/pdbs_secondary_structure_statistics

Linux GUI Program to calculate the percentage of each secondary structure for each input pdb file in a user specified directory

Primary LanguagePythonMIT LicenseMIT

pdbs secondary structure statistics DOI

Linux GUI Program to calculate the percentage of each secondary structure for each input pdb file in a user specified directory

Depedences

  1. linux OS (tested on ubuntu 20.04 LTS)
  2. python 3.8.2 or later
  3. anaconda or miniconda
  4. Gooey conda install -c conda-forge gooey(if you get errors during installation or runtime try installing gtk sudo apt-get install libgtk-3-dev)
  5. DSSP conda install -c salilab dssp
  6. biopython pip install biopython
  7. pandas pip install pandas

linux desktop app installation

  1. open a linux text editor and edit in the python file the shebang and the PATH to the dssp executable. To find where they are located in the system type:
which python3
which dssp
  1. convert to executable with chmod +x pdbs_secondary_structure_statistics_gui.py
  2. open a linux text editor and edit the PATHs in the .desktop file
  3. move the file to /usr/share/applications
  4. reboot your machine

Example output

The program's output file will look like:

For output explanation look up the DSSP codes