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use super::atom::Atom;
use super::bond::BondType;
use petgraph::graph::{NodeIndex, UnGraph};
/// The core molecular graph type.
pub type MolGraph = UnGraph<Atom, BondType>;
/// Extension trait adding chemistry-aware methods to MolGraph.
pub trait MolGraphExt {
/// Number of atoms (heavy atoms only, no implicit hydrogens).
fn num_atoms(&self) -> usize;
/// Number of bonds in the graph.
fn num_bonds(&self) -> usize;
/// Access atom data by node index.
fn atom(&self, idx: NodeIndex) -> &Atom;
/// Mutably access atom data by node index.
fn atom_mut(&mut self, idx: NodeIndex) -> &mut Atom;
/// Bond type between two atoms, or `None` if not bonded.
fn bond_between(&self, a: NodeIndex, b: NodeIndex) -> Option<BondType>;
/// All non-hydrogen neighbor indices.
fn heavy_neighbors(&self, idx: NodeIndex) -> Vec<NodeIndex>;
/// Number of neighbors (graph degree).
fn degree(&self, idx: NodeIndex) -> usize;
/// Compute implicit H count for an atom.
/// - If explicit_h is set (bracket atom with H spec), return that.
/// - For bracket atoms without H spec (explicit_h is None AND atom is bracket),
/// we return 0 — caller decides based on context.
/// - For organic subset atoms, compute from default valences:
/// implicit_H = min_valence_geq_bond_sum - bond_sum
fn compute_implicit_h(&self, idx: NodeIndex) -> u8;
/// Set h_count on all atoms. Call after graph is fully constructed.
fn assign_implicit_hydrogens(&mut self);
}
impl MolGraphExt for MolGraph {
fn num_atoms(&self) -> usize {
self.node_count()
}
fn num_bonds(&self) -> usize {
self.edge_count()
}
fn atom(&self, idx: NodeIndex) -> &Atom {
&self[idx]
}
fn atom_mut(&mut self, idx: NodeIndex) -> &mut Atom {
&mut self[idx]
}
fn bond_between(&self, a: NodeIndex, b: NodeIndex) -> Option<BondType> {
self.find_edge(a, b).map(|e| self[e])
}
fn heavy_neighbors(&self, idx: NodeIndex) -> Vec<NodeIndex> {
self.neighbors(idx).collect()
}
fn degree(&self, idx: NodeIndex) -> usize {
self.neighbors(idx).count()
}
fn compute_implicit_h(&self, idx: NodeIndex) -> u8 {
let atom = &self[idx];
// Bracket atoms with explicit H count
if let Some(h) = atom.explicit_h {
return h;
}
// Bracket atoms without H spec → 0 (e.g., [Fe], [C])
// We detect bracket vs organic by whether explicit_h was ever set.
// But we can't distinguish here without more context stored on the atom.
// Convention: if element is NOT in organic subset, return 0.
if !atom.element.is_organic_subset() {
return 0;
}
// Sum bond orders for the atom
let bond_sum: u8 = self
.edges(idx)
.map(|e| e.weight().valence_contribution())
.sum();
let valences = atom.element.default_valences();
if valences.is_empty() || (valences.len() == 1 && valences[0] == 0) {
return 0;
}
if atom.aromatic {
// For aromatic atoms, the pi system contributes 1 to the effective bond sum.
// However, if the atom's normal valence is already exactly satisfied by its bonds
// (e.g., aromatic N bonded to methyl + 2 ring atoms = 3 bonds, valence 3),
// do NOT add the +1 or we'd incorrectly jump to a higher valence (e.g., N valence 5).
for &v in valences {
if v >= bond_sum {
let h_raw = v.saturating_sub(bond_sum);
let charge_adj = atom.charge.unsigned_abs();
if h_raw == 0 {
// All valence bonds used; no pi-electron adjustment needed.
return 0_u8.saturating_sub(charge_adj);
}
// Atom still has available valence: apply the +1 aromatic pi adjustment.
let effective_sum = bond_sum + 1;
for &v2 in valences {
if v2 >= effective_sum {
return v2.saturating_sub(effective_sum).saturating_sub(charge_adj);
}
}
return 0;
}
}
return 0;
}
// Non-aromatic: find smallest valence >= bond_sum
for &v in valences {
if v >= bond_sum {
let charge_adj = atom.charge.unsigned_abs();
return v.saturating_sub(bond_sum).saturating_sub(charge_adj);
}
}
0
}
fn assign_implicit_hydrogens(&mut self) {
let indices: Vec<NodeIndex> = self.node_indices().collect();
for idx in indices {
if self[idx].element == super::atom::Element::H {
continue; // skip H/D atoms themselves
}
let h_implicit = self.compute_implicit_h(idx);
// Count explicit H/D neighbor atoms in the graph (e.g. [2H] deuterium)
let h_explicit: u8 = self
.neighbors(idx)
.filter(|&nb| self[nb].element == super::atom::Element::H)
.count()
.min(255) as u8;
self[idx].h_count = h_implicit + h_explicit;
}
}
}
#[cfg(test)]
mod tests {
use super::super::atom::Element;
use super::*;
fn make_ethanol() -> MolGraph {
let mut g = MolGraph::new_undirected();
let c1 = g.add_node(Atom::new(Element::C));
let c2 = g.add_node(Atom::new(Element::C));
let o = g.add_node(Atom::new(Element::O));
g.add_edge(c1, c2, BondType::Single);
g.add_edge(c2, o, BondType::Single);
g.assign_implicit_hydrogens();
g
}
#[test]
fn test_ethanol_structure() {
let g = make_ethanol();
assert_eq!(g.num_atoms(), 3);
assert_eq!(g.num_bonds(), 2);
}
#[test]
fn test_ethanol_implicit_h() {
let g = make_ethanol();
// C-C-O: C1 has 1 heavy neighbor → 3H, C2 has 2 → 2H, O has 1 → 1H
assert_eq!(g[NodeIndex::new(0)].h_count, 3);
assert_eq!(g[NodeIndex::new(1)].h_count, 2);
assert_eq!(g[NodeIndex::new(2)].h_count, 1);
}
#[test]
fn test_benzene_implicit_h() {
let mut g = MolGraph::new_undirected();
let atoms: Vec<NodeIndex> = (0..6)
.map(|_| {
let mut a = Atom::new(Element::C);
a.aromatic = true;
g.add_node(a)
})
.collect();
for i in 0..5 {
g.add_edge(atoms[i], atoms[i + 1], BondType::Aromatic);
}
g.add_edge(atoms[5], atoms[0], BondType::Aromatic);
g.assign_implicit_hydrogens();
// Each aromatic C: bond_sum=2 (two aromatic bonds, each contrib 1),
// effective_sum = 2+1 = 3, valence 4, h = 4-3 = 1
for &a in &atoms {
assert_eq!(g[a].h_count, 1, "aromatic C should have 1H");
}
}
#[test]
fn test_heavy_neighbors() {
let g = make_ethanol();
let c2 = NodeIndex::new(1);
let neighbors = g.heavy_neighbors(c2);
assert_eq!(neighbors.len(), 2);
}
}