/usr/lib/R/site-library/bio3d/matrices/similarity.mat is in r-other-bio3d 1.1-5-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | # Similarity Matrix derived from the PET91 matrix
# of Jones, Taylor and Thornton 1991 with values
# sacled to 0 or 1. Input with 'read.table'
A R N D C Q E G H I L K M F P S T W Y V B Z X -
A 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 0
R 0 1 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0
N 0 0 1 1 0 0 1 0 1 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0
D 0 0 1 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0
C 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0
Q 0 1 0 0 0 1 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0
E 0 0 1 1 0 1 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0
G 1 0 0 1 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
H 0 1 1 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0
I 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 1 0 0 1 0 0 0 0
L 0 0 0 0 0 0 0 0 0 1 1 0 1 1 0 0 0 0 0 1 0 0 0 0
K 0 1 1 0 0 1 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0
M 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0
F 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0
P 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0
S 1 0 1 0 1 0 0 1 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0
T 1 0 1 0 0 0 0 0 0 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0
W 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
Y 0 0 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0
V 1 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0
B 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0
Z 0 1 0 1 0 1 1 0 1 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0
X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|