的Python：轉換列向量名爲.xyz文件格式

Question

我有一個分子結構的列向量格式

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

我想這個轉換成一個名爲.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 

這很容易完成？如果難以添加原子類型，那麼只需將座標重新排列到列上就可以了（至少可以減少手動操作）。

Answer 1

我不明白什麼字母O，H，C的意思是如何添加這些信息（我不是化學家）。他們存放在哪裏？但是如果你是一個科學家，你可能使用numpy模塊。因此，這裏是一個簡單的解決方案，轉你的行三乘三：

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) 

輸出：

[['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