Plotting two 3D points from a textscan output

I have the following text file:

Eu3+             1

       10.06037350        -4.673610300        -1.834337367    
     1.22604929765      -2.02696902730      0.734136756877    
     10517.3113705      -9795.46057045      -2441.96899290   
  Eu3+             2
      -11.25268764         3.982158778        -4.411302032    
    0.239696547775E-01  0.719865908056      0.654664578760    
    -3423.27694546      -2308.86356341      -348.027397200

Whereby the entries are to be considered as (1) atom type (2) atom number (3)(4)(5) xyz coordinates (6)(7)(8)(9)(10)(11) irrelevant, and then repeated. I want to be able to represent a huge list of such data entries as atom positions and ultimately perform further calculations upon them, but currently I am only able to plot a single atom, using this code:

fid = fopen('twoatom.txt','r'); %read as a single cell

A = textscan(fid,'%s'); %perform textscan

A = A{1,1}(1:5); %Attain data as 1x5 cell array

a1 = A(1,:); %Atom type to vector

a2=str2double(A(2:end,:)); %Atom coordinates to vector

scatter3(a2(2),a2(3),a2(4))

But I have already had to ask for quite a bit of help to get this far, and am struggling to extend the code to accommodate a second atom. Could anyone enlighten me as to how this would be done? I am hoping that if someone can I will be able to extend the code myself to accommodate every atom in the file.

Any help would be greatly appreciated.

Kind regards,

Tom

[Cedric]

Could you attach one of these text files?

Answer 1

[sixwwwwww]

Dear Tom, you can do it as follows:

ID = fopen('filename.txt', 'r');
data = textscan(ID, '%s');
fclose(ID);
data = data{:};
atom_type = data(1:11:length(data));
atom_number = str2double(data(2:11:length(data)));
count = 1;
for i = 3:11:length(data)
    xyz(count, :) = str2double(data(i:i+2));
    count = count + 1;
end
scatter3(xyz(:,1), xyz(:,2), xyz(:,3));

I hope it helps. Good luck!

[Tom]

Hi sixww...

Thanks for your response, I am Matblabless for the next fews hours but I look forward to giving that a try! I may have a few questions for you, if you wouldn't mind answering them I would have to buy you a steak!

Kind regards,

Tom

[sixwwwwww]

You are welcome. Yes you can ask questions. If i will be able to help you then I will surely help you

[Tom]

sixww..

This really is exactly what I needed, I cannot thank you enough! Would you mind explaining to me however, what is the purpose of the line: data = data{:}; ? Also, what is the purpose of colons ':' generally?

Again, thankyou thankyou thankyou!

Tom

[sixwwwwww]

As you can see 'data' in line 2 of the code is one cell which contains all the values read from the text file and this 'data' in line 2 further has cells which contain actual data separated by white space delimination. so i used

data = data{:};

to unwrap those cells for further processing. You can use break points in the code and can see data at each step.

Basically ':' is used for vectorization in MATLAB. The purpose of colon can be explained with the help of above code as:

data = data{:}; % here ':' means all the elements in the cell 'data'
1:11:length(data) % here ':' is used to make an array starting from 1 and incrementing 11 till the length of vector

I hope it explains you some how the purpose of ':'. You are welcome if you can't understand anything further

[Tom]

Ah, I checked data between steps and I see what you are saying. Excellent stuff. I remember the usage of colons in defining vectors, but I hadn't encountered it in the first situation you described before. I have a complex task ahead of me after a long period away from Matlab, perhaps I might ask for your guidance again if you don't mind :)

Kind regards,

Tom

[sixwwwwww]

You are welcome anytime