contact map

蛋白质接触图使用二元二维矩阵表示三维蛋白质结构的所有可能的氨基酸残基对之间的距离。

 计算contact map

导入库

import pandas as pd
import numpy as np
from Bio import SeqIO
import matplotlib.pyplot as plt
import requests 
from sklearn.metrics import pairwise_distances
%matplotlib inline

定义坐标提取函数

def get_ca_coords(pdb='1LUC', chain='A'):
    
    url = f'https://files.rcsb.org/download/{pdb}.pdb'
    r = requests.get(url)
    r.raise_for_status()
    
    lines = r.text.splitlines()
    
    out = []
    
    for line