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Read all glycan names
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@douweschulte
douweschulte committed Oct 20, 2023
1 parent e605928 commit 80edcb2
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Showing 2 changed files with 161 additions and 60 deletions.
29 changes: 20 additions & 9 deletions src/build/gnome.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,23 +55,34 @@ fn parse_gnome(_debug: bool) -> Vec<GNOmeModification> {

fn parse_gnome_structures(_debug: bool) -> Vec<(String, GlycanStructure)> {
let mut glycans = Vec::new();
let mut errors = 0;
for line in parse_csv("databases/glycosmos_glycans_list.csv.gz", b',')
.unwrap()
.skip(1)
{
let line = line.unwrap();
if !line[1].is_empty() {
glycans.push((
line[0].to_string(),
GlycanStructure::from_short_iupac(
&line.line,
line.fields[1].clone(),
line.line_index + 1,
)
.unwrap(),
));
match GlycanStructure::from_short_iupac(
&line.line,
line.fields[1].clone(),
line.line_index + 1,
) {
Ok(glycan) => glycans.push((line[0].to_string(), glycan)),
Err(error) => {
if errors < 5 {
println!("{error}");
}
errors += 1;
}
}
}
}
if errors > 0 {
panic!(
"Total glycan structure reading errors: {errors} total read {}",
glycans.len()
);
}
glycans
}

Expand Down
192 changes: 141 additions & 51 deletions src/shared/glycan.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -196,62 +196,77 @@ impl MonoSaccharide {
// Postfix mods
while index < bytes.len() {
index += line[index..].ignore(&["-"]);
let mut single_amount = 0;
let mut double_amount = 0;
// Location
let mut amount = 1;
if bytes[index].is_ascii_digit() || bytes[index] == b'?' {
match bytes[index + 1] {
b',' => {
let num = bytes[index + 1..]
.iter()
.take_while(|c| c.is_ascii_digit() || **c == b',' || **c == b'?')
.count();
index += num + 1;
amount = num / 2 + 1;
// X,X{mod} (or 3/4/5/etc mods)
}
b'-' => {
index += 7;
index += line[index..].ignore(&["(X)", "(R)", "(S)"]);

if let Some(o) =
line[index..].take_any(DOUBLE_LINKED_POSTFIX_SUBSTITUENTS, |e| {
sugar.substituents.extend(e.iter().cloned());
})
{
index += o;
} else {
return Err(CustomError::error(
"Invalid iupac monosaccharide name",
"No detected double linked glycan substituent was found, while the pattern for location is for a double linked substituent",
Context::Line {
linenumber: line_number,
line: line.to_string(),
offset: index,
length: 2,
},
));
}
continue; // Do not accepts an additional mod immediately
} // X-X,X-X (Py)
_ => index += 1, // X{mod}
let (offset, mut amount, mut double) = line[index..].parse_location();
index += offset;
if double {
double_amount = amount;
} else {
single_amount = amount;
}
if bytes[index] == b':' {
// additional place
let (offset, amt, dbl) = line[index + 1..].parse_location();
index += offset + 1;
amount += amt;
if double {
double_amount += amount;
} else {
single_amount += amount;
}
double |= dbl; // if any is double
}

index += line[index..].ignore(&["-"]);
index += line[index..].ignore(&["(X)", "(R)", "(S)"]);
// Mod or an element
if let Some(o) = line[index..].take_any(POSTFIX_SUBSTITUENTS, |e| {
sugar
.substituents
.extend(std::iter::repeat(e.clone()).take(amount));
}) {
index += o;
} else if let Some(o) = line[index..].take_any(ELEMENT_PARSE_LIST, |e| {
sugar
.substituents
.extend(std::iter::repeat(GlycanSubstituent::Element(*e)).take(amount));
}) {
index += o;
if double {
if let Some(o) = line[index..].take_any(DOUBLE_LINKED_POSTFIX_SUBSTITUENTS, |e| {
sugar.substituents.extend(
e.iter()
.flat_map(|s| std::iter::repeat(s).take(double_amount))
.cloned(),
);
if single_amount > 0 {
sugar.substituents.extend(
e.iter()
.filter(|s| **s != GlycanSubstituent::Water)
.flat_map(|s| std::iter::repeat(s).take(single_amount))
.cloned(),
);
}
}) {
index += o;
} else {
return Err(CustomError::error(
"Invalid iupac monosaccharide name",
"No detected double linked glycan substituent was found, while the pattern for location is for a double linked substituent",
Context::Line {
linenumber: line_number,
line: line.to_string(),
offset: index,
length: 2,
},
));
}
} else {
break;
// Mod or an element
if let Some(o) = line[index..].take_any(POSTFIX_SUBSTITUENTS, |e| {
sugar
.substituents
.extend(std::iter::repeat(e.clone()).take(amount));
}) {
index += o;
} else if let Some(o) = line[index..].take_any(ELEMENT_PARSE_LIST, |e| {
sugar
.substituents
.extend(std::iter::repeat(GlycanSubstituent::Element(*e)).take(amount));
}) {
index += o;
} else {
break;
}
}
// Amount
if amount != 1 {
Expand Down Expand Up @@ -279,6 +294,7 @@ impl MonoSaccharide {
trait ParseHelper {
fn ignore(self, ignore: &[&str]) -> usize;
fn take_any<T>(self, parse_list: &[(&str, T)], f: impl FnMut(&T)) -> Option<usize>;
fn parse_location(self) -> (usize, usize, bool);
}

impl ParseHelper for &str {
Expand All @@ -303,6 +319,61 @@ impl ParseHelper for &str {
}
found
}

// Get a location, return the new index, the amount of the mod to place and if it is doubly linked or not
fn parse_location(self) -> (usize, usize, bool) {
let bytes = self.as_bytes();
let mut index = 0;
let mut amount = 1;
let mut double = false;
if bytes[0].is_ascii_digit() || bytes[0] == b'?' {
match bytes[1] {
b',' => {
let num = bytes[1..]
.iter()
.take_while(|c| c.is_ascii_digit() || **c == b',' || **c == b'?')
.count();
index += num + 1;
amount = num / 2 + 1;
// X,X{mod} (or 3/4/5/etc mods)
}
b'-' if bytes[index] != b'?' => {
index += 7;
double = true;
} // X-X,X-X (Py)
b'/' => {
let num = bytes[2..]
.iter()
.take_while(|c| c.is_ascii_digit() || **c == b'/')
.count();
index += num + 2;
// X/X/X...{mod} multiple possible locations
}
c if (c.is_ascii_digit() || c == b'?') && bytes[0] == b'?' => {
if bytes[2] == b',' {
let num = bytes[2..]
.iter()
.take_while(|c| c.is_ascii_digit() || **c == b',' || **c == b'?')
.count();
index += num + 2;
amount = num / 2 + 1;
// ?X,X{mod} (or 3/4/5/etc mods)
} else if bytes[2] == b'/' {
let num = bytes[3..]
.iter()
.take_while(|c| c.is_ascii_digit() || **c == b'/')
.count();
index += num + 3;
// ?X/X{mod} multiple possible locations
} else {
index += 2; // ?X{mod}
}
}
_ => index += 1, // X{mod}
}
}
(index, amount, double)
}
}

impl Chemical for MonoSaccharide {
Expand Down Expand Up @@ -714,6 +785,8 @@ pub enum GlycanSubstituent {
Deoxy,
///3,4Hb 3,4-dihydroxybutyryl
DiHydroxyButyryl,
///DiMe two methyl
DiMethyl,
///AmMe2 N-(N,N-dimethyl-acetimidoyl)
DiMethylAcetimidoyl,
///Gr2,3Me2 2,3-di-O-methyl-glyceryl
Expand Down Expand Up @@ -800,6 +873,7 @@ const POSTFIX_SUBSTITUENTS: &[(&str, GlycanSubstituent)] = &[
("Lt", GlycanSubstituent::Lactyl),
("Lac", GlycanSubstituent::Lac),
("Me", GlycanSubstituent::Methyl),
("CMe", GlycanSubstituent::Methyl), // unsure about the difference with Me
("NAc", GlycanSubstituent::NAcetyl),
("Pyr", GlycanSubstituent::CargoxyEthylidene),
("Tau", GlycanSubstituent::Tauryl),
Expand All @@ -817,6 +891,7 @@ const POSTFIX_SUBSTITUENTS: &[(&str, GlycanSubstituent)] = &[
("CE", GlycanSubstituent::Glycyl), // Same molecular formula
("Suc", GlycanSubstituent::Suc),
("NFo", GlycanSubstituent::NFo),
("DiMe", GlycanSubstituent::DiMethyl),
("A", GlycanSubstituent::Acid),
("P", GlycanSubstituent::Phosphate),
("p", GlycanSubstituent::Phosphate),
Expand Down Expand Up @@ -858,6 +933,7 @@ impl Display for GlycanSubstituent {
Self::Deoxy => "d".to_string(),
Self::Didehydro => "en".to_string(),
Self::DiHydroxyButyryl => "3,4Hb".to_string(),
Self::DiMethyl => "DiMe".to_string(),
Self::DiMethylAcetimidoyl => "AmMe2".to_string(),
Self::DiMethylGlyceryl => "Gr2,3Me2".to_string(),
Self::Ethanolamine => "Etn".to_string(),
Expand Down Expand Up @@ -909,6 +985,7 @@ impl Chemical for GlycanSubstituent {
Self::Deoxy => molecular_formula!(H 1), // Together with the replacement below this is O-1
Self::Didehydro => molecular_formula!(H -1 O 1), // Together with the replacement below this is H-2
Self::DiHydroxyButyryl => molecular_formula!(H 7 C 4 O 3),
Self::DiMethyl => molecular_formula!(H 5 C 2), // assumed to replace the both the OH and H on a single carbon
Self::DiMethylAcetimidoyl => molecular_formula!(H 9 C 4 N 1),
Self::DiMethylGlyceryl => molecular_formula!(H 9 C 5 O 3),
Self::Ethanolamine => molecular_formula!(H 6 C 2 N 1 O 1),
Expand Down Expand Up @@ -1469,4 +1546,17 @@ mod tests {
))
);
}

fn iupac_masses() {
assert_eq!(
MonoSaccharide::from_short_iupac("Gal3DiMe(b1-4)GlcNAc(b1-", 0, 0)
.unwrap()
.0
.formula()
.monoisotopic_mass()
.unwrap()
.round(),
411.0
);
}
}

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