Basic routines for internal to cartesian coordinate conversion #1311
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I hope there is agreement as to how something like this could be useful. I included a test to show how you can place atoms based on internal coordinates using a Z-matrix-like entry.
swails
reviewed
Jun 9, 2023
| u /= sqrt(np.dot(u, u)) | ||
| return u | ||
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| # Skipping type annotations for Atom bc it causes a circular import |
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At the bottom of the file you can do this:
if TYPE_CHECKING: # must be imported from typing
from .topologyobjects import AtomThen you can use strings as type hints:
def local_axes(atom1: "Atom", atom2: "Atom", atom3: "Atom") -> np.ndarray:|
There are a number of places where it'd be useful to do Zmat to cartesian transformations (e.g., CHARMM RTF files). I'm good adding this. |
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I hope there is agreement as to how something like this could be useful. I included a test to show how you can place atoms based on internal coordinates using a Z-matrix-like entry.