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//! RustSASA is a Rust library for computing the absolute solvent accessible surface area (ASA/SASA) of each atom in a given protein structure using the Shrake-Rupley algorithm[1].
mod consts;
mod test;
mod utils;
use crate::consts::POLAR_AMINO_ACIDS;
use crate::utils::{serialize_chain_id, simd_sum};
use nalgebra::{Point3, Vector3};
use pdbtbx::PDB;
use rayon::prelude::*;
use rstar::{PointDistance, RTree, RTreeObject, AABB};
use snafu::prelude::*;
use snafu::OptionExt;
use std::collections::HashMap;
use std::sync::Arc;
/// This struct represents an individual Atom
#[derive(Clone)]
pub struct Atom {
/// The 3D position of the atom
pub position: Point3<f32>,
/// The Van Der Walls radius of the atom
pub radius: f32,
/// A unique Id for the atom
pub id: usize,
/// Parent Id
pub parent_id: Option<isize>,
}
/// Can be used to specify output resolution of SASA computation for convenience.
pub enum SASALevel {
Atom,
Residue,
Chain,
Protein,
}
#[derive(Debug, PartialEq)]
pub struct ChainResult {
pub name: String,
pub value: f32,
}
#[derive(Debug, PartialEq)]
pub struct ResidueResult {
pub serial_number: isize,
pub value: f32,
pub name: String,
pub is_polar: bool,
}
#[derive(Debug, PartialEq)]
pub struct ProteinResult {
/// The total SASA value for the entire protein
pub global_total: f32,
/// The total polar SASA value for the entire protein
pub polar_total: f32,
/// The total *non*-polar SASA value for the entire protein
pub non_polar_total: f32,
}
#[derive(Debug, PartialEq)]
pub enum SASAResult {
Atom(Vec<f32>),
Residue(Vec<ResidueResult>),
Chain(Vec<ChainResult>),
Protein(ProteinResult),
}
#[derive(Debug, Snafu)]
pub enum SASACalcError {
#[snafu(display("Element missing for atom"))]
ElementMissing,
#[snafu(display("Van der Waals radius missing for element"))]
VanDerWaalsMissing,
#[snafu(display("Failed to map atoms back to level element"))]
AtomMapToLevelElementFailed,
#[snafu(display("Failed to get residue name"))]
FailedToGetResidueName,
}
impl RTreeObject for Atom {
type Envelope = AABB<[f32; 3]>;
fn envelope(&self) -> Self::Envelope {
AABB::from_point(<[f32; 3]>::from(self.position))
}
}
impl PointDistance for Atom {
fn distance_2(&self, other: &[f32; 3]) -> f32 {
let xyz = self.position.coords.xyz();
let z = xyz[2];
let y = xyz[1];
let x = xyz[0];
// No square root as that is required by the package
(other[2] - z).mul_add(
other[2] - z,
(other[1] - y).mul_add(other[1] - y, (other[0] - x).powi(2)),
)
}
}
/// Generates points on a sphere using the Golden Section Spiral algorithm
fn generate_sphere_points(n_points: usize) -> Vec<Vector3<f32>> {
let mut points = Vec::with_capacity(n_points);
let golden_ratio = (1.0 + 5f32.sqrt()) / 2.0;
let angle_increment = 2.0 * std::f32::consts::PI * golden_ratio;
for i in 0..n_points {
let t = i as f32 / n_points as f32;
let inclination = (1.0 - 2.0 * t).acos();
let azimuth = angle_increment * i as f32;
let x = inclination.sin() * azimuth.cos();
let y = inclination.sin() * azimuth.sin();
let z = inclination.cos();
points.push(Vector3::new(x, y, z));
}
points
}
fn is_accessible_rstar(
test_point: &Point3<f32>,
atom: &Atom,
atoms: &RTree<Atom>,
probe_radius: f32,
max_radii: f32,
) -> bool {
let xyz = test_point.coords.xyz();
let sr = probe_radius + (max_radii * 2.0);
let candidates = atoms.locate_within_distance([xyz[0], xyz[1], xyz[2]], sr * sr);
for candidate in candidates {
if atom.id != candidate.id
&& (test_point - candidate.position).norm() < (candidate.radius + probe_radius)
{
return false;
}
}
true
}
/// Takes the probe radius and number of points to use along with a list of Atoms as inputs and returns a Vec with SASA values for each atom.
/// For most users it is recommend that you use `calculate_sasa` instead. This method can be used directly if you do not want to use pdbtbx to load PDB/mmCIF files or want to load them from a different source.
/// Probe Radius Default: 1.4
/// Point Count Default: 100
/// ## Example using pdbtbx:
/// ```
/// use nalgebra::{Point3, Vector3};
/// use pdbtbx::StrictnessLevel;
/// use rust_sasa::{Atom, calculate_sasa_internal};
/// let (mut pdb, _errors) = pdbtbx::open(
/// "./example.cif",
/// StrictnessLevel::Medium
/// ).unwrap();
/// let mut atoms = vec![];
/// for atom in pdb.atoms() {
/// atoms.push(Atom {
/// position: Point3::new(atom.pos().0 as f32, atom.pos().1 as f32, atom.pos().2 as f32),
/// radius: atom.element().unwrap().atomic_radius().van_der_waals.unwrap() as f32,
/// id: atom.serial_number(),
/// parent_id: None
/// })
/// }
/// let sasa = calculate_sasa_internal(&atoms, None, None);
/// ```
pub fn calculate_sasa_internal(
atoms: &[Atom],
in_probe_radius: Option<f32>,
in_n_points: Option<usize>,
) -> Vec<f32> {
// Load defaults if not specified
let mut probe_radius = 1.4;
let mut n_points = 100;
if let Some(in_probe_radius) = in_probe_radius {
probe_radius = in_probe_radius;
}
if let Some(in_n_points) = in_n_points {
n_points = in_n_points;
}
//
let sphere_points = generate_sphere_points(n_points);
// Create R*-tree from atoms for spatial lookup
let tree = RTree::bulk_load(atoms.to_vec());
let tree_arc = Arc::new(tree); // Use Arc for safe sharing among threads
let mut max_radii = 0.0;
for atom in atoms {
if atom.radius > max_radii {
max_radii = atom.radius;
}
}
atoms
.par_iter()
.map(|atom| {
let mut accessible_points = 0;
for sphere_point in &sphere_points {
let test_point = atom.position + sphere_point * (atom.radius + probe_radius);
if is_accessible_rstar(&test_point, atom, &tree_arc, probe_radius, max_radii) {
accessible_points += 1;
}
}
4.0 * std::f32::consts::PI
* (atom.radius + probe_radius).powi(2)
* (accessible_points as f32)
/ (n_points as f32)
})
.collect()
}
/// This function calculates the SASA for a given protein. The output level can be specified with the level attribute e.g: (SASALevel::Atom,SASALevel::Residue,etc...).
/// Probe radius and n_points can be customized if not customized will default to 1.4, and 100 respectively.
/// If you want more fine-grained control you may want to use [calculate_sasa_internal] instead.
/// ## Example
/// ```
/// use pdbtbx::StrictnessLevel;
/// use rust_sasa::{Atom, calculate_sasa, calculate_sasa_internal, SASALevel};
/// let (mut pdb, _errors) = pdbtbx::open(
/// "./example.cif",
/// StrictnessLevel::Medium
/// ).unwrap();
/// let result = calculate_sasa(&pdb,None,None,SASALevel::Residue);
/// ```
pub fn calculate_sasa(
pdb: &PDB,
probe_radius: Option<f32>,
n_points: Option<usize>,
level: SASALevel,
) -> Result<SASAResult, SASACalcError> {
let mut atoms = vec![];
let mut parent_to_atoms = HashMap::new();
match level {
SASALevel::Atom => {
for atom in pdb.atoms() {
atoms.push(Atom {
position: Point3::new(
atom.pos().0 as f32,
atom.pos().1 as f32,
atom.pos().2 as f32,
),
radius: atom
.element()
.context(ElementMissingSnafu)?
.atomic_radius()
.van_der_waals
.context(VanDerWaalsMissingSnafu)? as f32,
id: atom.serial_number(),
parent_id: None,
})
}
}
SASALevel::Residue | SASALevel::Protein => {
let mut i = 0;
for residue in pdb.residues() {
let mut temp = vec![];
for atom in residue.atoms() {
atoms.push(Atom {
position: Point3::new(
atom.pos().0 as f32,
atom.pos().1 as f32,
atom.pos().2 as f32,
),
radius: atom
.element()
.context(ElementMissingSnafu)?
.atomic_radius()
.van_der_waals
.context(VanDerWaalsMissingSnafu)?
as f32,
id: atom.serial_number(),
parent_id: Some(residue.serial_number()),
});
temp.push(i);
i += 1;
}
parent_to_atoms.insert(residue.serial_number(), temp);
}
}
SASALevel::Chain => {
let mut i = 0;
for chain in pdb.chains() {
let mut temp = vec![];
let chain_id = serialize_chain_id(chain.id());
for atom in chain.atoms() {
atoms.push(Atom {
position: Point3::new(
atom.pos().0 as f32,
atom.pos().1 as f32,
atom.pos().2 as f32,
),
radius: atom
.element()
.context(ElementMissingSnafu)?
.atomic_radius()
.van_der_waals
.context(VanDerWaalsMissingSnafu)?
as f32,
id: atom.serial_number(),
parent_id: Some(chain_id),
});
temp.push(i);
i += 1
}
parent_to_atoms.insert(chain_id, temp);
}
}
}
let atom_sasa = calculate_sasa_internal(&atoms, probe_radius, n_points);
return match level {
SASALevel::Atom => Ok(SASAResult::Atom(atom_sasa)),
SASALevel::Chain => {
let mut chain_sasa = vec![];
for chain in pdb.chains() {
let chain_id = serialize_chain_id(chain.id());
let chain_atom_index = parent_to_atoms
.get(&chain_id)
.context(AtomMapToLevelElementFailedSnafu)?;
let chain_atoms: Vec<_> = chain_atom_index
.iter()
.map(|&index| atom_sasa[index])
.collect();
let sum = simd_sum(chain_atoms.as_slice());
chain_sasa.push(ChainResult {
name: chain.id().to_string(),
value: sum,
})
}
Ok(SASAResult::Chain(chain_sasa))
}
SASALevel::Residue => {
let mut residue_sasa = vec![];
for residue in pdb.residues() {
let residue_atom_index = parent_to_atoms
.get(&residue.serial_number())
.context(AtomMapToLevelElementFailedSnafu)?;
let residue_atoms: Vec<_> = residue_atom_index
.iter()
.map(|&index| atom_sasa[index])
.collect();
let sum = simd_sum(residue_atoms.as_slice());
let name = residue
.name()
.context(FailedToGetResidueNameSnafu)?
.to_string();
residue_sasa.push(ResidueResult {
serial_number: residue.serial_number(),
value: sum,
is_polar: POLAR_AMINO_ACIDS.contains(&name),
name,
})
}
Ok(SASAResult::Residue(residue_sasa))
}
SASALevel::Protein => {
let mut polar_total: f32 = 0.0;
let mut non_polar_total: f32 = 0.0;
for residue in pdb.residues() {
let residue_atom_index = parent_to_atoms
.get(&residue.serial_number())
.context(AtomMapToLevelElementFailedSnafu)?;
let residue_atoms: Vec<_> = residue_atom_index
.iter()
.map(|&index| atom_sasa[index])
.collect();
let sum = simd_sum(residue_atoms.as_slice());
let name = residue
.name()
.context(FailedToGetResidueNameSnafu)?
.to_string();
if POLAR_AMINO_ACIDS.contains(&name) {
polar_total += sum
} else {
non_polar_total += sum
}
}
let global_sum = simd_sum(atom_sasa.as_slice());
Ok(SASAResult::Protein(ProteinResult {
global_total: global_sum,
polar_total,
non_polar_total,
}))
}
};
}