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
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