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atse's Introduction

ATSE

This Code is an implementation for our paper "ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism"

Requirements

Python 3.x

Pytorch ~ 1.6

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atse's Issues

读取pssm矩阵的时候只读个位是bug吗?

def get_line_numpy(line, start=11, end=91, step=4):
    '''
    输入一行,返回处理后的np数组
    默认start是11,end是91,step是4
    start=10 end=69 step=3
    '''

    np_line = np.zeros([20])
    index = 0
    for symbol, num in zip(line[start:end:step], line[start + 1:end:step]):
        if symbol == '-':
            statu = -1
        else:
            statu = 1
        np_line[index] = statu * int(num)
        index = index + 1
    return np_line

难道不应该是:

def get_line_numpy(line, start=2, nums=20):
    """
    跳过行号和氨基酸符号,读取每行的20个值
    """
    return np.array(line.split()[start: start+nums], dtype=np.int)

不然,-10或者10都会读成0,而-11和11会变成1

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