Biomedical-final-project

# Using this reponsitory to realize 3 functions:
1. Generate a MODEL to evaluate stereochemical quality of a given protein structure (with coordinates);
2. Using interacted plot to view distribution of phi and psi of a single protein, a chain even a residue, or more;
3. 3D structure of the choosed .pdb file

Pre-processing

See details in 合并df.zip
data cleaning and merge.
Verify the data with Biopython output.
![image](gallery/verify.png)

RAMAplot model

See details in code_for_RAMA_plot.ipynb
References: Morris AL, MacArthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein structure coordinates. Proteins. 1992;12(4):345-364.

TOTAL WORKFLOW
Data process 1:
![image](gallery/process1.png)

Data process 2 (improved methods):
![image](/process2.png)

Interacted plot

The plot show the phi and psi based on above total dataframe from pre-processing
![image](gallery/verify.png)

Using NGLview

see details at https://github.com/nglviewer/nglview![image](https://user-images.githubusercontent.com/96851523/147740570-556d9e6c-b1a5-45f3-b674-7cb19329062f.png)
![image](gallery/3D_structure.png)