| import os |
|
|
| import numpy as np |
|
|
|
|
| def format(fname: str) -> str: |
| """ |
| Extract format extension from file name. |
| |
| Parameters |
| ---------- |
| fname : str |
| File name |
| |
| Returns |
| ------- |
| str |
| File extension |
| |
| Notes |
| ----- |
| The file extension is returned without the `.` character, i.e. for the file |
| `path/filename.ext` the string `ext` is returned. |
| |
| If a file is compressed, the `.gz` extension is ignored. |
| """ |
| name, ext = os.path.splitext(fname) |
|
|
| if ext == ".gz": |
| _, ext = os.path.splitext(name) |
|
|
| return ext[1:] |
|
|
|
|
| def molformat(fname: str) -> str: |
| """ |
| Extract an OpenBabel-friendly format from file name. |
| |
| Parameters |
| ---------- |
| fname : str |
| File name |
| |
| Returns |
| ------- |
| str |
| File extension in an OpenBabel-friendly format |
| |
| Notes |
| ----- |
| File types in OpenBabel do not always correspond to the file extension. This |
| function converts the file extension to an OpenBabel file type. |
| |
| The following table shows the different conversions performed by this function: |
| |
| ========= ========= |
| Extension File Type |
| --------- --------- |
| xyz XYZ |
| ========= ========= |
| """ |
|
|
| ext = format(fname) |
|
|
| if ext == "xyz": |
| |
| ext = "XYZ" |
|
|
| return ext |
|
|
|
|
| def deg_to_rad(angle: float) -> float: |
| """ |
| Convert angle in degrees to angle in radians. |
| |
| Parameters |
| ---------- |
| angle : float |
| Angle (in degrees) |
| |
| Returns |
| ------- |
| float |
| Angle (in radians) |
| """ |
|
|
| return angle * np.pi / 180.0 |
|
|
|
|
| def rotate( |
| v: np.ndarray, angle: float, axis: np.ndarray, units: str = "rad" |
| ) -> np.ndarray: |
| """ |
| Rotate vector. |
| |
| Parameters |
| ---------- |
| v: numpy.array |
| 3D vector to be rotated |
| angle : float |
| Angle of rotation (in `units`) |
| axis : numpy.array |
| 3D axis of rotation |
| units: {"rad", "deg"} |
| Units of `angle` (in radians `rad` or degrees `deg`) |
| |
| Returns |
| ------- |
| numpy.array |
| Rotated vector |
| |
| Raises |
| ------ |
| AssertionError |
| If the axis of rotation is not a 3D vector |
| ValueError |
| If `units` is not `rad` or `deg` |
| """ |
|
|
| assert len(axis) == 3 |
|
|
| |
| axis = axis / np.linalg.norm(axis) |
|
|
| if units.lower() == "rad": |
| pass |
| elif units.lower() == "deg": |
| angle = deg_to_rad(angle) |
| else: |
| raise ValueError( |
| f"Units {units} for angle is not supported. Use 'deg' or 'rad' instead." |
| ) |
|
|
| t1 = np.outer(axis, np.inner(axis, v)).T |
| t2 = np.cos(angle) * np.cross(np.cross(axis, v), axis) |
| t3 = np.sin(angle) * np.cross(axis, v) |
|
|
| return t1 + t2 + t3 |
|
|
|
|
| def center_of_geometry(coordinates: np.ndarray) -> np.ndarray: |
| """ |
| Center of geometry. |
| |
| Parameters |
| ---------- |
| coordinates: np.ndarray |
| Coordinates |
| |
| Returns |
| ------- |
| np.ndarray |
| Center of geometry |
| """ |
|
|
| assert coordinates.shape[1] == 3 |
|
|
| return np.mean(coordinates, axis=0) |
|
|
|
|
| def center(coordinates: np.ndarray) -> np.ndarray: |
| """ |
| Center coordinates. |
| |
| Parameters |
| ---------- |
| coordinates: np.ndarray |
| Coordinates |
| |
| Returns |
| ------- |
| np.ndarray |
| Centred coordinates |
| """ |
|
|
| return coordinates - center_of_geometry(coordinates) |
|
|
