python实现mask矩阵（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