This should do it...
import pybel
matrix = pybel.ob.matrix3x3()
matrix.RotAboutAxisByAngle(pybel.ob.vector3(1, 0, 0), 90)
my_array = pybel.ob.doubleArray(9)
matrix.GetArray(my_array)
mol = pybel.readstring("smi", "CC(=O)Cl")
mol.make3D()
print mol.write("xyz")
# 7
#
# C 1.05861 -0.06922 -0.08203
# C 2.56267 -0.02107 -0.02878
# O 3.14464 0.63176 0.83385
# Cl 3.31960 -0.96102 -1.27795
# H 0.69578 -0.68047 -0.91193
# H 0.67435 0.94707 -0.20685
# H 0.68295 -0.49475 0.85271
#
mol.OBMol.Rotate(my_array)
print mol.write("xyz")
# 7
#
# C 1.05861 -0.08203 0.06922
# C 2.56267 -0.02878 0.02107
# O 3.14464 0.83385 -0.63176
# Cl 3.31960 -1.27795 0.96102
# H 0.69578 -0.91193 0.68047
# H 0.67435 -0.20685 -0.94707
# H 0.68295 0.85271 0.49475
On 20 November 2010 15:02, Anders Christensen <[email protected]> wrote:
> Dear all,
>
> I am trying to use the Rotate() function through the python API.
> However, the method want as argument, something in the for of "double
> const [9]" (there are also other overloads, but the problem is the
> same). In what format do I pass a list/vector/matrix to Rotate()?
> Ideally, I want to use the output from RotAboutAxisByAngle(), but I
> can't just pass the resulting matrix3x3. However, I can get the
> elements of the generated rotation matrix through something along the
> lines of the following hoops+loops:
>
> some_rotation_matrix = openbabel.matrix3x3(1)
> some_rotation_matrix.RotAboutAxisByAngle(openbabel.vector3(1,2,3), 90)
>
> rotation_matrix =[ [0.0 for i in range(3)] for j in range(3)]
> for i in range(3):
> for j in range(3):
> print lol.Get(i,j)
> rotation_matrix[i][j] = some_rotation_matrix.Get(i,j)
>
> So how can I pass these elements on to Rotate(), in order to give my
> molecule a specific rotation?
>
> Best regards
> Anders
>
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