Check to ensure code is doing what I want it to (nlinfit)

조회 수: 2 (최근 30일)
Sam Mahdi
Sam Mahdi 2023년 6월 1일
답변: Karan Singh 2023년 8월 24일
I have an equation
y=b*((p+l+k-sqrt((p+l+k)^2-4pl))/2p)
where k and b are adjustable parameters to solve for with given p and l
The y is given from experimental data with this formula
y=sqrt(((x0-xi)/10)^2+(z0-zi)^2)
Where x0 is the first value at concentration ligand=0, and xi is all the other entries in the array (same with z0 and zi, so first entry 0 and all other entries differences from first). The data for x and z are in a series of text files, with p and l coming from the name of the text file.
I first read through all the text files and extract x,z,p, and l. Then I use x and z to calculate y (i.e. csp in my script). Finally, I fit the above function using nlinfit.
I have been told with this data set, you should get solutions from individual fits, but I cannot. I want to ensure that my script is setup correctly and doing what it needs to do, and the issue I am getting from matlab is not from a script setup, but from the data itself. Here is my code:
label=strings(242,numel(titration_files));
nitrogen=[];
hydrogen=[];
protein=[];
ligand=[];
for i=1:length(titration_files)
protein_concentration=regexp(titration_files(i).name,'pcna_(\d+\.\d*)','tokens');
ligand_concentration=regexp(titration_files(i).name,'brct_(\d+\.\d*)','tokens');
protein(i)=str2double(protein_concentration{1});
ligand(i)=str2double(ligand_concentration{1});
read_files=readtable(titration_files(i).name);
label(:,i)=convertCharsToStrings(read_files.Assignment);
nitrogen(:,i)=read_files.w1;
hydrogen(:,i)=read_files.w2;
end
[rows,columns]=size(nitrogen);
csp=[];
for i=1:rows
for j=1:columns
csp(i,j)=sqrt(((nitrogen(i,end)-nitrogen(i,j))/10)^2+((hydrogen(i,end)-hydrogen(i,j))^2));
end
end
x =[flip(protein.'),flip(ligand.')];
model=@(b,x)((x(:,1)+x(:,2)+b(2))-sqrt((x(:,1)+x(:,2)+b(2)).^2)-(4.*x(:,1).*x(:,2))).*(b(1)./(2.*x(:,1)));
beta0=[0.1,0.1];
for i=1:rows
labels=label(i);
if labels == 'G130N-H'
y=(flip(csp(i,:))).';
nlinfit(x,y,model,beta0)
end
end
Where the format of the data is (there are of course many more text/data files than this, I just wanted to give an example of the output. So one csp here for example would be for E20N-H csp=sqrt((118.384-118.380)/10)^2+(7.849 -7.838)^2), this would be just one entry for this p and l).
pcna_0.15_brct_1.1.txt
Assignment w1 w2
M4N-H 122.672 8.581
F5N-H 120.942 8.016
E6N-H 127.603 8.037
A7N-H 129.439 8.401
R8N-H 124.865 8.594
L9N-H 130.753 9.679
V10N-H 126.972 8.909
Q11N-H 119.272 7.964
G12N-H 111.714 8.069
S13N-H 114.817 8.403
I14N-H 122.036 7.834
L15N-H 117.768 7.246
K16N-H 116.918 7.089
K17N-H 117.737 7.954
V18N-H 120.989 8.310
L19N-H 120.731 7.772
E20N-H 118.380 7.838
A21N-H 119.412 7.436
#pcna_0.3_brct_0.0.txt
Assignment w1 w2
M4N-H 122.672 8.581
F5N-H 120.942 8.016
E6N-H 127.619 8.042
A7N-H 129.444 8.407
R8N-H 124.883 8.599
L9N-H 130.798 9.689
V10N-H 126.970 8.906
Q11N-H 119.254 7.963
G12N-H 111.724 8.070
S13N-H 114.779 8.407
I14N-H 122.068 7.840
L15N-H 117.762 7.244
K16N-H 116.949 7.095
K17N-H 117.733 7.960
V18N-H 120.902 8.303
L19N-H 120.743 7.775
E20N-H 118.386 7.849
A21N-H 119.412 7.436

답변 (1개)

Karan Singh
Karan Singh 2023년 8월 24일
Hey Sam, I have gone through your code once and while you seem to be on the right track there are somethings to be improved upon.
1.You have made a mistake in keeping the parenthesis for sqrt and I have corrected it. Here is the updated code snippet.
((x(:,1) + x(:,2) + b(2)) - sqrt((x(:,1) + x(:,2) + b(2)).^2 - (4 .* x(:,1) .* x(:,2)))) .* (b(1) ./ (2 .* x(:,1)))
2. In MATLAB, you cannot directly compare strings using the “== operator. Instead, you should use the “strcmp” function to compare strings.
These were all the discrepancies I could find, however I could assess it better if you can provide the dataset as well. I hope the above suggestions helped. Good luck!

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