mmLib.AtomMath

Package mmLib :: Module AtomMath

[show private | hide private]

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.

Generated by Epydoc 2.1 on Sun Apr 23 22:08:39 2006

http://epydoc.sf.net