propka.vector_algebra

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_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.
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.Vector(xi: float = 0.0, yi: float = 0.0, zi: float = 0.0, atom1: _XYZ | None = None, atom2: _XYZ | None = None)

cross(other: _XYZ)

Cross product.

length() → float

Return vector length.

orthogonal()

Returns a vector orthogonal to self

rescale(new_length: float)

Rescale vector to new length while preserving direction

sq_length()

Return vector squared-length

propka.vector_algebra.angle(avec: Vector, bvec: Vector) → float

Get the angle between two vectors.

Parameters:

• avec – vector 1

• bvec – vector 2

Returns:

angle in radians

propka.vector_algebra.angle_degrees(avec: Vector, bvec: Vector) → float

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: float) → Matrix4x4

Get rotation matrix for y-axis.

Parameters:

theta – angle of rotation (radians)

Returns:

rotation matrix

propka.vector_algebra.rotate_atoms_around_z_axis(theta: float) → Matrix4x4

Get rotation matrix for z-axis.

Parameters:

theta – angle of rotation (radians)

Returns:

rotation matrix

propka.vector_algebra.rotate_vector_around_an_axis(theta: float, axis: Vector, vec: Vector) → Vector

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: Vector, bvec: Vector, axis: Vector) → float

Get signed angle of two vectors around axis in radians.

Parameters:

• avec – vector 1

• bvec – vector 2

• axis – axis

Returns:

angle in radians