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
|
from Numeric import *
from Bio.SVDSuperimposer import *
# start with two coordinate sets (Nx3 arrays - Float0)
x=array([[51.65, -1.90, 50.07],
[50.40, -1.23, 50.65],
[50.68, -0.04, 51.54],
[50.22, -0.02, 52.85]], Float0)
y=array([[51.30, -2.99, 46.54],
[51.09, -1.88, 47.58],
[52.36, -1.20, 48.03],
[52.71, -1.18, 49.38]], Float0)
sup=SVDSuperimposer()
# set the coords
# y will be rotated and translated on x
sup.set(x, y)
# do the lsq fit
sup.run()
# get the rmsd
rms=sup.get_rms()
# get rotation (right multiplying!) and the translation
rot, tran=sup.get_rotran()
# rotate y on x manually
y_on_x1=matrixmultiply(y, rot)+tran
# same thing
y_on_x2=sup.get_transformed()
def simple_matrix_print(matrix) :
"""Simple string to display a floating point matrix
This should give the same output on multiple systems. This is
needed because a simple "print matrix" uses scientific notation
which varies between platforms."""
#This uses a fancy double nested list expression.
#If and when Biopython requires Python 2.4 or later,
#it would be slightly nicer to use generator expressions.
return "[" \
+ "\n ".join(["[" \
+ " ".join(["% 1.6f" % val for val in row]) \
+ "]" for row in matrix]) \
+ "]"
# output results
print simple_matrix_print(y_on_x1)
print
print simple_matrix_print(y_on_x2)
print
print "%.2f" % rms
|
