She Zhang

Fixed a bug in calculating the height of clades when building a UPGMA tree

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This pull request addresses the issue that the UPGMA constructor yields a tree with wrong branch lengths. In some cases, it may even yield a tree with unequal distances from...

Hi, is there a way to obtain the isomeric SMILES string for a query? I've seen `canonical_smiles` under `molecule_structures` but I can't seem to find an entry for isomeric ones....

We should consider adding a callback function in `buildPDBEnsemble` to give users access to intermediate variables such as `atommap` and `unmapped`, replacing the current mechanism of output arguments. The callback...

Add support for weighted PCA and ICA/tICA?

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I think it is worth considering adding support for weighted PCA and ICA/tICA in ProDy. The former should be fairly easy, since it already exists to an extent in the...

The load function warns about ignoring the top keyword argument when top is not supplied

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With mdtraj 1.9.9, ``` import mdtraj mdtraj.load("some_hdf5_file.h5") ``` will trigger the following warning: ``` /Users/shezhang/miniconda3/envs/openeye-cryptic-pocket-detection-floes/lib/python3.9/site-packages/mdtraj/core/trajectory.py:439: UserWarning: top= kwargs ignored since this file parser does not support it warnings.warn('top= kwargs ignored...

Preserve bond orders when writing out/reading in HDF5 trajectory files

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Hi Developers, I noticed that the current HDF5 file interface doesn’t appear to support storing or reading bond orders: [Link to Code](https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/hdf5.py#L309-L368) Are there any plans to add this functionality?...