Team members: Harold Knoll, Rian Touchent, Armand Du Parc Locmaria, Kim NOEL
Last edit: March 31 2019
The files are:
- convert data minifold to python drawing.xls: This file is used to prepare the coordinates of the amino acid of the protein
- draw_protein_3.py: This file is used to draw in 3D the amino acid chain in 3D
The purpose is to plot in 3D the proteins avalaible in the project MiniFold. The dataset was exctracted from ProteinNet project.
In this projet we are able to plot the proteins in 3D based on the coordinates of the amino acids.
The protein data are available here and the structure of the data is explained here. The compressed folders can be extracted with 7-zip.
The data to retreive are located in the 'Tertiary structure section'.
- Line 2 is to identify each 3x3 matrix
- From line 3 to 5 is to paste the text from the data of the Tertiary structure section
- Lines 7 to 10 are dedicated to replace the decimal separator, when needed
- Line 11 is used to paste the chain of amino acid. It is possible to split the string into multiple single symbol by using the python function list(string)
- Lines 13 to 16 are used to concatenate the coordinates in a format easy to use in python script.
- Line 16 is used to concatenate the amino acids in a format easy to use in python script.
- Cells B22 and B23 are to be copy and paste into the following python file into the variables data and amine_acid
- Line 66 is where the processed data of the 3x3 matrices from the previous file can be paste
- Line 70 is where the processed data of the amino acid from the previous file can be paste
See the gallery on the Facebook page Plot MiniFold
