function request: IsoelectricPoint class private function _chargeR

[dobrevnm]

Setup

I am requesting a feature for the IsoelectricPoint class from Biopython:

import sys; print(sys.version)
import platform; print(platform.python_implementation()); print(platform.platform())
import Bio; print(Bio.__version__)

(Please copy and run the above in your Python, and copy-and-paste the output)
I am using Biopython version 1.70

Expected behaviour

The IsoelectricPoint class allows calculation only of the pI of a given protein. It has a private function _chargeR, which allows calculating the charge of the protein at given pH.
It will be great if this function is not private, but it can be used as a method or to be integrated as a new class in order to be able to calculate the charge of the protein over a range of pIs.

For example, it can output:
pH Charge
4.00 11.4
4.50 4.0
5.00 -2.6
5.50 -6.2
6.00 -7.8
6.50 -8.8
7.00 -9.6
7.50 -10.2
8.00 -10.9
8.50 -11.8
9.00 -13.3
9.50 -16.2
10.00 -21.0

This will be a really nice feature.

P.S. This is my very first issue, which I am submitting. I am not sure that is the right way for requesting a feature.

[MarkusPiotrowski]

Sounds like a sensible idea. _chargeR, as it is, cannot been made public easily, it's tightly integrated in the process of calculating the IEP. Also, the class IsoelectricPoint can hardly been used on its own, you need to invoke it with the sequence and the AA composition. It is usually called from the method isoelectric_point of class ProteinAnalysis in module SeqUtils.ProtParam.
One can either think about adding a new method, e.g. charge_at_ph either in ProteinAnalysis or in the SeqUtils module.
I may give it a try together with issue #1863 (ProteinAnalysis should handle ambiguous amino acids).

[dobrevnm]

Thanks,
You are completely right!
It will be really great if it will be completely new method.