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#![allow(dead_code)]
use crate::structs::*;
use crate::transformation::*;
use std::cmp::Ordering;
#[derive(Debug, Clone, PartialEq, Eq)]
pub struct Model {
serial_number: usize,
chains: Vec<Chain>,
}
impl Model {
pub fn new(serial_number: usize) -> Model {
Model {
serial_number,
chains: Vec::new(),
}
}
pub fn serial_number(&self) -> usize {
self.serial_number
}
pub fn set_serial_number(&mut self, new_number: usize) {
self.serial_number = new_number;
}
pub fn chain_count(&self) -> usize {
self.chains.len()
}
pub fn residue_count(&self) -> usize {
self.chains()
.fold(0, |sum, chain| chain.residue_count() + sum)
}
pub fn conformer_count(&self) -> usize {
self.chains()
.fold(0, |sum, chain| chain.conformer_count() + sum)
}
pub fn atom_count(&self) -> usize {
self.chains().fold(0, |sum, chain| chain.atom_count() + sum)
}
pub fn chain(&self, index: usize) -> Option<&Chain> {
self.chains().nth(index)
}
pub fn chain_mut(&mut self, index: usize) -> Option<&mut Chain> {
self.chains_mut().nth(index)
}
pub fn residue(&self, index: usize) -> Option<&Residue> {
self.residues().nth(index)
}
pub fn residue_mut(&mut self, index: usize) -> Option<&mut Residue> {
self.residues_mut().nth(index)
}
pub fn conformer(&self, index: usize) -> Option<&Conformer> {
self.conformers().nth(index)
}
pub fn conformer_mut(&mut self, index: usize) -> Option<&mut Conformer> {
self.conformers_mut().nth(index)
}
pub fn atom(&self, index: usize) -> Option<&Atom> {
self.atoms().nth(index)
}
pub fn atom_mut(&mut self, index: usize) -> Option<&mut Atom> {
self.atoms_mut().nth(index)
}
pub fn chains(&self) -> impl DoubleEndedIterator<Item = &Chain> + '_ {
self.chains.iter()
}
pub fn chains_mut(&mut self) -> impl DoubleEndedIterator<Item = &mut Chain> + '_ {
self.chains.iter_mut()
}
pub fn residues(&self) -> impl DoubleEndedIterator<Item = &Residue> + '_ {
self.chains.iter().flat_map(|a| a.residues())
}
pub fn residues_mut(&mut self) -> impl DoubleEndedIterator<Item = &mut Residue> + '_ {
self.chains.iter_mut().flat_map(|a| a.residues_mut())
}
pub fn conformers(&self) -> impl DoubleEndedIterator<Item = &Conformer> + '_ {
self.chains.iter().flat_map(|a| a.conformers())
}
pub fn conformers_mut(&mut self) -> impl DoubleEndedIterator<Item = &mut Conformer> + '_ {
self.chains.iter_mut().flat_map(|a| a.conformers_mut())
}
pub fn atoms(&self) -> impl DoubleEndedIterator<Item = &Atom> + '_ {
self.chains.iter().flat_map(|a| a.atoms())
}
pub fn atoms_mut(&mut self) -> impl DoubleEndedIterator<Item = &mut Atom> + '_ {
self.chains.iter_mut().flat_map(|a| a.atoms_mut())
}
pub fn add_atom(
&mut self,
new_atom: Atom,
chain_id: &str,
residue_id: (isize, Option<&str>),
conformer_id: (&str, Option<&str>),
) {
let mut found = false;
let mut new_chain =
Chain::new(chain_id.trim()).expect("Invalid characters in chain creation");
let mut current_chain = &mut new_chain;
for chain in &mut self.chains {
if chain.id() == chain_id.trim() {
current_chain = chain;
found = true;
break;
}
}
#[allow(clippy::unwrap_used)]
if !found {
self.chains.push(new_chain);
current_chain = (&mut self.chains).last_mut().unwrap();
}
current_chain.add_atom(new_atom, residue_id, conformer_id);
}
pub fn add_chain(&mut self, chain: Chain) {
self.chains.push(chain);
}
pub fn remove_atoms_by<F>(&mut self, predicate: F)
where
F: Fn(&Atom) -> bool,
{
for residue in self.residues_mut() {
residue.remove_atoms_by(&predicate);
}
}
pub fn remove_conformers_by<F>(&mut self, predicate: F)
where
F: Fn(&Conformer) -> bool,
{
for chain in self.chains_mut() {
chain.remove_conformers_by(&predicate);
}
}
pub fn remove_residues_by<F>(&mut self, predicate: F)
where
F: Fn(&Residue) -> bool,
{
for chain in self.chains_mut() {
chain.remove_residues_by(&predicate);
}
}
pub fn remove_chains_by<F>(&mut self, predicate: F)
where
F: Fn(&Chain) -> bool,
{
self.chains.retain(|chain| !predicate(chain));
}
pub fn remove_chain(&mut self, index: usize) -> Chain {
self.chains.remove(index)
}
pub fn remove_chain_by_id(&mut self, id: String) -> bool {
let index = self.chains().position(|a| a.id() == id);
if let Some(i) = index {
self.remove_chain(i);
true
} else {
false
}
}
pub fn remove_empty(&mut self) {
self.chains.iter_mut().for_each(|c| c.remove_empty());
self.chains.retain(|c| c.residue_count() > 0);
}
pub fn apply_transformation(&mut self, transformation: &TransformationMatrix) {
for atom in self.atoms_mut() {
atom.apply_transformation(transformation);
}
}
pub fn join(&mut self, other: Model) {
self.chains.extend(other.chains);
}
pub fn extend<T: IntoIterator<Item = Chain>>(&mut self, iter: T) {
self.chains.extend(iter);
}
pub fn sort(&mut self) {
self.chains.sort();
}
}
use std::fmt;
impl fmt::Display for Model {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
write!(
f,
"MODEL SerialNumber:{}, Chains: {}",
self.serial_number,
self.chains.len()
)
}
}
impl PartialOrd for Model {
fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
Some(self.serial_number.cmp(&other.serial_number))
}
}
impl Ord for Model {
fn cmp(&self, other: &Self) -> Ordering {
self.serial_number.cmp(&other.serial_number)
}
}
#[cfg(test)]
mod tests {
use super::*;
#[test]
fn test_equality() {
let a = Model::new(0);
let b = a.clone();
let c = Model::new(1);
assert_eq!(a, b);
assert_ne!(a, c);
assert_ne!(b, c);
assert!(a < c);
}
#[test]
#[allow(clippy::unwrap_used)]
fn test_children() {
let mut a = Model::new(0);
a.add_chain(Chain::new("A").unwrap());
let mut iter = a.chains();
assert_eq!(iter.next(), Some(&Chain::new("A").unwrap()));
assert_eq!(iter.next(), None);
assert_eq!(a.chain_count(), 1);
assert_eq!(a.conformer_count(), 0);
assert_eq!(a.residue_count(), 0);
assert_eq!(a.atom_count(), 0);
}
#[test]
#[allow(clippy::unwrap_used)]
fn test_remove() {
let mut a = Model::new(0);
a.add_chain(Chain::new("A").unwrap());
a.add_chain(Chain::new("C").unwrap());
assert_eq!(a.remove_chain(0), Chain::new("A").unwrap());
a.remove_chain_by_id("C".to_string());
assert_eq!(a.chain_count(), 0);
}
#[test]
fn test_display() {
let a = Model::new(0);
format!("{:?}", a);
format!("{}", a);
}
}