How to calculate centroid in python

Question

I am starting to program in python. I am working on structural coordinates. I have a pdb structure that has xyz coordinate information (last three col)

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 requests.

How can I calculate the centroid structure from xyz coordinates.
From the centroid, I want to draw a sphere of radius 20 cm.

 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 center point like ??????

Answer 1

First of all, an easier way to read your file is with the numpy genfromtxt function. You do not need to import a string, and you do not need to iterate over all the lines and add text or count characters.

 from __future__ import division import numpy as nx data = nx.genfromtxt('file.pdb') 

Then, the last three columns can be accessed as:

 data[:, -3:] 

If the first : means "all rows", and -3: means from the third to the last column to the last column.

So, you can average them as such:

 nx.mean(data[:,-3:], axis=0) 

where the axis=0 argument tells nx.mean to take the average of the first ( 0th ) axis. It looks like this:

 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:

1) delete this line: import math as mean , which imports the entire math module and renames it mean . What you intended was from math import mean , which imports the mean function from the math module. But in your code, you still use the math function from the numpy ( nx ) module, so you never used the math version.

2) your loop has no indentation, which means that you either incorrectly inserted into StackOverflow, or your loops incorrectly indented. This is probably what your code looks like:

 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 idcord gets every empty cycle every time and calculates a new centroid for each particle. You don’t even need a loop if you immediately import a data file as described above. In fact, all of your code could be:

 from __future__ import division import numpy as nx data = nx.genfromtxt('file.pdb') nx.mean(data[:,-3:], axis=0) 

Answer 2

try it

 import numpy as nx X = nx.rand(10,3) # generate some number centroid = nx.mean(X) print centroid