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Add pKa and hydrophobicity to amino acid #66

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Merged
douweschulte merged 8 commits into from
Apr 1, 2025
Merged

Add pKa and hydrophobicity to amino acid #66

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97b46fe
Added pka to aminoacid
aukeheerdink Feb 11, 2025
0da256e
Restructure into trait definition
douweschulte Feb 11, 2025
2168f19
Used trait IsAminoAcid
douweschulte Feb 10, 2025
635b8cc
Added pKa and Hydro. module
aukeheerdink Feb 13, 2025
15a7ca7
Added isoelectric point calculation
aukeheerdink Feb 28, 2025
107bc13
Refactored pka and added docs
aukeheerdink Apr 1, 2025
229e5a8
Small improvements
douweschulte Apr 1, 2025
5a777b6
Merge branch 'main' into pr/aukeheerdink/66
douweschulte Apr 1, 2025
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1 change: 1 addition & 0 deletions rendered_glycans.html
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14 changes: 11 additions & 3 deletions rustyms-generate-imgt/src/structs.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ use std::str::FromStr;

use crate::imgt_gene::IMGTGene;
use crate::shared::{AnnotatedSequence, Gene, Species};
use rustyms::AminoAcid;
use rustyms::{AminoAcid, IsAminoAcid};

#[derive(Debug)]
pub struct DataItem {
Expand Down Expand Up @@ -57,7 +57,12 @@ impl Display for Region {
// self.found_seq.0,
self.found_seq
.as_ref()
.map(|seq| seq.1 .0.iter().map(|a| a.char()).collect::<String>())
.map(|seq| seq
.1
.0
.iter()
.map(|a| a.pro_forma_definition())
.collect::<String>())
.unwrap_or_else(|e| format!("<NO SEQ!>: {e}")),
)
}
Expand Down Expand Up @@ -237,7 +242,10 @@ impl std::fmt::Debug for AASequence {
write!(
f,
"[{}]",
self.0.iter().map(|a| a.char()).collect::<String>()
self.0
.iter()
.map(|a| a.pro_forma_definition())
.collect::<String>()
)
}
}
Expand Down
6 changes: 3 additions & 3 deletions rustyms-py/src/lib.rs
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Expand Up @@ -6,7 +6,7 @@ use std::num::NonZeroU16;
use ordered_float::OrderedFloat;
use pyo3::{exceptions::PyValueError, prelude::*, types::PyType};

use rustyms::{AnnotatableSpectrum, Chemical, Linked, MultiChemical};
use rustyms::{AnnotatableSpectrum, Chemical, IsAminoAcid, Linked, MultiChemical};

/// Mass mode enum.
#[pyclass(eq, eq_int)]
Expand Down Expand Up @@ -440,7 +440,7 @@ impl AminoAcid {
}

fn __str__(&self) -> String {
self.0.char().to_string()
self.0.pro_forma_definition().to_string()
}

fn __repr__(&self) -> String {
Expand Down Expand Up @@ -1124,7 +1124,7 @@ impl Peptidoform {
self.0
.sequence()
.iter()
.map(|x| x.aminoacid.char())
.map(|x| x.aminoacid.pro_forma_definition())
.collect()
}

Expand Down
2 changes: 1 addition & 1 deletion rustyms/src/align/multi_alignment.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ impl<Complexity> MultiAlignmentLine<'_, Complexity> {
{
print!(
"{}{}",
piece.1.aminoacid.char(),
piece.1.aminoacid,
"·".repeat(piece.0.step as usize - 1)
);
}
Expand Down
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