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charnley / rmsd

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
BSD 2-Clause "Simplified" License
495 stars 114 forks source link

rmsd package requires typing_extensions but missing from setup.py #95

Closed epeisach closed 1 year ago

epeisach commented 1 year ago

Create a new virtual environment:

% python3 -m venv /tmp/v3 % source /tmp/v3/bin/activate (v3) % pip install rmsd Collecting rmsd Using cached rmsd-1.5.0-py3-none-any.whl (17 kB) Collecting scipy Using cached scipy-1.9.3-cp310-cp310-macosx_10_9_x86_64.whl (34.3 MB) Collecting numpy Using cached numpy-1.24.0-cp310-cp310-macosx_10_9_x86_64.whl (19.8 MB) Installing collected packages: numpy, scipy, rmsd Successfully installed numpy-1.24.0 rmsd-1.5.0 scipy-1.9.3

% python3 Python 3.10.9 (main, Dec 15 2022, 18:25:35) [Clang 14.0.0 (clang-1400.0.29.202)] on darwin Type "help", "copyright", "credits" or "license" for more information.

from rmsd.calculate_rmsd import (NAMES_ELEMENT, centroid, check_reflections, rmsd)

Traceback (most recent call last): File "", line 1, in File "/private/tmp/v3/lib/python3.10/site-packages/rmsd/init.py", line 2, in from .calculate_rmsd import * File "/private/tmp/v3/lib/python3.10/site-packages/rmsd/calculate_rmsd.py", line 25, in from typing_extensions import Protocol ModuleNotFoundError: No module named 'typing_extensions'

charnley commented 1 year ago

Better typing control (removed typing_extension) and dropped support for Python 3.7.