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"description": "# moltransform \ud83d\udcbb\u2697\ufe0f\n\n\n\n\n\n\n\n\nMolecular transformations for graphic displaying using Cartesian coordinates.\n\n## How to use it\n\n#### Generalities:\nThis 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.\n\n### Opening a file\n\nTo load a file, we will use the `read_xyz` function by passing to it the path to the corresponding file to be opened.\n\nAn example on how to load a `.xyz` file:\n```bash\n>>> from moltransform.io import read_xyz\n>>> positions_matrix = read_xyz(\"path/to/file.xyz\")\n```\n\n### Centering coordinates\n\nCenter the molecules' coordinates by finding the center position of all `(x, y, z)` coordinates.\n```bash\n>>> from moltransform.transform import center\n>>> centered_positions = center(positions_matrix)\n```\n\n### Translating coordinates\n\nTranslate a molecule using a specific vector `(a, b, c)`. This implies:\n\n\t![](\"https://latex.codecogs.com/svg.latex?\\fn_cm&space;\\hspace*{-18}&space;x&space;\\rightarrow&space;x&space;+&space;a,\\newline&space;y&space;\\rightarrow&space;y&space;+&space;b,\\newline&space;z&space;\\rightarrow&space;z&space;+&space;c\" "\\"\\hspace*{-18}")
\n\n\n```bash\n>>> from moltransform.transform import translate\n>>> translated_positions = translate(positions_matrix, [a, b, c])\n```\n\n\n### Scaling coordinates\n\nScale the molecule along the 3-axis by a vector `(a, b, c)`. This implies:\n\n\t![](\"https://latex.codecogs.com/svg.latex?\\fn_cm&space;\\hspace*{-18}&space;x&space;\\rightarrow&space;ax,\\newline&space;y&space;\\rightarrow&space;by,\\newline&space;z&space;\\rightarrow&space;cz\" "\\"\\hspace*{-18}")
\n\n\n```bash\n>>> from moltransform.transform import scale\n>>> scaled_positions = scale(positions_matrix, [a, b, c])\n```\n\n### Saving into a file\n\nTo 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**.\n\nAn example on how to save into a `.xyz` file:\n```bash\n>>> from moltransform.io import write_xyz\n>>> write_xyz(\"path/to/file.xyz\", positions_matrix)\n```",
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