joseph-ellaway / ramachandran_plotter Goto Github PK

Currently, the Ramachandran plotter program requires the installation of the Phenix Suite in order to generate dihedral angles of the user's given protein. This is being changed to remove the reliance on the Phenix Suite (regardless of its power and standalone utility) to instead use the Python module Biopython. This will enable more widespread use of the plotting algorithm.

Describe the bug
The plot is not drawn because latex could not be found.

To Reproduce
Steps to reproduce the behavior:

1. Go to Google Colab
2. install dependencies:
   !pip install numpy pandas matplotlib scipy biopython matplotlib argparse opencv-python
3. fetch a .pdb file:
   !wget https://files.rcsb.org/download/6GVE.pdb
4. Install Ramachandran_Plotter:
   !git clone https://github.com/Joseph-Ellaway/Ramachandran_Plotter.git
5. Change directory:
   %cd Ramachandran_Plotter and move 6GVE.pdb into the directory.
6. Run program:
   !python RamachandranPlotter.py --pdb 6GVE.pdb --plot_type 0
7. See error:

Traceback (most recent call last):
  File "/usr/local/lib/python3.7/dist-packages/matplotlib/texmanager.py", line 306, in _run_checked_subprocess
    stderr=subprocess.STDOUT)
  File "/usr/lib/python3.7/subprocess.py", line 411, in check_output
    **kwargs).stdout
  File "/usr/lib/python3.7/subprocess.py", line 488, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/usr/lib/python3.7/subprocess.py", line 800, in __init__
    restore_signals, start_new_session)
  File "/usr/lib/python3.7/subprocess.py", line 1551, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'latex': 'latex'

Expected behavior
The plot should be drawn.

Desktop (please complete the following information):

• OS: Mac 10.14
• Browser [chrome]

Additional context
I assume that Latex is used to draw the phi and psi symbols. It may be more universal to use the ASCI codes ( u03A6, u03A8).

Change cv function to parse background through memory instead of save-delete step.

Utilise mmCIF parsing, potentially using Gemmi.

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

Describe the solution you'd like
A clear and concise description of what you want to happen.

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.