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Arc based atom bonds #94

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Arc based atom bonds #94

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aaf3a35
Preliminairy work on Arc based atom bonds (#80)
douweschulte Jul 21, 2022
27ca612
Closer to atom level bonds (WIP)
douweschulte Jul 24, 2022
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2 changes: 1 addition & 1 deletion Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ include = ["src/**/*", "LICENSE", "README.md"]

[dependencies]
rstar = { version = "^0.9.2", optional = true}
serde = { version = "~1.0", optional = true, features = ["derive"] }
serde = { version = "~1.0", optional = true, features = ["derive", "rc"] }
rayon = {version = "^1", optional = true}
doc-cfg = "0.1"
indexmap = "^1.8"
Expand Down
44 changes: 23 additions & 21 deletions src/read/pdb/parser.rs
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Expand Up @@ -607,41 +607,43 @@ fn add_modifications(pdb: &mut PDB, modifications: Vec<(Context, LexItem)>) -> V
/// Adds all bonds to the PDB, has to be done after all Atoms are already in place
#[allow(clippy::unwrap_used)]
fn add_bonds(pdb: &mut PDB, bonds: Vec<(Context, LexItem)>) -> Vec<PDBError> {
let mut errors = Vec::new();
for (context, bond) in bonds {
let errors = Vec::new();
for (_context, bond) in bonds {
match bond {
LexItem::SSBond(atom1, atom2, ..) => {
let find = |atom: (String, isize, Option<String>, String)| {
pdb.chains()
.find(|c| c.id() == atom.3)
.and_then(|c| {
c.residues()
.find(|r| {
r.serial_number() == atom.1
&& r.insertion_code() == atom.2.as_deref()
})
.map(|r| {
r.conformers().find(|c| c.name() == atom.0).map(|c| {
c.atoms().find(|a| a.name() == "SG").map(Atom::counter)
})
})
})
.flatten()
.flatten()
let h = pdb
.find(
Term::ConformerName(atom.0)
& Term::ResidueSerialNumber(atom.1)
& Term::ResidueInsertionCode(atom.2),
)
.next()
.unwrap();
(
h.atom().serial_number().to_owned(),
h.conformer()
.alternative_location()
.map(std::borrow::ToOwned::to_owned),
)
};
let ref1 = find(atom1);
let ref2 = find(atom2);

pdb.add_bond(
(ref1.0, ref1.1.as_deref()),
(ref2.0, ref2.1.as_deref()),
Bond::Disulfide,
);
/*
if let (Some(counter1), Some(counter2)) = (ref1, ref2) {
pdb.add_bond_counters(counter1, counter2, Bond::Disulfide);
} else {
errors.push(PDBError::new(
ErrorLevel::InvalidatingError,
"Could not find a bond partner",
"One of the atoms could not be found while parsing a disulfide bond.",
context,
));
}
} */
}
_ => {
panic!(
Expand Down
34 changes: 22 additions & 12 deletions src/structs/atom.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,15 @@
use crate::reference_tables;
use crate::structs::*;
use crate::transformation::TransformationMatrix;
use std::cell::{Ref, RefCell};
use std::cmp::Ordering;
use std::convert::TryInto;
use std::fmt;
use std::sync::atomic::{AtomicUsize, Ordering as AtomicOrdering};

static ATOM_COUNTER: AtomicUsize = AtomicUsize::new(0);

use std::sync::Arc;
/// A struct to represent a single Atom in a protein.
#[cfg_attr(feature = "serde", derive(serde::Serialize, serde::Deserialize))]
#[derive(Debug)]
pub struct Atom {
/// The unique serial number given to this atom
counter: usize,
/// Determines if this atom is a hetero atom (true), a non standard atom, or a normal atom (false)
hetero: bool,
/// The serial number of the Atom, should be unique within its model
Expand All @@ -37,6 +33,8 @@ pub struct Atom {
charge: isize,
/// The anisotropic temperature factors, if applicable
atf: Option<[[f64; 3]; 3]>,
/// Bonds
bonds: Vec<(Arc<RefCell<Atom>>, Bond)>,
}

impl Atom {
Expand Down Expand Up @@ -81,7 +79,6 @@ impl Atom {
None
};
Some(Atom {
counter: ATOM_COUNTER.fetch_add(1, AtomicOrdering::SeqCst),
hetero,
serial_number,
name: atom_name.trim().to_ascii_uppercase(),
Expand All @@ -93,17 +90,13 @@ impl Atom {
element,
charge,
atf: None,
bonds: Vec::new(),
})
} else {
None
}
}

/// Get a unique immutable counter for this atom.
pub(crate) const fn counter(&self) -> usize {
self.counter
}

/// Determine if this atom is an hetero atom (`true`), a non standard atom, or a normal atom (`false`).
pub const fn hetero(&self) -> bool {
self.hetero
Expand Down Expand Up @@ -350,6 +343,23 @@ impl Atom {
self.atf = Some(factors);
}

/// Add a bond to this Atom, do not forget to add the reverse bond as well yourself.
pub fn add_bond(&mut self, atom: Arc<RefCell<Atom>>, bond: Bond) {
self.bonds.push((atom, bond));
//atom.add_bond(self, bond);
}

/// Get the number of bonds on this Atom.
pub fn bond_count(&self) -> usize {
self.bonds.len()
}

/// Get all bonds to this Atom, it returns an `Arc<Atom>` which is a reference counted pointer to the Atom,
/// meaning it cannot ever be freed while the value is still being used somewhere.
pub fn bonds(&self) -> impl DoubleEndedIterator<Item = (Ref<'_, Atom>, Bond)> + '_ {
self.bonds.iter().map(|(a, b)| (a.borrow(), *b))
}

/// Determine whether this atom is likely to be a part of the backbone of a protein.
/// This is based on this Atom only, for a more precise definition use [`hierarchy::ContainsAtomConformer::is_backbone`].
pub fn is_backbone(&self) -> bool {
Expand Down
125 changes: 63 additions & 62 deletions src/structs/chain.rs
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
#![allow(dead_code)]
use crate::structs::*;
use crate::transformation::TransformationMatrix;
use doc_cfg::doc_cfg;
#[cfg(feature = "rayon")]
use rayon::prelude::*;
//use doc_cfg::doc_cfg;
//#[cfg(feature = "rayon")]
//use rayon::prelude::*;
use std::cell::{Ref, RefMut};
use std::cmp::Ordering;

#[cfg_attr(feature = "serde", derive(serde::Serialize, serde::Deserialize))]
Expand Down Expand Up @@ -87,21 +88,21 @@ impl<'a> Chain {
}

/// Get the number of Conformers making up this Chain in parallel
#[doc_cfg(feature = "rayon")]
pub fn par_conformer_count(&self) -> usize {
self.par_residues().map(Residue::conformer_count).sum()
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_conformer_count(&self) -> usize {
// self.par_residues().map(Residue::conformer_count).sum()
//}

/// Get the number of Atoms making up this Chain
pub fn atom_count(&self) -> usize {
self.residues().map(Residue::atom_count).sum()
}

/// Get the number of Atoms making up this Chain in parallel
#[doc_cfg(feature = "rayon")]
pub fn par_atom_count(&self) -> usize {
self.par_residues().map(Residue::par_atom_count).sum()
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_atom_count(&self) -> usize {
// self.par_residues().map(Residue::par_atom_count).sum()
//}

/// Get a reference to a specific Residue from list of Residues making up this Chain.
///
Expand Down Expand Up @@ -154,7 +155,7 @@ impl<'a> Chain {
///
/// ## Fails
/// It returns `None` if the index is out of bounds.
pub fn atom(&self, index: usize) -> Option<&Atom> {
pub fn atom(&self, index: usize) -> Option<Ref<'_, Atom>> {
self.atoms().nth(index)
}

Expand All @@ -165,7 +166,7 @@ impl<'a> Chain {
///
/// ## Fails
/// It returns `None` if the index is out of bounds.
pub fn atom_mut(&mut self, index: usize) -> Option<&mut Atom> {
pub fn atom_mut(&mut self, index: usize) -> Option<RefMut<'_, Atom>> {
self.atoms_mut().nth(index)
}

Expand Down Expand Up @@ -289,10 +290,10 @@ impl<'a> Chain {
}

/// Get a parallel iterator of references to Residues making up this Chain.
#[doc_cfg(feature = "rayon")]
pub fn par_residues(&self) -> impl ParallelIterator<Item = &Residue> + '_ {
self.residues.par_iter()
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_residues(&self) -> impl ParallelIterator<Item = &Residue> + '_ {
// self.residues.par_iter()
//}

/// Get an iterator of mutable references to Residues making up this Chain.
/// Double ended so iterating from the end is just as fast as from the start.
Expand All @@ -301,10 +302,10 @@ impl<'a> Chain {
}

/// Get a parallel iterator of mutable references to Residues making up this Chain.
#[doc_cfg(feature = "rayon")]
pub fn par_residues_mut(&mut self) -> impl ParallelIterator<Item = &mut Residue> + '_ {
self.residues.par_iter_mut()
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_residues_mut(&mut self) -> impl ParallelIterator<Item = &mut Residue> + '_ {
//self.residues.par_iter_mut()
//}

/// Get an iterator of references to Conformers making up this Chain.
/// Double ended so iterating from the end is just as fast as from the start.
Expand All @@ -313,10 +314,10 @@ impl<'a> Chain {
}

/// Get a parallel iterator of references to Conformers making up this Chain.
#[doc_cfg(feature = "rayon")]
pub fn par_conformers(&self) -> impl ParallelIterator<Item = &Conformer> + '_ {
self.par_residues().flat_map(Residue::par_conformers)
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_conformers(&self) -> impl ParallelIterator<Item = &Conformer> + '_ {
//self.par_residues().flat_map(Residue::par_conformers)
//}

/// Get an iterator of mutable references to Conformers making up this Chain.
/// Double ended so iterating from the end is just as fast as from the start.
Expand All @@ -325,35 +326,35 @@ impl<'a> Chain {
}

/// Get a parallel iterator of mutable references to Conformers making up this Chain.
#[doc_cfg(feature = "rayon")]
pub fn par_conformers_mut(&mut self) -> impl ParallelIterator<Item = &mut Conformer> + '_ {
self.par_residues_mut()
.flat_map(Residue::par_conformers_mut)
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_conformers_mut(&mut self) -> impl ParallelIterator<Item = &mut Conformer> + '_ {
//self.par_residues_mut()
//.flat_map(Residue::par_conformers_mut)
//}

/// Get an iterator of references to Atoms making up this Chain.
/// Double ended so iterating from the end is just as fast as from the start.
pub fn atoms(&self) -> impl DoubleEndedIterator<Item = &Atom> + '_ {
pub fn atoms(&self) -> impl DoubleEndedIterator<Item = Ref<'_, Atom>> + '_ {
self.residues().flat_map(Residue::atoms)
}

/// Get a parallel iterator of references to Atoms making up this Chain.
#[doc_cfg(feature = "rayon")]
pub fn par_atoms(&self) -> impl ParallelIterator<Item = &Atom> + '_ {
self.par_residues().flat_map(Residue::par_atoms)
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_atoms(&self) -> impl ParallelIterator<Item = &Atom> + '_ {
// self.par_residues().flat_map(Residue::par_atoms)
//}

/// Get an iterator of mutable references to Atoms making up this Chain.
/// Double ended so iterating from the end is just as fast as from the start.
pub fn atoms_mut(&mut self) -> impl DoubleEndedIterator<Item = &mut Atom> + '_ {
pub fn atoms_mut(&mut self) -> impl DoubleEndedIterator<Item = RefMut<'_, Atom>> + '_ {
self.residues_mut().flat_map(Residue::atoms_mut)
}

/// Get a parallel iterator of mutablereferences to Atoms making up this Chain.
#[doc_cfg(feature = "rayon")]
pub fn par_atoms_mut(&mut self) -> impl ParallelIterator<Item = &mut Atom> + '_ {
self.par_residues_mut().flat_map(Residue::par_atoms_mut)
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_atoms_mut(&mut self) -> impl ParallelIterator<Item = &mut Atom> + '_ {
// self.par_residues_mut().flat_map(Residue::par_atoms_mut)
//}

/// Get an iterator of references to a struct containing all atoms with their hierarchy making up this Chain.
pub fn atoms_with_hierarchy(
Expand Down Expand Up @@ -424,7 +425,7 @@ impl<'a> Chain {
/// Remove all Atoms matching the given predicate. As this is done in place this is the fastest way to remove Atoms from this Chain.
pub fn remove_atoms_by<F>(&mut self, predicate: F)
where
F: Fn(&Atom) -> bool,
F: Fn(Ref<'_, Atom>) -> bool,
{
for residue in self.residues_mut() {
residue.remove_atoms_by(&predicate);
Expand Down Expand Up @@ -481,17 +482,17 @@ impl<'a> Chain {
///
/// ## Arguments
/// * `id` - the id construct of the Residue to remove (see Residue.id())
#[doc_cfg(feature = "rayon")]
pub fn par_remove_residue_by_id(&mut self, id: (isize, Option<&str>)) -> bool {
let index = self.residues.par_iter().position_first(|a| a.id() == id);

if let Some(i) = index {
self.remove_residue(i);
true
} else {
false
}
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_remove_residue_by_id(&mut self, id: (isize, Option<&str>)) -> bool {
// let index = self.residues.par_iter().position_first(|a| a.id() == id);
//
// if let Some(i) = index {
// self.remove_residue(i);
// true
// } else {
// false
// }
//}

/// Remove all empty Residues from this Chain, and all empty Conformers from the Residues.
pub fn remove_empty(&mut self) {
Expand All @@ -508,11 +509,11 @@ impl<'a> Chain {

/// Apply a transformation to the position of all atoms making up this Chain, the new position is immediately set.
/// Done in parallel.
#[doc_cfg(feature = "rayon")]
pub fn par_apply_transformation(&mut self, transformation: &TransformationMatrix) {
self.par_atoms_mut()
.for_each(|atom| atom.apply_transformation(transformation));
}
//#[doc_cfg(feature = "rayon")]
//pub fn par_apply_transformation(&mut self, transformation: &TransformationMatrix) {
// self.par_atoms_mut()
// .for_each(|atom| atom.apply_transformation(transformation));
//}

/// Join this Chain with another Chain, this moves all atoms from the other Chain
/// to this Chain. All other (meta) data of this Chain will stay the same.
Expand All @@ -525,11 +526,11 @@ impl<'a> Chain {
self.residues.sort();
}

/// Sort the residues of this chain in parallel
#[doc_cfg(feature = "rayon")]
pub fn par_sort(&mut self) {
self.residues.par_sort();
}
// Sort the residues of this chain in parallel
//#[doc_cfg(feature = "rayon")]
//pub fn par_sort(&mut self) {
// self.residues.par_sort();
//}
}

use std::fmt;
Expand Down
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