stacker.vector module

Vector class used for SSF and PSF Calculation

This module defines the Vector datatype that’s used to store position (x,y,z) information for the atoms and residues in an MD Simulation. Documentation is provided for reference.

class Vector(x, y, z)

Bases: object

Represents a 3D vector with x, y, and z components.

This class defines a data type ‘Vector’ that represents a 3D vector with x, y, and z components, assuming the vector originates at the origin (0,0,0). Expands the numpy.array object.

Attributes:

xfloat

The x-component of the vector.

yfloat

The y-component of the vector.

zfloat

The z-component of the vector.

Methods

calculate_cross_product(b)	Calculate the cross product of two vectors.
calculate_projection(b)	Calculate the projection of this vector onto vector b.
magnitude()	Calculate the magnitude (length) of the vector.
scale(a)	Scale the vector by a scalar a.

__init__(x, y, z)

Initialize a Vector instance.

Parameters:

xfloat

The x-component of the vector.

yfloat

The y-component of the vector.

zfloat

The z-component of the vector.

calculate_cross_product(b)

Calculate the cross product of two vectors.

Calculates the cross product of two vectors, which is the unit vector that is perpendicular to both vectors.

Parameters:

bVector

The second vector to calculate the cross product with.

Returns:

Vector

The resulting vector from the cross product.

magnitude()

Calculate the magnitude (length) of the vector.

Returns:

float

The magnitude (length) of the vector.

calculate_projection(b)

Calculate the projection of this vector onto vector b.

Parameters:

bVector

The vector to project onto.

Returns:

Vector

The resulting vector from the projection.

scale(a)

Scale the vector by a scalar a.

Parameters:

afloat

The scalar to scale the vector by.

Returns:

Vector

The scaled vector.