I am not sure that I understand your question.
Are you looking to write a computer program that does something? If so, what language are you planning on using?

The function that calculates the normalized contrast angle of two vectors is here:
https://github.com/ProteoWizard/pwiz/blob/master/pwiz_tools/Skyline/Util/Statistics.cs#L1371

Can you describe more what you are trying to do?
-- Nick

Hi Nick,

Thank you for your response.
Yes, I am trying to write a computer program that can calculate rdotp score.
I am seeking the package or library which can be easily implemented to my program.
I am using Python mainly. Maybe the source you kindly shared can help. However, if you have any information about the way of implement rdotp score calculation into my Python script, it is that I trully look for.

Could you please give me some comments or advice?

Best,
TY

I asked ChatGPT to write some python code to calculate the normalized contrast angle of the square root of two vectors:
https://chatgpt.com/share/67c7db02-3014-800a-971e-c17f955c827d

My knowledge of python is not very good so I can't be sure it's correct.

I am not sure I understand why you are specifically saying "rdotp".
There are several dot products in Skyline:
1. Library dot product ("dotp"): measure of the similarity between the chromatogram peak areas of MS2 transitions and the intensities from a library spectrum
2. Isotope dot product ("idotp"): measure of the similarity between chromatogram peak areas of MS1 transitions and the predicted distribution based on isotope abundances
3. Ratio dot product ("rdotp"): when calculating the ratio of the light molecule to the heavy molecule, a measure of whether the ratios of the individual transition peak areas are the same as the ratio of the sum of all of the transitions

Let me know if you have any questions about the ratio dot product.
-- Nick