python实现mask矩阵示例(根据列表所给元素)

行和列的位置都在以下三个列表中的一列中，则对应位置为1，其余位置全为0

​ ——[7-56,239-327,438-454,522-556,574-586]

​ ——[57-85,96-112,221-238]

​ ——[113-220,328-437,455-521,557-573]

代码实现

def generateMaskBasedOnDom(dom_path, length):
  """
  :param dom_path: this is a file path, which contains the following information:
  [7-56,239-327,438-454,522-556,574-586][57-85,96-112,221-238][113-220,328-437,455-521,557-573]
  each [...] means one domain
  :param length: this is the length of this protein
  :return: the mask matrix with size length x length, 1 means inner domain residue pair, otherwise 0
  """
  # 读取文件
  with open(dom_path, "r", encoding="utf-8") as file:
    contents = file.readlines()

  # 获得mask位置数据
  list0 = []
  list1 = []
  list2 = []
  for list_idx, content in enumerate(contents):
    num_range_list = content.strip()[1:-1].split(",")
    for num_range in num_range_list:
      start_num = int(num_range.split("-")[0])
      end_num = int(num_range.split("-")[1])
      for num in range(start_num, end_num+1):
        if list_idx == 0:
          list0.append(num)
        elif list_idx == 1:
          list1.append(num)
        else:
          list2.append(num)

  mask = np.zeros((length, length))
  # 遍历矩阵每个元素
  for row in range(mask.shape[0]):
    for col in range(mask.shape[1]):
      if (row in list0 and col in list0) or (row in list1 and col in list1) or (row in list2 and col in list2):
        mask[row][col] = 1

  return mask

if __name__ == "__main__":

  # if no dom file ,please get dom file first
  with open("dom.txt", "w", encoding="utf-8") as f:
    f.write("[7-56,239-327,438-454,522-556,574-586]" + "\n" + "[57-85,96-112,221-238]" + "\n" + "[113-220,328-437,455-521,557-573]")

  file_path = "./dom.txt"
  protein_length = 1000  # mask_matrix size
  mask_matrix = generateMaskBasedOnDom(file_path, protein_length)
  print("*************Generate Mask Matrix Successful!*************")

  # 随机测试几组
  print(mask_matrix[7][56]) # 1
  print(mask_matrix[7][239]) # 1
  print(mask_matrix[8][57])  # 0
  print(mask_matrix[57][95]) # 0
  print(mask_matrix[113][573]) # 1

到此这篇关于python实现mask矩阵示例(根据列表所给元素)的文章就介绍到这了,更多相关python实现mask矩阵 内容请搜索我们以前的文章或继续浏览下面的相关文章希望大家以后多多支持我们！