MolecularNodes

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TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'

17

**Describe the bug** loading MD lammps cg spica trajectory gives error and does not load. **To Reproduce** Topology: 4ypg-e.psf Trajectory: 4ypg-20fs.lammpsdump "Load" **Expected behavior** load md lammps trajectory without error...

alphataubio

v4.0.11 surface

3

**Is your feature request related to a problem? Please describe.** In [v4.0.11](https://github.com/BradyAJohnston/MolecularNodes/releases/tag/v4.0.11) a new way to depict surfaces was introduced. As far as I can tell the old method was...

Jojo109x

Missing VDW radius values for rarely used elements

1

The `molcularnodes/data.py::elements` dictionary contains information about elements, where the element symbols are keys to access a subdictionary for each element. The subdictionaries have keys such as 'name', 'atomic_number', 'standard_mass', and...

rbdavid

Molecule class implementation

6

Here's some notes that I have for the current implementation of the Molecule class: 1. I'm noticing some methods associated with the Molecule superclass that utilize `self.data` (see below), which...

rbdavid

Add trajectory smoothing when importing via MDAnalysis

4

Support potentially trajectory smoothing when importing an MD trajectory via MDAnalysis. (https://docs.mdanalysis.org/stable/documentation_pages/transformations/positionaveraging.html) Potential for in theory to add enable / disable support for a variety of transformations. Some of these...

BradyAJohnston

Guessing atom attributes based on atom names can lead to misinterpretations

3

Depending on the files being read into blender to instantiate a Molecule object, various atom attributes are likely to be missing that the MN Molecule object is expecting to have....

rbdavid

Currently the calculated centroid offset field is output, but this means it is recalculated and will be 0 when used outside of the node group (first image).  To fix,...

BradyAJohnston

Trouble loading trajectory

1

**Describe the bug** When I try to load my MD trajectory (in psf/dcd format) it crashes and the error indicates there are no coordinates in the MDA universe. If I...

msinclair-py

For `Style Ball and Stick` adds an option for visually splitting the single and double bonds.

BradyAJohnston

Blender has [changed their licensing requirements](https://extensions.blender.org/approval-queue/molecularnodes/#activity) for the extensions platform, requiring the change of the license to GPLv3 to continue uploading new versions to the extensions platform for hosting: >...

BradyAJohnston