Package mmLib :: Module AtomMath
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Module mmLib.AtomMath

Mathmatical operations performed on mmLib.Strcuture.Atom objects.
Function Summary
  addquaternion(q1, q2)
Adds quaterions q1 and q2.
  calc_angle(a1, a2, a3)
Return the angle between the three argument atoms.
  calc_anisotropy(U)
Calculates the anisotropy of a atomic ADP tensor U.
  calc_atom_centroid(atom_iter)
Calculates the centroid of all contained Atom instances and returns a Vector to the centroid.
  calc_atom_mean_temp_factor(atom_iter)
Calculates the adverage temperature factor of all contained Atom instances and returns the adverage temperature factor.
  calc_CCuij(U, V)
Calculate the cooralation coefficent for anisotropic ADP tensors U and V.
  calc_distance(a1, a2)
Returns the distance between two argument atoms.
  calc_DP2uij(U, V)
Calculate the square of the volumetric difference in the probability density function of anisotropic ADP tensors U and V.
  calc_inertia_tensor(atom_iter, origin)
Calculate a moment-of-intertia tensor at the given origin assuming all atoms have the same mass.
  calc_Suij(U, V)
Calculate the similarity of anisotropic ADP tensors U and V.
  calc_torsion_angle(a1, a2, a3, a4)
Calculates the torsion angle between the four argument atoms.
  cross(u, v)
Cross product of u and v: Cross[u,v] = {-u3 v2 + u2 v3, u3 v1 - u1 v3, -u2 v1 + u1 v2}
  dmatrix(alpha, beta, gamma)
Returns the displacement matrix based on rotation about Euler angles alpha, beta, and gamma.
  dmatrixu(u, theta)
Return a displacement matrix caused by a right hand rotation of theta radians around vector u.
  length(u)
Calculates the length of u.
  normalize(u)
Returns the normalized vector along u.
  quaternionrmatrix(R)
Return a quaternion calculated from the argument rotation matrix R.
  rmatrix(alpha, beta, gamma)
Return a rotation matrix based on the Euler angles alpha, beta, and gamma in radians.
  rmatrixquaternion(q)
Create a rotation matrix from q quaternion rotation.
  rmatrixu(u, theta)
Return a rotation matrix caused by a right hand rotation of theta radians around vector u.
  rmatrixz(vec)
Return a rotation matrix which transforms the coordinate system such that the vector vec is aligned along the z axis.
  rquaternionu(u, theta)
Returns a quaternion representing the right handed rotation of theta radians about vector u.Quaternions are typed as Numeric Python numpy.arrays of length 4.
  test_module()

Function Details

addquaternion(q1, q2)

Adds quaterions q1 and q2. Quaternions are typed as Numeric Python numpy.arrays of length 4.

calc_angle(a1, a2, a3)

Return the angle between the three argument atoms.

calc_anisotropy(U)

Calculates the anisotropy of a atomic ADP tensor U. Anisotropy is defined as the smallest eigenvalue of U divided by the largest eigenvalue of U.

calc_atom_centroid(atom_iter)

Calculates the centroid of all contained Atom instances and returns a Vector to the centroid.

calc_atom_mean_temp_factor(atom_iter)

Calculates the adverage temperature factor of all contained Atom instances and returns the adverage temperature factor.

calc_CCuij(U, V)

Calculate the cooralation coefficent for anisotropic ADP tensors U and V.

calc_distance(a1, a2)

Returns the distance between two argument atoms.

calc_DP2uij(U, V)

Calculate the square of the volumetric difference in the probability density function of anisotropic ADP tensors U and V.

calc_inertia_tensor(atom_iter, origin)

Calculate a moment-of-intertia tensor at the given origin assuming all atoms have the same mass.

calc_Suij(U, V)

Calculate the similarity of anisotropic ADP tensors U and V.

calc_torsion_angle(a1, a2, a3, a4)

Calculates the torsion angle between the four argument atoms.

cross(u, v)

Cross product of u and v: Cross[u,v] = {-u3 v2 + u2 v3, u3 v1 - u1 v3, -u2 v1 + u1 v2}

dmatrix(alpha, beta, gamma)

Returns the displacement matrix based on rotation about Euler angles alpha, beta, and gamma.

dmatrixu(u, theta)

Return a displacement matrix caused by a right hand rotation of theta radians around vector u.

length(u)

Calculates the length of u.

normalize(u)

Returns the normalized vector along u.

quaternionrmatrix(R)

Return a quaternion calculated from the argument rotation matrix R.

rmatrix(alpha, beta, gamma)

Return a rotation matrix based on the Euler angles alpha, beta, and gamma in radians.

rmatrixquaternion(q)

Create a rotation matrix from q quaternion rotation. Quaternions are typed as Numeric Python numpy.arrays of length 4.

rmatrixu(u, theta)

Return a rotation matrix caused by a right hand rotation of theta radians around vector u.

rmatrixz(vec)

Return a rotation matrix which transforms the coordinate system such that the vector vec is aligned along the z axis.

rquaternionu(u, theta)

Returns a quaternion representing the right handed rotation of theta radians about vector u.Quaternions are typed as Numeric Python numpy.arrays of length 4.

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