Hi, I will start with a brief overview of what I am trying to achieve in this code.
I have a sample piece of data I want manipulate below. It stores the xyz coordinates and velocities of atoms in solution.
1SOL OW 1 4.309 5.254 4.135 -0.2790 0.3440 0.2064 1SOL HW1 2 4.314 5.169 4.082 -1.5406 0.3918 -0.0293 1SOL HW2 3 4.388 5.312 4.114 -1.3375 0.9272 -2.6151 2SOL OW 4 1.743 1.687 2.366 0.2136 0.2777 0.3181 2SOL HW1 5 1.818 1.750 2.387 0.3115 0.1542 0.3431 4502OCTA H13545 2.108 5.326 1.045 -1.2169 0.4890 -2.6144 4502OCTA H13546 2.068 5.492 1.036 0.7609 0.6650 0.8612 4502OCTA H13547 2.285 5.388 1.207 3.0144 2.5562 1.0920 4502OCTA H13548 2.121 5.425 1.265 -1.2460 -1.3635 1.4829 4502OCTA Oc13549 2.131 5.677 1.238 -0.0183 -0.0221 -1.0402 4502OCTA Oh13550 2.353 5.635 1.208 -0.6036 0.2241 -0.8140 4502OCTA H13551 2.383 5.198 0.399 0.4893 0.7154 -0.9915 4502OCTA Ho13552 2.413 5.565 1.189 -0.4685 -0.0421 -2.1107What I need to do is add a specific value, for instance add 1 to the numbers in the columns 4 and 5 and rows 3 to 8. Basically, I want to translate the positions of certain atoms. It is important that I keep the original file's format.
There were two challenging aspects to this code: The first being that the second and the third column merge when the numbers in the third column (atom IDs) go into the 5 digits. I've worked around that, albeit not elegantly.
The second issue which I haven't been able to solve is how to write the new coordinates into a file. Matlab ignores the empty spaces before each row begins, and ignores the spaces in between the columns, and ignores the spaces after the rows end. I've tried using horzcat, mat2str, strcat, and maybe some others without success. I will leave my code below for you to examine.
function output = Gro_editor(filename, x1, y1, y2,addval) %Initialize Values%
filend = 0; fin = 0; data = cell(15,22); Xpos = 1; %X-coordinate
Ypos = 1; %Y-coordinate
%Open and get permission to write target file%
fid = fopen(filename,'r'); if fid == -1 disp('Could not open file'); else disp('File Open...'); %Index the entire file with meaningful partitions.
%First 15 are indexed individually, following seven are read as blocks.
while filend == 0 if Xpos < 16 data(Ypos,Xpos) = {cellstr(fscanf(fid,'%c',1))}; elseif Xpos > 15 data(Ypos,Xpos) = {fscanf(fid,'%f',1)}; end if Xpos == 22 Xpos = 1; Ypos = Ypos + 1; fscanf(fid,'%c',2); elseif Xpos < 22 Xpos = Xpos + 1; end if Ypos == 20 filend = 1; end end closeresult = fclose(fid); if closeresult == 0 disp('File closed') else disp('File close unsuccessful') end %Writing new cell array
while fin == 0 data{y1,x1} = data{y1,x1}+addval if y1 < y2 y1 = y1+1; elseif y1 == y2 fin = 1; end end %So far so good. I don't know what I am doing after here.%
---------------------------------------------------------- output=data; fid = fopen('output.txt','w'); [nrows,ncols] = size(data); formatSpec = '%c%c%c%c%c%c%c%c%c%c%c%c%c%c%c%c\n'; for row = 1:nrows for col = 1:ncols line = horzcat(data(nrows,1:15)) fprintf(fid,formatSpec,line(col)); end end fclose(fid); type output.txt end
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