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//! Debug: exercise SSSR ring perception on assorted ring systems.
//!
//! Category: debug
use sci_form::graph::Molecule;
fn main() {
let molecules = [
"C1C2CC1C2", // bicyclo[1.1.1]pentane
"CC12CC(C1)C2", // norbornane-like
"C1CC2CCC12", // bicyclo[2.2.0]hexane
"C1C2C3CC2C13", // tricyclic
"CC1C2CC1C2", // methylbicyclopentane
"CC1(C)C2CC1C2", // dimethyl
"OC1C2CC1C2", // OH-bicyclopentane
"C1CC2CC1C2", // bicyclo[2.1.1]hexane
"C12CC3CC(C1)CC(C2)C3", // adamantane
];
for smi in &molecules {
let mol = match Molecule::from_smiles(smi) {
Ok(m) => m,
Err(_) => {
println!("{:30} PARSE_FAIL", smi);
continue;
}
};
let n = mol.graph.node_count();
let bounds = {
let raw = sci_form::distgeom::calculate_bounds_matrix_opts(&mol, true);
let mut b = raw;
if sci_form::distgeom::triangle_smooth_tol(&mut b, 0.05) {
b
} else {
let raw2 = sci_form::distgeom::calculate_bounds_matrix_opts(&mol, false);
let mut b2 = raw2.clone();
if sci_form::distgeom::triangle_smooth_tol(&mut b2, 0.0) {
b2
} else {
let mut b3 = raw2;
sci_form::distgeom::triangle_smooth_tol(&mut b3, 0.05);
b3
}
}
};
let chiral_sets = sci_form::distgeom::identify_chiral_sets(&mol);
let tet_centers = sci_form::distgeom::identify_tetrahedral_centers(&mol);
let use_4d = !chiral_sets.is_empty();
let embed_dim = if use_4d { 4 } else { 3 };
let mut rng = sci_form::distgeom::MinstdRand::new(42);
let mut step_fails = [0u32; 7]; // 0:eigen 1:energy 2:tet 3:chiral 4:planar 5:dblbond 6:smooth_fail
let max_iter = 10 * n;
let mut ok = false;
for _iter in 0..max_iter {
let dists = sci_form::distgeom::pick_rdkit_distances(&mut rng, &bounds);
let coords_opt =
sci_form::distgeom::compute_initial_coords_rdkit(&mut rng, &dists, embed_dim);
let mut coords = match coords_opt {
Some(c) => c,
None => {
step_fails[0] += 1;
continue;
}
};
{
let mut need = 1;
let mut restarts = 0;
while need != 0 && restarts < 5 {
need = sci_form::forcefield::bounds_ff::minimize_bfgs_rdkit(
&mut coords,
&bounds,
&chiral_sets,
400,
1e-3,
5.0,
0.1,
1.0,
);
restarts += 1;
}
}
let c32 = coords.map(|v| v as f32);
let e =
sci_form::forcefield::bounds_ff::bounds_violation_energy_basin(&c32, &bounds, 5.0)
+ if !chiral_sets.is_empty() {
sci_form::forcefield::bounds_ff::chiral_violation_energy(&c32, &chiral_sets)
} else {
0.0
};
if e / n as f32 >= 0.05 {
step_fails[1] += 1;
continue;
}
if !sci_form::distgeom::check_tetrahedral_centers(&coords, &tet_centers) {
step_fails[2] += 1;
continue;
}
if !chiral_sets.is_empty()
&& !sci_form::distgeom::check_chiral_centers(&coords, &chiral_sets)
{
step_fails[3] += 1;
continue;
}
if use_4d {
let mut need = 1;
let mut restarts = 0;
while need != 0 && restarts < 5 {
need = sci_form::forcefield::bounds_ff::minimize_bfgs_rdkit(
&mut coords,
&bounds,
&chiral_sets,
200,
1e-3,
5.0,
1.0,
0.2,
);
restarts += 1;
}
}
let coords3d = coords.columns(0, 3).into_owned();
let ff = sci_form::forcefield::etkdg_3d::build_etkdg_3d_ff_with_torsions(
&mol,
&coords3d,
&bounds,
&[],
);
let refined = sci_form::forcefield::etkdg_3d::minimize_etkdg_3d_bfgs(
&mol, &coords3d, &ff, 300, 1e-3,
);
let ref_f32 = refined.map(|v| v as f32);
{
let n_improper_atoms = ff.inversion_contribs.len() / 3;
let planarity_energy =
sci_form::forcefield::etkdg_3d::planarity_check_energy(&ref_f32, &ff);
if planarity_energy > n_improper_atoms as f32 * 0.7 {
step_fails[4] += 1;
continue;
}
}
if !sci_form::distgeom::check_double_bond_geometry(&mol, &refined) {
step_fails[5] += 1;
continue;
}
println!(
"{:30} OK iter={:3} eig={} ene={} tet={} chi={} pla={} dbl={}",
smi,
_iter,
step_fails[0],
step_fails[1],
step_fails[2],
step_fails[3],
step_fails[4],
step_fails[5]
);
ok = true;
break;
}
if !ok {
println!(
"{:30} FAIL iters={} eig={} ene={} tet={} chi={} pla={} dbl={}",
smi,
max_iter,
step_fails[0],
step_fails[1],
step_fails[2],
step_fails[3],
step_fails[4],
step_fails[5]
);
}
}
}