David Koes
David Koes
Fix issue with protonating charged ARG OB was placing a third H on NH1 using a random bond vector. The AssignBonds, which is suppose to match known protein residue bonding...
It would be great if there was a way to download the whole ChEMBL tarball and populate the cache in one command. This would be much faster than incrementally populating...
In colab output cells are sandboxed so viewers can only be updated from their associated cell. Could work around this by using broadcast channels. https://colab.research.google.com/notebooks/snippets/advanced_outputs.ipynb
Should support linear gradient with user supplied start and stop colors and a divergent gradient with start, stop and midpoint colors. Need to also support declarative usage for py3Dmol.
References examples that don't exist. Doesn't specify that builtin gradients can be specified by name.
For example, prody/mdanalysis/pybel/rdkit/openbabel molecule/atomgroup python objects. Some of these toolkit have embedded support for 3dmol (e.g. prody showProtein) but we could support them independently in py3Dmol (convert to a standard...
Shapes use an alpha property to indicate transparency while styles use opacity. This is confusing. Standardize on one and deprecate the other.
Stick style should show aromatic bonds with solid/dashed representation.
Currently zoomTo is agnostic to the visual radius of the atoms and uses a fixed minimum distance to ensure small molecules are viewable. A better approach would be to calculate...
probably implement this by interpreting spectrum is a property map of the resi with a gradient from the smallest to largest resi in the selection