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Adds centre of geometry and centre of mass functionality #47
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Added a new keyword: center; Defaults to 'Geometry' for future proofing. get_molecules now calculates the center of the molecules.
Added a new keyword: center; Defaults to 'Geometry' for future proofing. get_molecules now calculates the center of the molecules.
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Can you add the new tutorial so that it will appear on the documentation pages. This would involve editing the notebooks.md
file and adding this tutorial to the list.
"import matplotlib.pyplot as plt\n", | ||
"from kinisi.analyze import DiffusionAnalyzer\n", | ||
"import warnings\n", | ||
"warnings.filterwarnings(\"ignore\", category=UserWarning)" |
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Does an error get raised if you don't have this?
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This suppresses warnings about missing atom mass data from MDAnalysis, although these warnings are very small:
"UserWarning: Failed to guess the mass for the following atom types: SI warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))"
docs/source/mda_COG.ipynb
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] | ||
}, | ||
{ | ||
"cell_type": "code", |
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Can you delete the final empty cell please.
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Done.
kinisi/parser.py
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new_drift_indices = list(range(n_molecules, n_molecules + len(drift_indices))) | ||
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if new_coords.shape[2] != 1: | ||
new_coords = np.expand_dims(new_coords, axis=2) |
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Is there code duplication that we can avoid here?
I think this is ready to merge. Are you happy for me to go ahead @jd15489? |
I am happy for it to be merged. |
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