mmLib.AtomMath

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)`
	`calc_CCuij(U, V)`
	`calc_distance(a1, a2)` Returns the distance between two argument atoms.
	`calc_DP2uij(U, V)`
	`calc_Suij(U, 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 displacment 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.
	`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(u)` Return a rotation matrix which transforms the coordinate system such that the vector u is aligned along the z axis.
	`rquaternionu(u, theta)` Returns a quaternion representing the right handed rotation of theta radians about vector u.

Function Details

addquaternion(q1, q2)

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

calc_angle(a1, a2, a3)

Return the angle between the three argument atoms.

calc_distance(a1, a2)

Returns the distance between two argument atoms.

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 displacment 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.

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 arrays of length 4.

rmatrixu(u, theta)

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

rmatrixz(u)

Return a rotation matrix which transforms the coordinate system such that the vector u 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 arrays of length 4.

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