Enum Modification 

pub enum Modification {
    Simple(SimpleModification),
    CrossLink {
        peptide: usize,
        sequence_index: SequencePosition,
        linker: SimpleModification,
        name: CrossLinkName,
        side: CrossLinkSide,
    },
    Ambiguous {
        group: String,
        id: usize,
        modification: SimpleModification,
        localisation_score: Option<OrderedFloat<f64>>,
        preferred: bool,
    },
}

A modification on an amino acid

Variants

Simple(SimpleModification)

Any of the simple modifications

CrossLink

A cross link to another (or the same) peptide, a branch is also seen as a cross-link but then the name is None.

Fields

peptide: usize

The index of the peptide this cross-link is bound to (can be the index for this peptide if it is an intra link)

sequence_index: SequencePosition

The sequence index where this cross-link is bound to

linker: SimpleModification

The linker that defines the chemical structure that is the actual linker

name: CrossLinkName

The name of the cross-linker, if CrossLinkName::Branch it is a branch instead of cross-link

side: CrossLinkSide

To determine if the cross-link is placed symmetrically or if asymmetrically if this is the left or right side

Ambiguous

An ambiguous modification, that can be placed at multiple locations

Fields

group: String

The name of the group

id: usize

The id to compare be able to find the other locations where this modifications can be placed

modification: SimpleModification

The modification itself

localisation_score: Option<OrderedFloat<f64>>

If present the localisation score, meaning the chance/ratio for this modification to show up on this exact spot

preferred: bool

If this is the preferred location or not

Implementations

impl Modification

pub const fn is_simple(&self) -> bool

Check if this modification is a simple modification.

pub const fn is_cross_link(&self) -> bool

Check if this modification is a cross-link.

pub const fn is_ambiguous(&self) -> bool

Check if this modification is an ambiguous modification.

pub fn formula(&self) -> MolecularFormula

Get the formula for a modification, if it is a cross linked modification only get the cross link

pub const fn simple(&self) -> Option<&SimpleModification>

Check if this is a simple modification

pub fn into_simple(self) -> Option<SimpleModification>

Check if this is a simple modification

pub fn ontology_url(&self) -> Option<String>

Get a url for more information on this modification. Only defined for modifications from ontologies.

pub fn is_possible<T>( &self, seq: &SequenceElement<T>, position: SequencePosition, ) -> RulePossible

Check to see if this modification can be placed on the specified element

impl Modification

pub fn display( &self, f: &mut impl Write, specification_compliant: bool, display_ambiguous: bool, ) -> Result

Display a modification either normalised to the internal representation or as fully valid ProForma (no glycan structure or custom modifications). display_ambiguous shows or hides the modification definition of any ambiguous modifications (eg true results in ‘+1#1’ false in ‘#1’).

Errors

When the given writer errors.

impl Modification

pub fn sloppy_modification( line: &str, location: Range<usize>, position: Option<&SequenceElement<SemiAmbiguous>>, custom_database: Option<&CustomDatabase>, ) -> Result<SimpleModification, CustomError>

Parse a modification defined by sloppy names

Errors

If the name is not in Unimod, PSI-MOD, the custom database, or the predefined list of common trivial names. Or if this is the case when the modification follows a known structure (eg mod (AAs)).

Trait Implementations

impl Clone for Modification

fn clone(&self) -> Modification

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Modification

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<'de> Deserialize<'de> for Modification

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Display for Modification

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl From<Arc<SimpleModificationInner>> for Modification

fn from(value: SimpleModification) -> Self

Converts to this type from the input type.

impl From<SimpleModificationInner> for Modification

fn from(value: SimpleModificationInner) -> Self

Converts to this type from the input type.

impl Hash for Modification

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for Modification

fn cmp(&self, other: &Modification) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for Modification

fn eq(&self, other: &Modification) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for Modification

fn partial_cmp(&self, other: &Modification) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

Tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

Tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

Tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl Serialize for Modification

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl Eq for Modification

impl StructuralPartialEq for Modification