的Python：转换列向量名为.xyz文件格式

Question

我有一个分子结构的列向量格式

x1 
y1 
z1 
x2 
y2 
z2 
x3 
y3 
z3 
x4 
y4 
z4 
x5 
y5 
z5 
x6 
y6 
z6 
x7 
y7 
z7 
x8 
y8 
z8 

我想这个转换成一个名为.xyz文件格式：

number of atoms 
comment line 
C x1 y1 z1 
H x2 y2 z2 
H x3 y3 z3 
C x4 y4 z4 
H x5 y5 z5 
H x6 y6 z6 
O x7 y7 z7 
O x8 y8 z8 

这很容易完成？如果难以添加原子类型，那么只需将坐标重新排列到列上就可以了（至少可以减少手动操作）。

Answer 1

我不明白什么字母O，H，C的意思是如何添加这些信息（我不是化学家）。他们存放在哪里？但是如果你是一个科学家，你可能使用numpy模块。因此，这里是一个简单的解决方案，转你的行三乘三：

import numpy as np 
import csv 

#assuming your vector is in a text file 
vector = np.genfromtxt('yourfilename.txt',dtype='str') 

a = np.array(vector) 
a = a.reshape((-1, 3)) 

print(a) 

输出：

[['x1' 'y1' 'z1'] 
['x2' 'y2' 'z2'] 
['x3' 'y3' 'z3'] 
['x4' 'y4' 'z4'] 
['x5' 'y5' 'z5'] 
['x6' 'y6' 'z6'] 
['x7' 'y7' 'z7'] 
['x8' 'y8' 'z8']] 

""" 
The output is a list of lists in which each element is a row. 
Numpy has a simple method to write a 2D array in a csv file : 
np.savetxt("youfilename.csv", a, delimiter=",") 
but since I get a bug in this moment, I will use a classical method. 
""" 
with open("output.csv", "w") as f: 
    writer = csv.writer(f) 
    writer.writerows(a) 

CSV文件：

x1,y1,z1 

x2,y2,z2 

x3,y3,z3 

x4,y4,z4 

x5,y5,z5 

x6,y6,z6 

x7,y7,z7 

x8,y8,z8