11 -0.06 -0.32 -0.13 0.23 -0.02 -0.23
peptides/datasets/ChouZhang1995/alpha+beta/mean.csv 0 → 100644
View file @ 7631e195
A,0.0845
C,0.0310
D,0.0547
E,0.0579
F,0.0399
G,0.0684
H,0.0219
I,0.0460
K,0.0684
L,0.0727
M,0.0176
N,0.0487
P,0.0491
Q,0.0375
R,0.0441
S,0.0710
T,0.0638
V,0.0684
W,0.0132
Y,0.0472
peptides/datasets/ChouZhang1995/alpha/eigen.txt 0 → 100644
View file @ 7631e195
# eig A C D E F G H I K L M N P Q R S T V W Y
0.0 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22
1.6 -0.06 -0.13 0.01 0.04 -0.21 0.06 0.14 -0.25 -0.03 -0.29 0.23 0.16 -0.25 -0.25 0.06 -0.01 0.14 -0.10 0.73 0.00
10.9 0.10 -0.46 -0.13 0.23 0.21 0.05 0.11 -0.20 -0.04 -0.12 0.27 -0.04 0.05 -0.24 0.11 -0.11 0.13 -0.10 -0.36 0.52
13.4 0.10 0.22 -0.26 0.06 -0.03 0.08 0.15 0.00 0.06 -0.04 -0.08 0.19 -0.54 -0.04 0.05 -0.02 0.51 0.10 -0.36 -0.30
30.8 0.10 0.02 -0.13 -0.26 -0.11 -0.57 0.43 0.28 -0.14 -0.04 0.37 -0.02 0.09 -0.09 0.22 -0.06 -0.17 0.19 -0.03 -0.07
33.4 0.00 -0.21 0.08 -0.02 -0.33 0.22 0.05 0.23 -0.06 -0.09 -0.30 0.41 0.41 -0.20 0.28 -0.33 0.17 -0.03 -0.11 -0.18
53.7 -0.19 0.09 0.11 0.29 0.03 0.40 -0.06 0.01 -0.25 -0.24 0.51 -0.07 0.11 0.01 0.06 0.03 -0.32 0.07 -0.17 -0.40
69.6 -0.11 0.34 -0.01 -0.10 0.48 -0.01 0.09 -0.25 -0.14 -0.14 -0.15 -0.25 0.12 0.06 0.33 -0.51 0.16 0.01 0.13 -0.04
74.5 0.06 -0.57 0.28 0.08 0.15 -0.07 -0.11 0.28 0.01 -0.03 0.01 -0.17 -0.28 0.36 -0.02 -0.30 0.11 0.26 0.12 -0.19
78.0 -0.07 -0.06 0.39 -0.42 -0.13 0.20 -0.03 -0.08 0.31 0.08 0.05 -0.31 -0.21 -0.19 0.51 0.18 -0.04 -0.02 -0.16 0.01
82.9 0.05 0.11 0.09 0.00 0.38 0.03 -0.20 0.35 -0.07 0.25 0.03 0.32 -0.34 -0.45 0.03 -0.22 -0.32 -0.17 0.07 0.06
148.8 -0.16 -0.10 -0.34 -0.42 0.03 0.31 0.12 0.16 0.20 0.12 0.30 0.07 0.03 0.37 -0.11 -0.21 -0.01 -0.43 0.04 0.03
169.3 0.01 0.04 0.29 0.00 -0.08 0.18 0.59 -0.08 -0.31 -0.09 -0.28 0.14 -0.30 0.26 -0.07 -0.01 -0.29 -0.09 -0.12 0.21
197.3 -0.02 -0.13 0.43 -0.12 0.28 -0.31 0.09 -0.38 0.12 0.08 0.14 0.37 0.16 0.02 -0.17 0.08 0.10 -0.27 -0.13 -0.35
256.3 -0.01 -0.18 -0.34 -0.17 0.19 0.05 -0.14 -0.29 0.16 -0.15 -0.12 0.43 -0.06 0.19 0.27 0.13 -0.37 0.41 0.01 -0.01
263.5 -0.01 0.26 0.27 -0.18 -0.32 -0.02 -0.26 -0.19 0.07 -0.03 0.28 0.13 -0.03 0.07 -0.24 -0.44 0.01 0.33 -0.12 0.33
510.6 -0.62 -0.03 0.07 -0.21 0.26 0.05 0.16 0.27 0.07 -0.28 -0.07 0.04 0.05 -0.22 -0.30 0.18 0.19 0.29 -0.03 0.12
672.3 -0.08 -0.11 -0.02 -0.30 0.02 0.08 -0.20 -0.08 -0.73 0.36 0.09 0.09 0.00 0.07 0.11 0.22 0.27 0.10 0.05 0.07
774.5 0.09 0.15 0.12 -0.07 0.04 -0.20 -0.34 0.26 -0.11 -0.60 0.02 0.15 -0.06 0.27 0.21 0.20 0.11 -0.35 -0.07 0.19
1315.4 0.66 -0.02 0.01 -0.40 0.18 0.29 0.04 0.02 -0.07 -0.28 -0.01 -0.12 0.12 -0.20 -0.33 0.06 0.00 0.12 0.04 -0.11
peptides/datasets/ChouZhang1995/alpha/mean.csv 0 → 100644
View file @ 7631e195
A,0.1106
C,0.0097
D,0.0555
E,0.0745
F,0.0398
G,0.0603
H,0.0286
I,0.0402
K,0.0859
L,0.1127
M,0.0255
N,0.0392
P,0.0273
Q,0.0432
R,0.0458
S,0.0563
T,0.0453
V,0.0597
W,0.0104
Y,0.0294
peptides/datasets/ChouZhang1995/alpha_beta/eigen.txt 0 → 100644
View file @ 7631e195
# eig A C D E F G H I K L M N P Q R S T V W Y
0.0 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22
1.3 -0.06 0.30 -0.04 -0.07 -0.16 0.00 -0.07 0.19 -0.08 -0.18 -0.37 0.30 0.32 0.16 0.29 -0.04 0.23 -0.10 -0.11 -0.53
2.5 0.00 0.81 -0.11 -0.11 -0.26 -0.10 -0.17 -0.12 0.02 0.17 -0.01 0.02 0.00 -0.05 -0.22 -0.09 -0.11 -0.05 0.08 0.30
4.9 -0.08 0.14 0.10 -0.25 0.04 -0.14 0.43 0.08 -0.19 -0.33 0.18 -0.01 -0.18 0.13 -0.08 -0.14 -0.15 0.10 0.60 -0.23
8.2 -0.06 0.19 0.22 0.26 -0.04 -0.09 0.58 -0.36 0.14 -0.09 -0.04 0.10 -0.14 0.00 -0.07 0.26 -0.17 -0.11 -0.42 -0.14
11.8 0.14 0.30 0.01 -0.07 0.63 -0.23 -0.23 0.08 -0.05 -0.20 0.07 -0.11 -0.25 -0.17 -0.03 0.08 0.15 0.29 -0.27 -0.17
15.4 -0.07 0.01 -0.03 0.02 0.16 -0.09 0.21 0.33 -0.08 0.34 -0.48 -0.43 0.23 0.14 -0.30 0.14 -0.21 0.16 0.00 -0.07
28.5 0.00 0.02 -0.29 0.45 0.12 0.07 -0.13 -0.42 -0.08 -0.01 -0.02 -0.09 -0.05 0.47 -0.30 -0.07 0.31 0.01 0.20 -0.18
39.0 -0.14 0.00 0.22 -0.06 -0.20 -0.15 -0.18 0.09 -0.21 -0.04 0.60 -0.18 0.38 0.28 -0.20 0.19 -0.05 0.03 -0.26 -0.14
41.0 0.15 -0.03 -0.21 -0.08 0.10 0.10 0.18 0.31 -0.24 -0.11 0.01 0.29 -0.16 0.44 -0.14 -0.32 -0.10 -0.11 -0.39 0.31
45.7 0.14 0.06 -0.09 -0.01 0.12 -0.01 -0.06 -0.10 0.21 -0.56 -0.12 -0.40 0.26 0.23 0.29 0.12 -0.22 -0.23 0.05 0.30
54.9 0.07 -0.02 0.20 -0.08 -0.21 -0.03 0.25 0.12 0.12 -0.24 -0.08 -0.27 0.07 -0.16 -0.30 -0.19 0.13 0.16 -0.16 -0.13
63.5 -0.27 0.07 -0.32 -0.31 -0.16 0.17 0.09 0.08 0.40 0.15 0.15 -0.29 -0.36 0.28 0.24 0.09 0.13 0.16 -0.16 -0.13
116.2 -0.15 0.09 0.39 -0.18 0.12 0.71 -0.10 -0.24 -0.04 -0.09 -0.10 -0.09 0.08 0.02 -0.10 -0.26 -0.14 0.24 -0.10 -0.05
143.6 -0.03 -0.07 0.52 -0.03 -0.20 -0.23 -0.28 -0.01 -0.11 -0.02 -0.32 0.05 -0.41 0.38 0.09 0.22 0.07 0.12 0.05 0.19
165.6 -0.13 -0.11 0.14 -0.39 0.34 -0.19 -0.10 -0.12 0.51 0.12 -0.03 0.28 0.14 0.18 -0.32 -0.03 0.01 -0.32 0.07 -0.05
221.2 -0.39 0.00 -0.13 0.30 -0.08 0.16 -0.16 0.36 0.25 -0.41 -0.04 0.24 -0.07 -0.13 -0.35 0.25 -0.11 0.17 0.07 0.07
363.4 0.22 -0.15 -0.11 -0.04 -0.21 -0.30 0.03 -0.21 0.27 -0.10 -0.06 0.16 0.23 0.07 -0.02 -0.52 -0.14 0.69 -0.08 0.02
465.0 -0.39 -0.05 -0.24 -0.31 0.16 -0.02 0.15 -0.29 -0.37 -0.04 -0.09 0.18 0.20 -0.04 0.07 0.35 0.23 0.19 -0.01 0.33
546.6 0.60 -0.06 -0.15 -0.33 -0.19 0.28 -0.02 -0.05 -0.04 -0.07 -0.05 0.08 -0.07 -0.02 -0.29 0.50 -0.02 -0.01 0.05 -0.16
peptides/datasets/ChouZhang1995/alpha_beta/mean.csv 0 → 100644
View file @ 7631e195
A,0.0948
C,0.0103
D,0.0649
E,0.0633
F,0.0365
G,0.0860
H,0.0231
I,0.0611
K,0.0632
L,0.0766
M,0.0220
N,0.0431
P,0.0409
Q,0.0404
R,0.0386
S,0.0555
T,0.0524
V,0.0808
W,0.0122
Y,0.0363
peptides/datasets/ChouZhang1995/beta/eigen.txt 0 → 100644
View file @ 7631e195
# eig A C D E F G H I K L M N P Q R S T V W Y
0.0 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22 -0.22
2.8 -0.12 0.16 -0.16 0.16 0.02 0.09 0.50 -0.15 -0.03 0.10 -0.23 0.02 0.01 0.08 -0.08 -0.11 0.24 0.01 -0.68 0.17
9.0 -0.05 -0.04 -0.23 0.11 0.27 0.00 -0.15 0.43 0.08 -0.05 0.24 -0.34 -0.40 -0.24 -0.05 0.30 -0.04 0.18 -0.25 0.24
21.4 -0.02 0.01 0.02 -0.16 0.22 -0.01 0.36 0.06 0.33 -0.12 -0.62 -0.34 -0.17 0.04 0.02 0.02 -0.08 0.14 0.34 -0.06
32.3 0.27 -0.14 -0.17 -0.15 0.22 -0.11 0.19 -0.32 0.25 0.08 0.44 -0.28 -0.21 0.12 0.20 -0.22 0.22 -0.32 0.04 -0.12
38.3 0.01 -0.04 0.30 -0.13 -0.01 -0.04 -0.22 0.07 0.23 -0.32 -0.08 0.10 -0.08 0.24 0.53 0.14 0.01 0.07 -0.45 -0.31
51.4 -0.13 0.23 0.15 0.14 0.30 0.41 -0.36 -0.16 0.24 0.02 -0.11 -0.23 0.25 -0.10 -0.22 0.14 0.09 -0.43 -0.08 -0.13
63.8 0.09 -0.02 -0.27 0.29 0.31 -0.16 -0.50 -0.20 -0.06 -0.04 -0.28 0.07 -0.05 0.28 0.09 -0.31 0.20 0.23 0.07 0.23
77.8 -0.22 0.23 0.45 -0.42 0.34 -0.13 -0.06 -0.09 -0.30 0.21 0.16 -0.19 -0.05 0.14 -0.18 -0.16 0.05 0.32 -0.08 -0.02
128.7 -0.22 0.24 0.00 0.28 0.05 0.10 0.16 -0.16 -0.10 -0.42 0.22 0.14 -0.10 0.44 -0.22 0.12 -0.20 -0.08 0.16 -0.09
149.6 0.15 0.21 0.21 0.08 -0.03 -0.26 -0.10 -0.11 0.13 0.47 -0.21 0.34 -0.55 -0.17 -0.05 0.16 -0.02 -0.21 -0.02 -0.02
179.2 -0.07 0.18 -0.06 0.45 -0.03 0.00 0.08 -0.16 -0.27 0.14 0.04 -0.24 -0.01 -0.30 0.29 0.03 0.07 0.30 0.09 -0.56
201.1 -0.58 0.05 -0.17 -0.27 0.06 0.07 0.00 -0.25 0.03 -0.10 0.04 0.26 -0.07 -0.29 0.34 0.18 0.31 -0.01 0.19 0.22
296.8 -0.12 -0.20 -0.23 -0.13 0.02 0.55 -0.07 -0.12 0.11 0.43 0.02 0.11 -0.14 0.17 0.12 -0.11 -0.47 0.20 -0.06 -0.09
320.6 0.12 -0.17 0.33 0.19 -0.01 -0.07 0.05 -0.57 0.10 -0.13 0.06 -0.15 0.08 -0.21 0.08 0.16 -0.36 0.18 -0.08 0.41
466.6 0.33 0.37 -0.22 -0.24 0.13 0.05 -0.01 -0.12 0.27 -0.28 0.11 0.32 0.05 -0.34 -0.25 -0.13 -0.08 0.32 -0.08 -0.13
487.9 -0.05 -0.34 0.41 0.20 0.04 0.33 0.05 0.14 0.06 -0.17 0.03 0.15 -0.28 -0.29 -0.08 -0.51 0.23 0.04 0.04 0.00
682.9 -0.14 0.25 0.03 0.01 -0.65 0.03 -0.19 -0.05 0.42 0.07 0.11 -0.29 -0.10 0.14 -0.11 -0.13 0.22 0.23 0.05 0.11
979.5 0.09 -0.49 -0.02 -0.06 -0.02 0.06 -0.02 -0.22 0.01 0.04 -0.04 0.08 -0.03 0.12 -0.39 0.47 0.40 0.27 -0.01 -0.24
1822.8 0.45 0.20 0.01 -0.23 -0.19 0.46 -0.07 -0.09 -0.45 -0.13 -0.15 -0.17 -0.25 -0.01 -0.17 0.12 0.17 -0.06 0.05 0.18
peptides/datasets/ChouZhang1995/beta/mean.csv 0 → 100644
View file @ 7631e195
A,0.0600
C,0.0274
D,0.0496
E,0.0497
F,0.0498
G,0.0759
H,0.0141
I,0.0505
K,0.0612
L,0.0711
M,0.0182
N,0.0513
P,0.0549
Q,0.0424
R,0.0404
S,0.0808
T,0.0767
V,0.0670
W,0.0153
Y,0.0434
peptides/datasets/Nakashima1986/README.md 0 → 100644
View file @ 7631e195
# Nakashima, Nishikawa & Ooi (1986)
## Overview
These tables contain the average amino acid composition and standard deviation
of a set of 569 proteins with a resolved structure, grouped by their structural
class.
## Reference
Nakashima, H., K. Nishikawa, and T. Ooi.
*The Folding Type of a Protein Is Relevant to the Amino Acid Composition*.
Journal of Biochemistry. Jan 1986;99(1):158, Table II.
doi:10.1093/oxfordjournals.jbchem.a135454. PMID:3957893.
peptides/datasets/Nakashima1986/alpha+beta/sd.csv 0 → 100644
View file @ 7631e195
A,0.0912
C,0.0397
D,0.0405
E,0.0512
F,0.0301
G,0.0799
H,0.0125
I,0.0485
K,0.0595
L,0.0521
M,0.0062
N,0.0731
P,0.0488
Q,0.0333
R,0.0314
S,0.0804
T,0.0826
V,0.0654
W,0.0122
Y,0.0614
peptides/datasets/Nakashima1986/alpha/sd.csv 0 → 100644
View file @ 7631e195
A,0.1167
C,0.0181
D,0.0647
E,0.0656
F,0.0430
G,0.0705
H,0.0259
I,0.0372
K,0.1000
L,0.0918
M,0.0215
N,0.0399
P,0.0379
Q,0.0348
R,0.0312
S,0.0617
T,0.0441
V,0.0559
W,0.0130
Y,0.0264
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