CIR4MICS ("ceramics") is a pipeline that creates artificial datasets of rotationally symmetric structures. Out of the box, it generates structurally variable synthetic Nuclear Pore Complexes (NPCs) based on architectural models of the true NPC. Users can select one or more N- or C-terminally tagged NPC proteins, and simulate a wide range of geometric variations. Rotationally symmetric structures such as the NPC are also represented as a spring-model such that arbitrary deforming forces, of user-defined magnitudes, simulate irregularly shaped variations.
- python
- pip (https://pip.pypa.io/en/stable/installation/)
- git
- jupyter-lab (or any application capable of running the Ipython notebooks under /notebooks. Jupyter notebook or PyCharm are other options)
Open a terminal where you want to install the project
Recommended Windows command line shells are Windows powershell or cmd.exe. Alternatively use Windows Subsystem for Linux (WSL).
Open a terminal of choice
Clone this repository:
Tip: Copy/paste commands to avoid typos
git clone https://github.com/uhlmanngroup/cir4mics.git
Change to the directory folder:
cd cir4mics
pip install cir4mics
Skip to "Tutorials" if Installation via Option A was successfull
pip install poetry
or following: https://python-poetry.org/docs/
From the same directory as before
Create or start a virtual environment. Packages installed here will be isolated from the rest of the system, avoiding unfavourable crosstalk.
poetry shell
The name of the virtual environment should now be indicated in round brackets to the left of the command line prompt.
If there are issues with this, try first restarting the terminal and then closing any existing environments, such as conda environments.
Dependencies are installed according to pyproject.toml and poetry.lock
poetry install
If you are already aware of what's in call_functions.py (See Tutorials)
poetry run python cir4mics/call_functions.py
exit
Run from within the poetry shell and the right working directory (see above).
jupyter-lab notebooks/NPC_testlab.ipynb
- Start an IDE of your choice
- Load cir4mics/cir4mics/call_functions.py
New models can be defined manually, or using structural models from PDB.
jupyter-lab notebooks/Include_models.ipynb
Dynamics do not reflect true NPC dynamics, but might be useful when hard to predict dynamics are of interest
jupyter-lab notebooks/Dynamics.ipynb
jupyter-lab notebooks/Notes_on_imaging_datasets.ipynb
Windows: Git Bash struggles to open poetry shell
Solution: Use Powershell, cmd.exe, or WSL
see: python-poetry/poetry#6495
Windows: poetry install is unable to install debugpy
Solution: run poetry config installer.modern-installation false
see: microsoft/debugpy#1246
Windows: powershell does not execute poetry shell and returns
<filepath> cannot be loaded because running scripts is disabled on this system error
Solution:
- Open the powershell as administrator
- Run
Set-ExecutionPolicy RemoteSigned
See: https://www.sharepointdiary.com/2014/03/fix-for-powershell-script-cannot-be-loaded-because-running-scripts-is-disabled-on-this-system.html
Windows: Issues with Microsoft C++ Build Tools (https://visualstudio.microsoft.com/visual-cpp-build-tools/):
Solution: Use at most version 3.10
Windows: Powershell upon running poetry shell returns Virtual environment already activated.
Solution: Restart the computer
See: https://visualstudio.microsoft.com/visual-cpp-build-tools/