• [Question] Make CLI unit tests work (somehow they are not run in GHA but locally); check missing lines in cli.py
• [Question] Unit tests for CLI: capture the standard output (if there's any) and check that it contains substrings that are only present in a successful execution (and in reverse) > How to do this?

core infrastructure

• Add Ligand class - see #21
• Use superfeature colors as defined in dynophore-0.2 output instead of hard-coded feature colors in definitions; update plots/nglview accordingly - see #22
• Use Ligand as Dynophore attribute? If ligand PDB block were part of JSON/PML files, that would be fantastic! #31

Plots (static/interactive)

• Interactive plots: Too slow for 20k frames. Optimize.
• Plots: Heatmap: Add x/y labels
• Add slider for frame range (min/max)
• Add % to plot labels / legends
• Use matplotlib.pyplot.eventplot for occurrence plots instead of simple dot plots... - see #23
• Interactive plots: Also select envpartners (depending on superfeature)? > Set minimum percentage cutoff to filter out low-coverage envpartners and superfeatures - see #23
• [TBD] Distance plots: Add distance cutoffs or interaction on/off - see #35
  • [Medium] Add marker for feature cutoffs (needs feature definitions added to pml file)
  • [Minor] Or add widget that toggles between "all frames" and "only frames where superfeature occurs"
  • Distance line plot: Add interaction-relevant distances as dots on-top
  • Distance histogram: Plot interaction-relevant distances only
• [Minor] Add tick to collapse envpartners with same residue/different atoms for one superfeature (e.g. ASP 89) - see #36

3D viz

• Feature clouds by superfeature ID? At the moment, pml only contains H-123344123124 IDs - can we add H[1234, 1235, ...] to pml?
• Check if dcd file has appropriate number of frames (e.g. 1000 frames) > For 20k frames this was not a problem in the Jupyter Notebook
• Add interpolation to nglview trajectory > Added nglview.player.TrajectoryPlayer(view) to notebooks.
• Add frame index to points in PML?
• [Minor] Add pocket residue side chains: We do not have all pocket residues in PML/JSON output but we can add to each superfeature the environmental partners. #28
• [Major] Temporal resolution of dynophore clouds (use point frame index) - see #32
  • Color clouds by frame index: What kind of color gradient shall we use? Keep feature color and use sequential colormap? Matplotlib has colormaps but can we use our hex colors as endpoint? HSV color model: https://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_rgb_to_hsv.html
  • Select cloud points by frame index range: Add slider that allows to select cloud points for selected frame range only? Do we need this?

2D viz

• 2D viz: Add 2D ligand view with highlighted features, as done in KinFragLib - see #17

CLI

• Make dcd optional!
• Add dynoviz demo

Package

• Make package conda-installable (help from Jaime)
• Make raise_keyerror_if_invalid_superfeature_name private!!

Documentation

• Add prominent link to tutorials?
• Fix code formatting here: https://dynophores.readthedocs.io/en/latest/installing.html > Decided it is ok to have some words highlighted in a different color.
• [Question] How to save widget images? (Missing on GH and RTD) #29

The viz.view2d module contains a first version of the 2D view of the structure-bound ligand with highlighted superfeatures. Added in PR #17.

In case, we toggle on the atom serial numbers, the visualization does not look so nice at the moment.

For later version, come back to improve this.

Update CI config file (use latest cookiecutter-cms template):
https://github.com/MolSSI/cookiecutter-cms/blob/main/%7B%7Bcookiecutter.repo_name%7D%7D/.github/workflows/CI.yaml

• Comment on static figure save (to produce HR figure files) #53
• Comment on bin size (expose this as method argument?)
• Update installation (we have conda package now!)

Check if problem in dynophores:

nglview throws TypeError for add_sphere because sphere center given as numpy.float but must be now float.

Look here: volkamerlab/opencadd#104

How can I generate the json file used in the tutorial ?

Technical TODOs for v1.0.0

Python package

• [Minor] Move to @wolberlab https://github.com/wolberlab: #45
• [Minor] Update installing (once conda-installable) + add Jupyter extensions (not installable via yml)
  • jupyter labextension install @jupyter-widgets/jupyterlab-manager nglview-js-widgets @jupyterlab/toc
  • Is this still necessary? Via dynophore conda installation, this was not needed... Double check with test user.

DynophoreApp

• Remove README from output folder
• Installers without date, only version?

Barcode plots: Collapse all features that belong to one envpartner.

See this issue: volkamerlab/opencadd#126

Update docs here: https://dynophores.readthedocs.io/en/latest/installing.html

nglview is working now with JupyterLab 3 - try out our notebooks and if everything works update environment.

nglviewer/nglview#955

See the description in s-weigand/flake8-nb#249

See: matplotlib/ipympl#391

Affects dyno.plot.interactive.superfeatures_vs_envpartners(dynophore)

Hi,

I just installed dynophores using conda.

When running dynoviz -h I get the following error message:

Traceback (most recent call last):
File "/home/bmc/miniconda3/envs/dyno/lib/python3.12/site-packages/matplotlib/style/core.py", line 137, in use
style = _rc_params_in_file(style)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/bmc/miniconda3/envs/dyno/lib/python3.12/site-packages/matplotlib/init.py", line 866, in _rc_params_in_file
with _open_file_or_url(fname) as fd:
File "/home/bmc/miniconda3/envs/dyno/lib/python3.12/contextlib.py", line 137, in enter
return next(self.gen)
^^^^^^^^^^^^^^
File "/home/bmc/miniconda3/envs/dyno/lib/python3.12/site-packages/matplotlib/init.py", line 843, in _open_file_or_url
with open(fname, encoding='utf-8') as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'seaborn'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/bmc/miniconda3/envs/dyno/bin/dynoviz", line 6, in
from dynophores.cli import main
File "/home/bmc/miniconda3/envs/dyno/lib/python3.12/site-packages/dynophores/init.py", line 8, in
from .viz import plot, view2d, view3d
File "/home/bmc/miniconda3/envs/dyno/lib/python3.12/site-packages/dynophores/viz/plot/init.py", line 6, in
from . import static
File "/home/bmc/miniconda3/envs/dyno/lib/python3.12/site-packages/dynophores/viz/plot/static.py", line 13, in
plt.style.use("seaborn")
File "/home/bmc/miniconda3/envs/dyno/lib/python3.12/site-packages/matplotlib/style/core.py", line 139, in use
raise OSError(
OSError: 'seaborn' is not a valid package style, path of style file, URL of style file, or library style name (library styles are listed in style.available)

System: Ubuntu 22.04.4 LTS

Thanks for helping me resolve this issue this issue!

The setup.py does not install all necessary libraries. Maybe add Docker distribution?

Add more documentation in dynophore notebook

• For 3D view, add all args explicitly and explain them in Markdown cell above
• Give a short intro for each plot type, what kind of data is shown and what options for visualization are given

Prettify notebook plots

• Check figure.max_open_warning for environmental barcode plots
• Try to reproduce error in environmental barcode plots when ticking "Collapse" in certain settings
• Heatmap: Do not allow 1e+02 numbers
• Remove (fig, ax) prints below plots in notebooks (left-over TODO from #33)
  • jupyter-widgets/ipywidgets#712
  • Example: In notebook, between widget and plot:

    (<Figure size 576x396 with 2 Axes>,
     <AxesSubplot:xlabel='Superfeature IDs', ylabel='Environmental partner IDs'>)
    

Hello,

Can I ask how the input files for dynophores, like 1KE7_dynophore.json, 1KE7_dynophore.cgo, etc , are generated? Thank you!

By default, we show dynophores in 3D using the NGL SphereBuffer representation.

Alternatively, we would like to offer the NGL PointBuffer representation which shows rendering artifacts. With time on our hands, look into this and make it ready for use.

Description

Move repo to @wolberlab: https://github.com/wolberlab

Todos

• Transfer repo; GH documentation
• Update all https://github.com/dominiquesydow/dynophores references (note: old URL will redirect to new URL; we will do the update anyways to avoid future dominiquesydow/wolberlab mixtures in the docs ect.)
  • https://github.com/wolberlab/dynophores
    • README.md
    • docs/installing.rst
    • dynophores/visz/view3d/interactive.py
  • https://github.com/conda-forge/dynophores-feedstock
    • README.md
    • meta.yaml
  • https://dynophores.readthedocs.io/
    • Update https://readthedocs.org/dashboard/dynophores/edit/

Our weekly CI failed. All notebooks using ipywidgets are broken with new version 8; affects e.g. nglview.

Error message:
AttributeError: 'super' object has no attribute '_ipython_display_'

See discussions here:
nglviewer/nglview#1032
jupyter-widgets/ipywidgets#3552

Solution for now:
Pin ipywidgets to version 7, see nglviewer/nglview#1033.

https://github.com/volkamerlab/teachopencadd/blob/daeb016bb89feb93813be925085aff47885225ce/devtools/test_env.yml#L11

Transfer from https://codecov.io/gh/dominiquesydow/dynophores/branch/master to https://codecov.io/gh/wolberlab/dynophores/branch/master may not work out-of-the-box.

Check if URL works after first CI pass on master on wolberlab/dynophores > No.

--

CI triggers CodeCov:

CI fails:
https://github.com/wolberlab/dynophores/runs/3653565981?check_suite_focus=true#step:8:49