4.4.7. propka.vector_algebra

4.4.7.1. Vector calculations

Vector algebra for PROPKA.

Functions

angle(avec, bvec)	Get the angle between two vectors.
angle_degrees(avec, bvec)	Get the angle between two vectors in degrees.
rotate_atoms_around_y_axis(theta)	Get rotation matrix for y-axis.
rotate_atoms_around_z_axis(theta)	Get rotation matrix for z-axis.
rotate_multi_vector_around_an_axis(theta, …)	Rotate a multi-vector around an axis.
rotate_vector_around_an_axis(theta, axis, vec)	Rotate vector around an axis.
signed_angle_around_axis(avec, bvec, axis)	Get signed angle of two vectors around axis in radians.

Classes

Matrix4x4([a11i, a12i, a13i, a14i, a21i, …])	A 4-by-4 matrix class.
MultiVector([atom1, atom2])	Collection of vectors for multiple configurations of atoms.
Vector([xi, yi, zi, atom1, atom2])

class propka.vector_algebra.Matrix4x4(a11i=0.0, a12i=0.0, a13i=0.0, a14i=0.0, a21i=0.0, a22i=0.0, a23i=0.0, a24i=0.0, a31i=0.0, a32i=0.0, a33i=0.0, a34i=0.0, a41i=0.0, a42i=0.0, a43i=0.0, a44i=0.0)

A 4-by-4 matrix class.

class propka.vector_algebra.MultiVector(atom1=None, atom2=None)

Collection of vectors for multiple configurations of atoms.

TODO - this class does not appear to be used or covered by tests

do_job(job)

Append vectors to configuration.

Parameters

job – name of function to apply to vectors

Returns

TODO - figure out what this is

generic_operation(operation, other)

Perform a generic operation between two MultiVector objects.

Parameters

• operation – operation to perform (string)

• other – other MultiVector object

static generic_self_operation(_)

TODO - delete this.

property get_result

Return the latest result.

rescale(new_length)

Rescale multi-vector to new length.

Parameters

new_length – new length for multi-vector

Result:

MultiVector object

class propka.vector_algebra.Vector(xi=0.0, yi=0.0, zi=0.0, atom1=None, atom2=None)

length()

Return vector length.

orthogonal()

Returns a vector orthogonal to self

rescale(new_length)

Rescale vector to new length while preserving direction

sq_length()

Return vector squared-length

propka.vector_algebra.angle(avec, bvec)

Get the angle between two vectors.

Parameters

• avec – vector 1

• bvec – vector 2

Returns

angle in radians

propka.vector_algebra.angle_degrees(avec, bvec)

Get the angle between two vectors in degrees.

Parameters

• avec – vector 1

• bvec – vector 2

Returns

angle in degrees

propka.vector_algebra.rotate_atoms_around_y_axis(theta)

Get rotation matrix for y-axis.

Parameters

theta – angle of rotation (radians)

Returns

rotation matrix

propka.vector_algebra.rotate_atoms_around_z_axis(theta)

Get rotation matrix for z-axis.

Parameters

theta – angle of rotation (radians)

Returns

rotation matrix

propka.vector_algebra.rotate_multi_vector_around_an_axis(theta, axis, vec)

Rotate a multi-vector around an axis.

NOTE - both axis ans v must be MultiVectors.

Parameters

• theta – angle (in radians)

• axis – multi-vector axis

• vec – multi-vector vector

propka.vector_algebra.rotate_vector_around_an_axis(theta, axis, vec)

Rotate vector around an axis.

Parameters

• theta – rotation angle (in radians)

• axis – axis for rotation

• vec – vector to rotate

Returns

rotated vector

propka.vector_algebra.signed_angle_around_axis(avec, bvec, axis)

Get signed angle of two vectors around axis in radians.

Parameters

• avec – vector 1

• bvec – vector 2

• axis – axis

Returns

angle in radians