Added AA property classes according to IMGT

.vscode/settings.json

@@ -39,6 +39,7 @@
         "Heptopyranose",
         "Heptose",
         "heptoses",
+        "Hydropathy",
         "hydroxybutyryl",
         "Idose",
         "itertools",
@@ -48,6 +49,7 @@
         "Manno",
         "monoisotopic",
         "Nonose",
+        "Nonpolar",
         "novor",
         "Opair",
         "Phospho",

src/aminoacid_properties.rs

@@ -0,0 +1,279 @@
+//! All amino acid property classes according to
+//! > IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties
+//! >
+//! > Christelle Pommié, Séverine Levadoux, Robert Sabatier, Gérard Lefranc, Marie-Paule Lefranc
+//! >
+//! > <https://doi.org/10.1002/jmr.647>
+//!
+//! Adapted to include J,B,Z,U,O, and X.
+#![allow(missing_docs)]
+
+use serde::{Deserialize, Serialize};
+
+/// All amino acid property classes according to
+/// > IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties
+/// >
+/// > Christelle Pommié, Séverine Levadoux, Robert Sabatier, Gérard Lefranc, Marie-Paule Lefranc
+/// >
+/// > <https://doi.org/10.1002/jmr.647>
+///
+/// Adapted to include J,B,Z,U,O, and X.
+impl crate::AminoAcid {
+    pub const fn physiochemical_class(&self) -> PhysiochemicalClass {
+        match self {
+            Self::Alanine
+            | Self::Isoleucine
+            | Self::AmbiguousLeucine
+            | Self::Leucine
+            | Self::Valine => PhysiochemicalClass::Aliphatic,
+            Self::Proline => PhysiochemicalClass::Proline,
+            Self::Tyrosine => PhysiochemicalClass::Tyrosine,
+            Self::Tryptophan => PhysiochemicalClass::Tryptophan,
+            Self::Glycine => PhysiochemicalClass::Glycine,
+            Self::Phenylalanine => PhysiochemicalClass::Phenylalanine,
+            Self::Cysteine | Self::Methionine => PhysiochemicalClass::Sulphur,
+            Self::Serine | Self::Threonine => PhysiochemicalClass::Hydroxyl,
+            Self::AsparticAcid | Self::GlutamicAcid => PhysiochemicalClass::Acidic,
+            Self::Asparagine | Self::Glutamine => PhysiochemicalClass::Amide,
+            Self::Arginine | Self::Histidine | Self::Lysine => PhysiochemicalClass::Basic,
+            Self::AmbiguousAsparagine
+            | Self::AmbiguousGlutamine
+            | Self::Pyrrolysine
+            | Self::Selenocysteine
+            | Self::Unknown => PhysiochemicalClass::Unknown,
+        }
+    }
+    pub const fn chemical_class(&self) -> ChemicalClass {
+        match self {
+            Self::Alanine
+            | Self::Isoleucine
+            | Self::AmbiguousLeucine
+            | Self::Leucine
+            | Self::Proline
+            | Self::Glycine
+            | Self::Valine => ChemicalClass::Aliphatic,
+            Self::Tyrosine | Self::Tryptophan | Self::Phenylalanine => ChemicalClass::Aromatic,
+            Self::Cysteine | Self::Methionine => ChemicalClass::Sulphur,
+            Self::Serine | Self::Threonine => ChemicalClass::Hydroxyl,
+            Self::AsparticAcid | Self::GlutamicAcid => ChemicalClass::Acidic,
+            Self::Asparagine | Self::Glutamine => ChemicalClass::Amide,
+            Self::Arginine | Self::Histidine | Self::Lysine => ChemicalClass::Basic,
+            Self::AmbiguousAsparagine
+            | Self::AmbiguousGlutamine
+            | Self::Pyrrolysine
+            | Self::Selenocysteine
+            | Self::Unknown => ChemicalClass::Unknown,
+        }
+    }
+    pub const fn volume_class(&self) -> VolumeClass {
+        match self {
+            Self::Alanine | Self::Glycine | Self::Serine => VolumeClass::VerySmall,
+            Self::Proline
+            | Self::AsparticAcid
+            | Self::Asparagine
+            | Self::AmbiguousAsparagine
+            | Self::Threonine
+            | Self::Cysteine
+            | Self::Selenocysteine => VolumeClass::Small,
+            Self::GlutamicAcid
+            | Self::Glutamine
+            | Self::AmbiguousGlutamine
+            | Self::Histidine
+            | Self::Valine => VolumeClass::Medium,
+            Self::Arginine
+            | Self::Lysine
+            | Self::Isoleucine
+            | Self::AmbiguousLeucine
+            | Self::Leucine
+            | Self::Methionine => VolumeClass::Large,
+            Self::Tyrosine | Self::Tryptophan | Self::Phenylalanine | Self::Pyrrolysine => {
+                VolumeClass::VeryLarge
+            }
+            Self::Unknown => VolumeClass::Unknown,
+        }
+    }
+    pub const fn hydropathy_class(&self) -> HydropathyClass {
+        match self {
+            Self::Alanine
+            | Self::Cysteine
+            | Self::Selenocysteine
+            | Self::Isoleucine
+            | Self::AmbiguousLeucine
+            | Self::Leucine
+            | Self::Methionine
+            | Self::Phenylalanine
+            | Self::Tryptophan
+            | Self::Valine => HydropathyClass::Hydrophobic,
+            Self::Glycine
+            | Self::Serine
+            | Self::Histidine
+            | Self::Proline
+            | Self::Threonine
+            | Self::Tyrosine => HydropathyClass::Neutral,
+            Self::Lysine
+            | Self::AsparticAcid
+            | Self::Asparagine
+            | Self::AmbiguousAsparagine
+            | Self::GlutamicAcid
+            | Self::Glutamine
+            | Self::AmbiguousGlutamine
+            | Self::Pyrrolysine
+            | Self::Arginine => HydropathyClass::Hydrophilic,
+            Self::Unknown => HydropathyClass::Unknown,
+        }
+    }
+    pub const fn charge_class(&self) -> ChargeClass {
+        match self {
+            Self::Arginine | Self::Histidine | Self::Lysine => ChargeClass::Positive,
+            Self::AsparticAcid | Self::GlutamicAcid => ChargeClass::Negative,
+            Self::Alanine
+            | Self::Cysteine
+            | Self::Selenocysteine
+            | Self::Isoleucine
+            | Self::AmbiguousLeucine
+            | Self::Leucine
+            | Self::Methionine
+            | Self::Phenylalanine
+            | Self::Tryptophan
+            | Self::Valine
+            | Self::Glycine
+            | Self::Serine
+            | Self::Proline
+            | Self::Threonine
+            | Self::Tyrosine
+            | Self::Asparagine
+            | Self::Glutamine
+            | Self::Pyrrolysine => ChargeClass::Uncharged,
+            Self::Unknown | Self::AmbiguousAsparagine | Self::AmbiguousGlutamine => {
+                ChargeClass::Unknown
+            }
+        }
+    }
+    pub const fn polarity_class(&self) -> PolarityClass {
+        match self {
+            Self::Arginine
+            | Self::Histidine
+            | Self::Lysine
+            | Self::Pyrrolysine
+            | Self::AmbiguousAsparagine
+            | Self::AmbiguousGlutamine
+            | Self::AsparticAcid
+            | Self::Asparagine
+            | Self::Glutamine
+            | Self::Threonine
+            | Self::Tyrosine
+            | Self::Serine
+            | Self::GlutamicAcid => PolarityClass::Polar,
+            Self::Alanine
+            | Self::Cysteine
+            | Self::Selenocysteine
+            | Self::Isoleucine
+            | Self::AmbiguousLeucine
+            | Self::Leucine
+            | Self::Methionine
+            | Self::Phenylalanine
+            | Self::Tryptophan
+            | Self::Valine
+            | Self::Glycine
+            | Self::Proline => PolarityClass::Nonpolar,
+            Self::Unknown => PolarityClass::Unknown,
+        }
+    }
+    pub const fn hydrogen_bond_class(&self) -> HydrogenBondClass {
+        match self {
+            Self::Arginine | Self::Lysine | Self::Tryptophan => HydrogenBondClass::Donor,
+            Self::AsparticAcid | Self::GlutamicAcid => HydrogenBondClass::Acceptor,
+            Self::Histidine
+            | Self::Pyrrolysine
+            | Self::Asparagine
+            | Self::Threonine
+            | Self::Tyrosine
+            | Self::Serine => HydrogenBondClass::Both,
+            Self::Glutamine
+            | Self::Alanine
+            | Self::Cysteine
+            | Self::Selenocysteine
+            | Self::Isoleucine
+            | Self::AmbiguousLeucine
+            | Self::Leucine
+            | Self::Methionine
+            | Self::Phenylalanine
+            | Self::Valine
+            | Self::Glycine
+            | Self::Proline => HydrogenBondClass::None,
+            Self::AmbiguousAsparagine | Self::AmbiguousGlutamine | Self::Unknown => {
+                HydrogenBondClass::Unknown
+            }
+        }
+    }
+}
+
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
+pub enum PhysiochemicalClass {
+    Aliphatic,
+    Proline,
+    Tyrosine,
+    Tryptophan,
+    Glycine,
+    Phenylalanine,
+    Sulphur,
+    Hydroxyl,
+    Acidic,
+    Amide,
+    Basic,
+    Unknown,
+}
+
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
+pub enum ChemicalClass {
+    Aliphatic,
+    Sulphur,
+    Hydroxyl,
+    Acidic,
+    Amide,
+    Basic,
+    Aromatic,
+    Unknown,
+}
+
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
+pub enum VolumeClass {
+    VerySmall,
+    Small,
+    Medium,
+    Large,
+    VeryLarge,
+    Unknown,
+}
+
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
+pub enum HydropathyClass {
+    Hydrophobic,
+    Neutral,
+    Hydrophilic,
+    Unknown,
+}
+
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
+pub enum ChargeClass {
+    Uncharged,
+    Positive,
+    Negative,
+    Unknown,
+}
+
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
+pub enum PolarityClass {
+    Polar,
+    Nonpolar,
+    Unknown,
+}
+
+#[derive(Copy, Clone, Eq, PartialEq, Ord, PartialOrd, Hash, Debug, Serialize, Deserialize)]
+pub enum HydrogenBondClass {
+    Donor,
+    Acceptor,
+    Both,
+    None,
+    Unknown,
+}

src/lib.rs

@@ -22,6 +22,7 @@ mod helper_functions;
 mod formula;
 
 pub mod align;
+pub mod aminoacid_properties;
 mod aminoacids;
 mod complex_peptide;
 mod element;