Mathematical operations performed on mmLib.Strcuture.Atom objects.
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normalize(u)
Returns the normalized vector along u. |
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cross(u,
v)
Cross product of u and v: Cross[u,v] = {-u3 v2 + u2 v3, u3 v1 - u1
v3, -u2 v1 + u1 v2} |
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rmatrix(alpha,
beta,
gamma)
Return a rotation matrix based on the Euler angles alpha, beta, and
gamma in radians. |
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rmatrixu(u,
theta)
Return a rotation matrix caused by a right hand rotation of theta
radians around vector u. |
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dmatrix(alpha,
beta,
gamma)
Returns the displacement matrix based on rotation about Euler angles
alpha, beta, and gamma. |
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dmatrixu(u,
theta)
Return a displacement matrix caused by a right hand rotation of theta
radians around vector u. |
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rmatrixz(vec)
Return a rotation matrix which transforms the coordinate system such
that the vector vec is aligned along the z axis. |
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rquaternionu(u,
theta)
Returns a quaternion representing the right handed rotation of theta
radians about vector u. |
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quaternionrmatrix(R)
Return a quaternion calculated from the argument rotation matrix R. |
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calc_distance(a1,
a2)
Returns the distance between two argument atoms. |
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calc_angle(a1,
a2,
a3)
Return the angle between the three argument atoms. |
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calc_torsion_angle(a1,
a2,
a3,
a4,
sqrt=<built-in function sqrt>,
acos=<built-in function acos>)
Calculates the torsion angle between the four argument atoms. |
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calc_CCuij(U,
V)
Calculate the correlation coefficient for anisotropic ADP tensors U
and V. |
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calc_Suij(U,
V)
Calculate the similarity of anisotropic ADP tensors U and V. |
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calc_DP2uij(U,
V)
Calculate the square of the volumetric difference in the probability
density function of anisotropic ADP tensors U and V. |
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diff_trace_UV(U,
V)
Calculates the trace difference of anisotropic ADP tensors U and V. |
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sum_square_diff(U,
V)
Calculates the sum of the differences of anisotropic ADP tensors U
and V squared. |
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calc_atom_centroid(atom_iter)
Calculates the centroid of all contained Atom instances and returns a
Vector to the centroid. |
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calc_atom_mean_temp_factor(atom_iter)
Calculates the average temperature factor of all contained Atom
instances and returns the average temperature factor. |
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calc_inertia_tensor(atom_iter,
origin)
Calculate a moment-of-inertia tensor at the given origin assuming all
atoms have the same mass. |
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