如何在python中计算质心
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How to Calculate Centroid in python
提问by awanit
I'm beginner to python coding. I'm working over structural coordinates. I have pdb structure which have xyz coordinate information (last three col)
我是 python 编码的初学者。我正在研究结构坐标。我有 pdb 结构，其中包含 xyz 坐标信息（最后三个列）
ATOM 1 N SER A 1 27.130 7.770 34.390
ATOM 2 1H SER A 1 27.990 7.760 34.930
ATOM 3 2H SER A 1 27.160 6.960 33.790
ATOM 4 3H SER A 1 27.170 8.580 33.790
ATOM 5 CA SER A 1 25.940 7.780 35.250
ATOM 6 CB SER A 1 25.980 9.090 36.020
ATOM 7 OG SER A 1 26.740 10.100 35.320
ATOM 8 HG SER A 1 26.750 10.940 35.860
ATOM 9 C SER A 1 24.640 7.790 34.460
ATOM 10 O SER A 1 24.530 8.510 33.500
ATOM 11 N CYS A 2 23.590 7.070 34.760
ATOM 12 H CYS A 2 23.590 6.550 35.610
ATOM 13 CA CYS A 2 22.420 7.010 33.900
ATOM 14 CB CYS A 2 21.620 5.760 34.270
ATOM 15 SG CYS A 2 22.480 4.210 33.970
ATOM 16 C CYS A 2 21.590 8.220 34.040
ATOM 17 O CYS A 2 21.370 8.690 35.160
- I have 1000 atoms in my structure.
- I have two queries.
- 我的结构中有 1000 个原子。
- 我有两个疑问。
How I can calculate the centroid of the structure from xyz coordinates.
From the centroid I want to draw a sphere of radius 20cm.
我如何从 xyz 坐标计算结构的质心。
从质心我想画一个半径为 20 厘米的球体。
I try this
from __future__ import division
import math as mean
import numpy as nx
from string import*
infile = open('file.pdb', 'r') #open my file
text1 = infile.read().split('\n')
infile.close()
text = []
for i in text1:
if i != '':
text.append(i)
for j in text:
x1 = eval(replace(j[30:38], ' ', '')) #extract x-coordinate
y1 = eval(replace(j[38:46], ' ', '')) #extract y-coordinate
z1 = eval(replace(j[46:54], ' ', '')) #extract z-coordinate
idcord = []
idcord.append(x1); idcord.append(y1); idcord.append(z1)
centroid = nx.mean(idcord)
print centroid
it gives the centroid of each atom (xyz) i need a central point how??????
它给出了每个原子的质心（xyz）我需要一个中心点如何？？？？？？
回答by lsb123
try this
尝试这个
import numpy as nx
X = nx.rand(10,3) # generate some number
centroid = nx.mean(X)
print centroid
回答by askewchan
First of all, an easier way to read your file is with numpy's genfromtxtfunction. You don't need to import string, and you don't need to loop through all the lines and append text or count the characters.
首先，读取文件的更简单方法是使用 numpy 的genfromtxt函数。您不需要导入字符串，也不需要遍历所有行并附加文本或计算字符数。
from __future__ import division
import numpy as nx
data = nx.genfromtxt('file.pdb')
Then, the last three columns can be accessed as:
然后，可以通过以下方式访问最后三列：
data[:, -3:]
Where the first :means "all rows", and -3:means from the third-to-last column to the last column.
其中第一个:表示“所有行”，-3:表示从倒数第三列到最后一列。
So, you can average them as such:
因此，您可以将它们平均为：
nx.mean(data[:,-3:], axis=0)
where the axis=0argument tells nx.meanto take the average along the first (0th) axis. It looks like this:
其中axis=0参数告诉nx.mean取平均沿着第一（0th）轴。它看起来像这样：
In : data[:,-3:]
Out:
array([[ 27.13, 7.77, 34.39],
[ 27.99, 7.76, 34.93],
[ 27.16, 6.96, 33.79],
[ 27.17, 8.58, 33.79],
[ 25.94, 7.78, 35.25],
[ 25.98, 9.09, 36.02],
[ 26.74, 10.1 , 35.32],
[ 26.75, 10.94, 35.86],
[ 24.64, 7.79, 34.46],
[ 24.53, 8.51, 33.5 ],
[ 23.59, 7.07, 34.76],
[ 23.59, 6.55, 35.61],
[ 22.42, 7.01, 33.9 ],
[ 21.62, 5.76, 34.27],
[ 22.48, 4.21, 33.97],
[ 21.59, 8.22, 34.04],
[ 21.37, 8.69, 35.16]])
In : np.mean(data[:,-3:], axis=0)
Out: array([ 24.74647059, 7.81117647, 34.64823529])
Some other things:
其他一些事情：
1) remove this line: import math as mean, which imports the entire mathmodule and renames it mean. What you intended was from math import meanwhich imports the meanfunction from the mathmodule. But in your code, you end up using the mathfunction from the numpy(nx) module anyway, so you never used the mathversion.
1) 删除这一行: import math as mean，它导入整个math模块并将其重命名为mean. 你想要的是从模块中from math import mean导入mean函数math。但是在您的代码中，无论如何您最终都会使用( ) 模块中的math函数，因此您从未使用过该版本。numpynxmath
2) your loop is not indented, which means you either pasted incorrectly into StackOverflow, or your loop is incorrectly indented. Possibly, this is what your code actually looks like:
2) 你的循环没有缩进，这意味着你要么错误地粘贴到 StackOverflow 中，要么你的循环缩进不正确。可能，这就是您的代码实际的样子：
for j in text:
x1 = eval(replace(j[30:38], ' ', '')) #extract x-coordinate
y1 = eval(replace(j[38:46], ' ', '')) #extract y-coordinate
z1 = eval(replace(j[46:54], ' ', '')) #extract z-coordinate
idcord = []
idcord.append(x1); idcord.append(y1); idcord.append(z1)
centroid = nx.mean(idcord)
print centroid
But the problem is that idcordgets set to an empty list everytime the loop goes through, and a new centroid is calculated, for each particle. You don't even need the loop at all if you import the data file all at once as above. In fact, your entire code can be:
但问题是每次循环通过时idcord都会设置为一个空列表，并为每个粒子计算一个新的质心。如果您像上面那样一次性导入数据文件，您甚至根本不需要循环。事实上，你的整个代码可以是：
from __future__ import division
import numpy as nx
data = nx.genfromtxt('file.pdb')
nx.mean(data[:,-3:], axis=0)
