Basic routines for internal to cartesian coordinate conversion #1311
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 | ||
|
|
||
| # Skipping type annotations for Atom bc it causes a circular import |
Contributor
There was a problem hiding this comment.
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:
Contributor
|
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. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.