moltransform 0.1.2

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moltransform 💻⚗️

Molecular transformations for graphic displaying using Cartesian coordinates.

How to use it

Generalities:

This package aims to transform (x, y, z) coordinates of molecules by reading and writing directly from a .xyz file and specifying the transformation vector. For each transformation function in the transform module, a verbose flag can be set True to print the transformation matrix to be applied for all (x, y, z) coordinates.

Opening a file

To load a file, we will use the read_xyz function by passing to it the path to the corresponding file to be opened.

An example on how to load a .xyz file:

>>> from moltransform.io import read_xyz
>>> positions_matrix = read_xyz("path/to/file.xyz")

Centering coordinates

Center the molecules' coordinates by finding the center position of all (x, y, z) coordinates.

>>> from moltransform.transform import center
>>> centered_positions = center(positions_matrix)

Translating coordinates

Translate a molecule using a specific vector (a, b, c). This implies: $$x \rightarrow x + a\y \rightarrow y + b\z \rightarrow z + c$$

>>> from moltransform.transform import translate
>>> translated_positions = translate(positions_matrix, [a, b, c])

Scaling coordinates

Scale the molecule along the 3-axis by a vector (a, b, c). This implies: $$x \rightarrow ax\y \rightarrow by\z \rightarrow cz$$

>>> from moltransform.transform import scale
>>> scaled_positions = scale(positions_matrix, [a, b, c])

Saving into a file

To save transformed coordinates into a file, we will use the write_xyz function by passing to it the path to the corresponding file to be created.

An example on how to save into a .xyz file:

>>> from moltransform.io import write_xyz
>>> write_xyz("path/to/file.xyz", positions_matrix)