Add option to ignore N-/C-terminus effects in isoelectric point calculation#5022
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FriedLabJHU wants to merge 1 commit intobiopython:masterfrom
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Add option to ignore N-/C-terminus effects in isoelectric point calculation#5022FriedLabJHU wants to merge 1 commit intobiopython:masterfrom
FriedLabJHU wants to merge 1 commit intobiopython:masterfrom
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…lation This update introduces a new ignore_termini parameter to the IsoelectricPoint class, allowing users to exclude the N-terminus, C-terminus, or both from isoelectric point (pI) and charge calculations. Key Changes: Added ignore_termini argument to IsoelectricPoint.__init__, which accepts: "Nterm" – excludes N-terminal charge and pK contribution "Cterm" – excludes C-terminal charge and pK contribution "both" – excludes both N- and C-terminal contributions Purpose: In many use cases (e.g., peptide segments derived from a larger protein), the termini of a fragment may not be chemically exposed and therefore do not contribute to the molecule’s charge in physiological contexts. This enhancement enables more biologically realistic pI calculations for internal peptide fragments by omitting artificial terminal effects. Additionally, it allows for flexible modeling of peptides with only one exposed terminus, such as C-terminal peptides (ignore Nterm) or N-terminal peptides (ignore Cterm), which is useful in proteomics applications and fragment-based analyses.
Member
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I thought there might be a similar option in one of the existing |
Author
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@peterjc as far as I am aware, there aren't any other functions that explicitly ignore the protein termini (other than by indexing). If there is an existing option meant for ignoring termini, then I will change this PR to match that naming. |
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This update introduces a new ignore_termini parameter to the IsoelectricPoint class, allowing users to exclude the N-terminus, C-terminus, or both from isoelectric point (pI) and charge calculations.
Key Changes:
Added ignore_termini argument to IsoelectricPoint.init, which accepts:
"Nterm" – excludes N-terminal charge and pK contribution
"Cterm" – excludes C-terminal charge and pK contribution
"both" – excludes both N- and C-terminal contributions
Purpose:
In many use cases (e.g., peptide segments derived from a larger protein), the termini of a fragment may not be chemically exposed and therefore do not contribute to the molecule’s charge in physiological contexts. This enhancement enables more biologically realistic pI calculations for internal peptide fragments by omitting artificial terminal effects.
Additionally, it allows for flexible modeling of peptides with only one exposed terminus, such as C-terminal peptides (ignore Nterm) or N-terminal peptides (ignore Cterm), which is useful in proteomics applications and fragment-based analyses.