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Moved the new terminal generation into building_blocks
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@douweschulte
douweschulte committed Nov 8, 2023
1 parent 3c04b1f commit b7a8e00
Showing 1 changed file with 79 additions and 96 deletions.
175 changes: 79 additions & 96 deletions src/isobaric_sets.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,8 @@ impl TryFrom<&str> for MassTolerance {

/// A list of building blocks for a sequence defined by its sequence elements and its mass.
pub type BuildingBlocks = Vec<(SequenceElement, Mass)>;
/// A list of all combinations of terminal modifications and their accompanying amino acid
pub type TerminalBuildingBlocks = Vec<(SequenceElement, Modification, Mass)>;
/// Get the possible building blocks for sequences based on the given modifications.
/// Useful for any automated sequence generation, like isobaric set generation or de novo sequencing.
/// The result is for each location (N term, center, C term) the list of all possible building blocks with its mass, sorted on mass.
Expand All @@ -94,7 +96,11 @@ pub type BuildingBlocks = Vec<(SequenceElement, Mass)>;
pub fn building_blocks(
fixed: &[(Modification, Option<PlacementRule>)],
variable: &[(Modification, Option<PlacementRule>)],
) -> (BuildingBlocks, BuildingBlocks, BuildingBlocks) {
) -> (
TerminalBuildingBlocks,
BuildingBlocks,
TerminalBuildingBlocks,
) {
/// Enforce the placement rules of predefined modifications.
fn can_be_placed(
modification: &Modification,
Expand All @@ -111,6 +117,71 @@ pub fn building_blocks(
true
}
}
fn n_term_options(rule: &PlacementRule) -> Vec<AminoAcid> {
match rule {
PlacementRule::AminoAcid(aa, Position::AnyNTerm | Position::ProteinNTerm) => {
AA.iter().filter(|a| aa.contains(a)).copied().collect_vec()
}
PlacementRule::Terminal(Position::AnyNTerm | Position::ProteinNTerm) => {
AA.iter().copied().collect_vec()
}
_ => Vec::new(),
}
}
fn c_term_options(rule: &PlacementRule) -> Vec<AminoAcid> {
match rule {
PlacementRule::AminoAcid(aa, Position::AnyCTerm | Position::ProteinCTerm) => {
AA.iter().filter(|a| aa.contains(a)).copied().collect_vec()
}
PlacementRule::Terminal(Position::AnyCTerm | Position::ProteinCTerm) => {
AA.iter().copied().collect_vec()
}
_ => Vec::new(),
}
}
fn generate_terminal(
position: &impl Fn(&PlacementRule) -> Vec<AminoAcid>,
fixed: &[(Modification, Option<PlacementRule>)],
variable: &[(Modification, Option<PlacementRule>)],
) -> TerminalBuildingBlocks {
let mut options = fixed
.iter()
.chain(variable.iter())
.flat_map(|(modification, rule)| {
rule.as_ref().map_or_else(
|| {
if let Modification::Predefined(_, rules, _, _, _) = modification {
rules
.iter()
.flat_map(position)
.unique()
.map(|a| (SequenceElement::new(a, None), modification.clone()))
.collect_vec()
} else {
Vec::new()
}
},
|rule| {
position(rule)
.into_iter()
.map(|a| (SequenceElement::new(a, None), modification.clone()))
.collect_vec()
},
)
})
.map(|(a, m)| {
let mass = a
.formula_all()
.unwrap()
.monoisotopic_mass()
.unwrap_or_default()
+ m.formula().monoisotopic_mass().unwrap_or_default();
(a, m, mass)
})
.collect_vec();
options.sort_unstable_by(|a, b| a.2.partial_cmp(&b.2).unwrap());
options
}

let generate = |index| {
let mut options: Vec<(SequenceElement, Mass)> = AA
Expand Down Expand Up @@ -175,7 +246,11 @@ pub fn building_blocks(
};

// Create the building blocks
(generate(0), generate(1), generate(2))
(
generate_terminal(&n_term_options, fixed, variable),
generate(1),
generate_terminal(&c_term_options, fixed, variable),
)
}

/// Find the isobaric sets for the given mass with the given modifications and ppm error.
Expand All @@ -189,101 +264,9 @@ pub fn find_isobaric_sets(
fixed: &[(Modification, Option<PlacementRule>)],
variable: &[(Modification, Option<PlacementRule>)],
) -> IsobaricSetIterator {
fn n_term_options(rule: &PlacementRule) -> Vec<AminoAcid> {
match rule {
PlacementRule::AminoAcid(aa, Position::AnyNTerm | Position::ProteinNTerm) => {
AA.iter().filter(|a| aa.contains(a)).copied().collect_vec()
}
PlacementRule::Terminal(Position::AnyNTerm | Position::ProteinNTerm) => {
AA.iter().copied().collect_vec()
}
_ => Vec::new(),
}
}
fn c_term_options(rule: &PlacementRule) -> Vec<AminoAcid> {
match rule {
PlacementRule::AminoAcid(aa, Position::AnyCTerm | Position::ProteinCTerm) => {
AA.iter().filter(|a| aa.contains(a)).copied().collect_vec()
}
PlacementRule::Terminal(Position::AnyCTerm | Position::ProteinCTerm) => {
AA.iter().copied().collect_vec()
}
_ => Vec::new(),
}
}

let bounds = tolerance.bounds(mass);
let (_, center, _) = building_blocks(fixed, variable);
let n_term = fixed
.iter()
.chain(variable.iter())
.flat_map(|(modification, rule)| {
rule.as_ref().map_or_else(
|| {
if let Modification::Predefined(_, rules, _, _, _) = modification {
rules
.iter()
.flat_map(n_term_options)
.unique()
.map(|a| (SequenceElement::new(a, None), modification.clone()))
.collect_vec()
} else {
Vec::new()
}
},
|rule| {
n_term_options(rule)
.into_iter()
.map(|a| (SequenceElement::new(a, None), modification.clone()))
.collect_vec()
},
)
})
.map(|(a, m)| {
let mass = a
.formula_all()
.unwrap()
.monoisotopic_mass()
.unwrap_or_default()
+ m.formula().monoisotopic_mass().unwrap_or_default();
(a, m, mass)
})
.collect_vec();
let c_term = fixed
.iter()
.chain(variable.iter())
.flat_map(|(modification, rule)| {
rule.as_ref().map_or_else(
|| {
if let Modification::Predefined(_, rules, _, _, _) = modification {
rules
.iter()
.flat_map(c_term_options)
.unique()
.map(|a| (SequenceElement::new(a, None), modification.clone()))
.collect_vec()
} else {
Vec::new()
}
},
|rule| {
c_term_options(rule)
.into_iter()
.map(|a| (SequenceElement::new(a, None), modification.clone()))
.collect_vec()
},
)
})
.map(|(a, m)| {
let mass = a
.formula_all()
.unwrap()
.monoisotopic_mass()
.unwrap_or_default()
+ m.formula().monoisotopic_mass().unwrap_or_default();
(a, m, mass)
})
.collect_vec();
let (n_term, center, c_term) = building_blocks(fixed, variable);

IsobaricSetIterator::new(n_term, c_term, center, bounds)
}

Expand Down

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