ProtSpace3D

This is a bachelor thesis project, Development of protein-embedding visualization tool.

Installing dependencies

Python-poetry(https://python-poetry.org/) is used for installing the dependencies. Follow the instruction on the website to install poetry. After that run

poetry install

to install the dependencies for this project.

Running the script

The script to be executed is processing.py with the arguments:

->  -d          Name of the folder which holds the required data, .h5 .csv & .fasta (String)
->  -b          Name of the files which are in the data folder, requires equal names (String)
->  --sep       The character which seperates the columns in the .csv file (Character)
->  --uid_col   The column number which holds the unique ID, starting from 0 (Integer)
->  --html_cols If set, html file(s) of the selected column(s) is saved in data directory, starting from 1 ignoring the uid_col (Integer)
->  --pdb       Name of the directory in the data directory, which holds the .pdb files for viewing the molecule (String)

Example:

poetry run python app.py -d data/ex1 -b VA

or with molecule visualization

poetry run python protspace3d/app.py -b Conotoxins_try1_mapped -d data/ex3 --pdb pdb