-
Notifications
You must be signed in to change notification settings - Fork 8
/
Copy pathtopmat.mat
77 lines (77 loc) · 7.82 KB
/
topmat.mat
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
! This matrix is for aligning secondary structure topology strings
! encoded as follows:
! <--Distant--> <--Adjacent-->
! Sheet Helix Sheet Helix
! Up A G M S
! Right B H N T
! Down C I O U
! Left D J P V
! Back E K Q W
! Forward F L R X
!
! Lower case letters are used for buried, upper case for exposed
!
! Scores are as follows:
! Same SS Different SS
! Same orientation 10 3
! Out by 90degrees 8 1
! Out by 180degrees 2 0
!
! Scores are multiplied by .75 if there is a difference in adjacency
! i.e.
! Same SS Different SS
! Same orientation 8 2
! Out by 90degrees 6 1
! Out by 180degrees 1 0
!
! Similarly, scores are multiplied by .75 if there is a difference in accessibility
!
A B C D E F G H I J K L M N O P Q R S T U V W X a b c d e f g h i j k l m n o p q r s t u v w x
10 8 2 8 8 8 3 1 0 1 1 1 8 6 1 6 6 6 2 1 0 1 1 1 8 6 1 6 6 6 2 1 0 1 1 1 6 4 1 4 4 4 1 1 0 1 1 1
8 10 8 2 8 8 1 3 1 0 1 1 6 8 6 1 6 6 1 2 1 0 1 1 6 8 6 1 6 6 1 2 1 0 1 1 4 6 4 1 4 4 1 1 1 0 1 1
2 8 10 8 8 8 0 1 3 1 1 1 1 6 8 6 6 6 0 1 2 1 1 1 1 6 8 6 6 6 0 1 2 1 1 1 1 4 6 4 4 4 0 1 1 1 1 1
8 2 8 10 8 8 1 0 1 3 1 1 6 1 6 8 6 6 1 0 1 2 1 1 6 1 6 8 6 6 1 0 1 2 1 1 4 1 4 6 4 4 1 0 1 1 1 1
8 8 8 8 10 2 1 1 1 1 3 0 6 6 6 6 8 1 1 1 1 1 2 0 6 6 6 6 8 1 1 1 1 1 2 0 4 4 4 4 6 1 1 1 1 1 1 0
8 8 8 8 2 10 1 1 1 1 0 3 6 6 6 6 1 8 1 1 1 1 0 2 6 6 6 6 1 8 1 1 1 1 0 2 4 4 4 4 1 6 1 1 1 1 0 1
3 1 0 1 1 1 10 8 2 8 8 8 2 1 0 1 1 1 8 6 1 6 6 6 2 1 0 1 1 1 8 6 1 6 6 6 1 1 0 1 1 1 6 4 1 4 4 4
1 3 1 0 1 1 8 10 8 2 8 8 1 2 1 0 1 1 6 8 6 1 6 6 1 2 1 0 1 1 6 8 6 1 6 6 1 1 1 0 1 1 4 6 4 1 4 4
0 1 3 1 1 1 2 8 10 8 8 8 0 1 2 1 1 1 1 6 8 6 6 6 0 1 2 1 1 1 1 6 8 6 6 6 0 1 1 1 1 1 1 4 6 4 4 4
1 0 1 3 1 1 8 2 8 10 8 8 1 0 1 2 1 1 6 1 6 8 6 6 1 0 1 2 1 1 6 1 6 8 6 6 1 0 1 1 1 1 4 1 4 6 4 4
1 1 1 1 3 0 8 8 8 8 10 2 1 1 1 1 2 0 6 6 6 6 8 1 1 1 1 1 2 0 6 6 6 6 8 1 1 1 1 1 1 0 4 4 4 4 6 1
1 1 1 1 0 3 8 8 8 8 2 10 1 1 1 1 0 2 6 6 6 6 1 8 1 1 1 1 0 2 6 6 6 6 1 8 1 1 1 1 0 1 4 4 4 4 1 6
8 6 1 6 6 6 2 1 0 1 1 1 10 8 2 8 8 8 3 1 0 1 1 1 6 4 1 4 4 4 1 1 0 1 1 1 8 6 1 6 6 6 2 1 0 1 1 1
6 8 6 1 6 6 1 2 1 0 1 1 8 10 8 2 8 8 1 3 1 0 1 1 4 6 4 1 4 4 1 1 1 0 1 1 6 8 6 1 6 6 1 2 1 0 1 1
1 6 8 6 6 6 0 1 2 1 1 1 2 8 10 8 8 8 0 1 3 1 1 1 1 4 6 4 4 4 0 1 1 1 1 1 1 6 8 6 6 6 0 1 2 1 1 1
6 1 6 8 6 6 1 0 1 2 1 1 8 2 8 10 8 8 1 0 1 3 1 1 4 1 4 6 4 4 1 0 1 1 1 1 6 1 6 8 6 6 1 0 1 2 1 1
6 6 6 6 8 1 1 1 1 1 2 0 8 8 8 8 10 2 1 1 1 1 3 0 4 4 4 4 6 1 1 1 1 1 1 0 6 6 6 6 8 1 1 1 1 1 2 0
6 6 6 6 1 8 1 1 1 1 0 2 8 8 8 8 2 10 1 1 1 1 0 3 4 4 4 4 1 6 1 1 1 1 0 1 6 6 6 6 1 8 1 1 1 1 0 2
2 1 0 1 1 1 8 6 1 6 6 6 3 1 0 1 1 1 10 8 2 8 8 8 1 1 0 1 1 1 6 4 1 4 4 4 2 1 0 1 1 1 8 6 1 6 6 6
1 2 1 0 1 1 6 8 6 1 6 6 1 3 1 0 1 1 8 10 8 2 8 8 1 1 1 0 1 1 4 6 4 1 4 4 1 2 1 0 1 1 6 8 6 1 6 6
0 1 2 1 1 1 1 6 8 6 6 6 0 1 3 1 1 1 2 8 10 8 8 8 0 1 1 1 1 1 1 4 6 4 4 4 0 1 2 1 1 1 1 6 8 6 6 6
1 0 1 2 1 1 6 1 6 8 6 6 1 0 1 3 1 1 8 2 8 10 8 8 1 0 1 1 1 1 4 1 4 6 4 4 1 0 1 2 1 1 6 1 6 8 6 6
1 1 1 1 2 0 6 6 6 6 8 1 1 1 1 1 3 0 8 8 8 8 10 2 1 1 1 1 1 0 4 4 4 4 6 1 1 1 1 1 2 0 6 6 6 6 8 1
1 1 1 1 0 2 6 6 6 6 1 8 1 1 1 1 0 3 8 8 8 8 2 10 1 1 1 1 0 1 4 4 4 4 1 6 1 1 1 1 0 2 6 6 6 6 1 8
8 6 1 6 6 6 2 1 0 1 1 1 6 4 1 4 4 4 1 1 0 1 1 1 10 8 2 8 8 8 3 1 0 1 1 1 8 6 1 6 6 6 2 1 0 1 1 1
6 8 6 1 6 6 1 2 1 0 1 1 4 6 4 1 4 4 1 1 1 0 1 1 8 10 8 2 8 8 1 3 1 0 1 1 6 8 6 1 6 6 1 2 1 0 1 1
1 6 8 6 6 6 0 1 2 1 1 1 1 4 6 4 4 4 0 1 1 1 1 1 2 8 10 8 8 8 0 1 3 1 1 1 1 6 8 6 6 6 0 1 2 1 1 1
6 1 6 8 6 6 1 0 1 2 1 1 4 1 4 6 4 4 1 0 1 1 1 1 8 2 8 10 8 8 1 0 1 3 1 1 6 1 6 8 6 6 1 0 1 2 1 1
6 6 6 6 8 1 1 1 1 1 2 0 4 4 4 4 6 1 1 1 1 1 1 0 8 8 8 8 10 2 1 1 1 1 3 0 6 6 6 6 8 1 1 1 1 1 2 0
6 6 6 6 1 8 1 1 1 1 0 2 4 4 4 4 1 6 1 1 1 1 0 1 8 8 8 8 2 10 1 1 1 1 0 3 6 6 6 6 1 8 1 1 1 1 0 2
2 1 0 1 1 1 8 6 1 6 6 6 1 1 0 1 1 1 6 4 1 4 4 4 3 1 0 1 1 1 10 8 2 8 8 8 2 1 0 1 1 1 8 6 1 6 6 6
1 2 1 0 1 1 6 8 6 1 6 6 1 1 1 0 1 1 4 6 4 1 4 4 1 3 1 0 1 1 8 10 8 2 8 8 1 2 1 0 1 1 6 8 6 1 6 6
0 1 2 1 1 1 1 6 8 6 6 6 0 1 1 1 1 1 1 4 6 4 4 4 0 1 3 1 1 1 2 8 10 8 8 8 0 1 2 1 1 1 1 6 8 6 6 6
1 0 1 2 1 1 6 1 6 8 6 6 1 0 1 1 1 1 4 1 4 6 4 4 1 0 1 3 1 1 8 2 8 10 8 8 1 0 1 2 1 1 6 1 6 8 6 6
1 1 1 1 2 0 6 6 6 6 8 1 1 1 1 1 1 0 4 4 4 4 6 1 1 1 1 1 3 0 8 8 8 8 10 2 1 1 1 1 2 0 6 6 6 6 8 1
1 1 1 1 0 2 6 6 6 6 1 8 1 1 1 1 0 1 4 4 4 4 1 6 1 1 1 1 0 3 8 8 8 8 2 10 1 1 1 1 0 2 6 6 6 6 1 8
6 4 1 4 4 4 1 1 0 1 1 1 8 6 1 6 6 6 2 1 0 1 1 1 8 6 1 6 6 6 2 1 0 1 1 1 10 8 2 8 8 8 3 1 0 1 1 1
4 6 4 1 4 4 1 1 1 0 1 1 6 8 6 1 6 6 1 2 1 0 1 1 6 8 6 1 6 6 1 2 1 0 1 1 8 10 8 2 8 8 1 3 1 0 1 1
1 4 6 4 4 4 0 1 1 1 1 1 1 6 8 6 6 6 0 1 2 1 1 1 1 6 8 6 6 6 0 1 2 1 1 1 2 8 10 8 8 8 0 1 3 1 1 1
4 1 4 6 4 4 1 0 1 1 1 1 6 1 6 8 6 6 1 0 1 2 1 1 6 1 6 8 6 6 1 0 1 2 1 1 8 2 8 10 8 8 1 0 1 3 1 1
4 4 4 4 6 1 1 1 1 1 1 0 6 6 6 6 8 1 1 1 1 1 2 0 6 6 6 6 8 1 1 1 1 1 2 0 8 8 8 8 10 2 1 1 1 1 3 0
4 4 4 4 1 6 1 1 1 1 0 1 6 6 6 6 1 8 1 1 1 1 0 2 6 6 6 6 1 8 1 1 1 1 0 2 8 8 8 8 2 10 1 1 1 1 0 3
1 1 0 1 1 1 6 4 1 4 4 4 2 1 0 1 1 1 8 6 1 6 6 6 2 1 0 1 1 1 8 6 1 6 6 6 3 1 0 1 1 1 10 8 2 8 8 8
1 1 1 0 1 1 4 6 4 1 4 4 1 2 1 0 1 1 6 8 6 1 6 6 1 2 1 0 1 1 6 8 6 1 6 6 1 3 1 0 1 1 8 10 8 2 8 8
0 1 1 1 1 1 1 4 6 4 4 4 0 1 2 1 1 1 1 6 8 6 6 6 0 1 2 1 1 1 1 6 8 6 6 6 0 1 3 1 1 1 2 8 10 8 8 8
1 0 1 1 1 1 4 1 4 6 4 4 1 0 1 2 1 1 6 1 6 8 6 6 1 0 1 2 1 1 6 1 6 8 6 6 1 0 1 3 1 1 8 2 8 10 8 8
1 1 1 1 1 0 4 4 4 4 6 1 1 1 1 1 2 0 6 6 6 6 8 1 1 1 1 1 2 0 6 6 6 6 8 1 1 1 1 1 3 0 8 8 8 8 10 2
1 1 1 1 0 1 4 4 4 4 1 6 1 1 1 1 0 2 6 6 6 6 1 8 1 1 1 1 0 2 6 6 6 6 1 8 1 1 1 1 0 3 8 8 8 8 2 10