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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#TODO - Don't use "from XXX import *"
try:
from numpy import *
from numpy import dot #missing in PyPy's micronumpy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.SVDSuperimposer.")
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]], 'f')
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]], 'f')
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=dot(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.
Only 4 decimal places are used to avoid false test failures due
to slight differences in the calculation (e.g. due to different
versions of the underlying libraries or the compilation options
they used).
"""
#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(["% 1.4f" % 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
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