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HenriqueCSJ merged 2 commits into from
Feb 5, 2026
Merged

Claude/debug ni complex shape ewrvu #96

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37d7340
fix: improve OC-6 CShM accuracy with post-Kabsch refinement
claude Feb 5, 2026
0dc2e47
test: add debug tests for OC-6 investigation
claude Feb 5, 2026
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81 changes: 81 additions & 0 deletions src/services/shapeAnalysis/compareStructures.test.js
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/**
* Compare NiN4O2 (works) vs user's NiN6 (doesn't work)
*/

import calculateShapeMeasure from './shapeCalculator';
import { REFERENCE_GEOMETRIES } from '../../constants/referenceGeometries';

describe('Compare Working vs Non-Working OC-6 Structures', () => {

test('Compare the two structures', () => {
console.log("\n=== Comparing Two OC-6 Structures ===\n");

const ocRef = REFERENCE_GEOMETRIES[6]['OC-6 (Octahedral)'];

// NiN4O2 from benchmark (WORKS - 0.00% error)
// Ni at (-0.3317, 12.0165, 1.2469)
const niN4O2Metal = [-0.3317, 12.0165, 1.2469];
const niN4O2Ligands = [
[-0.4577 - niN4O2Metal[0], 9.7734 - niN4O2Metal[1], 1.2212 - niN4O2Metal[2]], // N1
[0.4360 - niN4O2Metal[0], 12.0165 - niN4O2Metal[1], 3.1526 - niN4O2Metal[2]], // N2
[1.5045 - niN4O2Metal[0], 12.0165 - niN4O2Metal[1], 0.3292 - niN4O2Metal[2]], // N3
[-2.2777 - niN4O2Metal[0], 12.0165 - niN4O2Metal[1], 2.2016 - niN4O2Metal[2]], // O1
[-1.2331 - niN4O2Metal[0], 12.0165 - niN4O2Metal[1], -0.6084 - niN4O2Metal[2]], // O2
[-0.4577 - niN4O2Metal[0], 14.2596 - niN4O2Metal[1], 1.2212 - niN4O2Metal[2]] // N4
];

// User's NiN6 (DOESN'T WORK - 15.81% error)
const userLigands = [
[0, 0.062076, -2.255810],
[1.417646, 1.531172, 0],
[1.459398, -1.474949, 0],
[0, 0.062076, 2.255810],
[-1.417646, 1.531172, 0],
[-1.459398, -1.474949, 0]
];

// Compute CShM
const niN4O2Result = calculateShapeMeasure(niN4O2Ligands, ocRef, 'intensive');
const userResult = calculateShapeMeasure(userLigands, ocRef, 'intensive');

console.log("NiN4O2 benchmark:");
console.log(" CShM:", niN4O2Result.measure.toFixed(5), "(SHAPE: 0.21577)");

console.log("\nUser's NiN6:");
console.log(" CShM:", userResult.measure.toFixed(5), "(SHAPE: 0.19694)");

// Analyze the structures
function analyzeStructure(coords, name) {
console.log(`\n--- ${name} Analysis ---`);

// Centroid of ligands
const centroid = [0, 0, 0];
for (const c of coords) {
centroid[0] += c[0] / 6;
centroid[1] += c[1] / 6;
centroid[2] += c[2] / 6;
}
console.log("Ligand centroid:", centroid.map(x => x.toFixed(6)));

// Bond lengths
const distances = coords.map(c => Math.sqrt(c[0]**2 + c[1]**2 + c[2]**2));
console.log("Bond lengths:", distances.map(d => d.toFixed(4)));
console.log(" Mean:", (distances.reduce((a,b) => a+b, 0) / 6).toFixed(4));
console.log(" Std:", Math.sqrt(distances.map(d => (d - distances.reduce((a,b) => a+b, 0)/6)**2).reduce((a,b) => a+b, 0) / 6).toFixed(4));

// Symmetry check: distances from centroid
const centeredCoords = coords.map(c => [c[0] - centroid[0], c[1] - centroid[1], c[2] - centroid[2]]);
const centroidDistances = centeredCoords.map(c => Math.sqrt(c[0]**2 + c[1]**2 + c[2]**2));
console.log("Distances from ligand centroid:", centroidDistances.map(d => d.toFixed(4)));

// Check if centroid is far from metal (at origin)
const metalToCentroid = Math.sqrt(centroid[0]**2 + centroid[1]**2 + centroid[2]**2);
console.log("Metal-to-centroid distance:", metalToCentroid.toFixed(6));
}

analyzeStructure(niN4O2Ligands, "NiN4O2");
analyzeStructure(userLigands, "User NiN6");

expect(true).toBe(true);
});
});
193 changes: 193 additions & 0 deletions src/services/shapeAnalysis/debugOC6.test.js
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/**
* Debug test for OC-6 CShM discrepancy
*/

import calculateShapeMeasure from './shapeCalculator';
import { REFERENCE_GEOMETRIES } from '../../constants/referenceGeometries';

describe('OC-6 Debug Analysis', () => {
// User's Ni complex coordinates (centered on metal)
const metalCoords = [6.016150, 1.141803, 11.745750];
const ligandCoordsRaw = [
[6.016150, 1.203879, 9.489940],
[7.433796, 2.672975, 11.745750],
[7.475548, -0.333146, 11.745750],
[6.016150, 1.203879, 14.001560],
[4.598504, 2.672975, 11.745750],
[4.556752, -0.333146, 11.745750]
];

// Center on metal
const ligandCoords = ligandCoordsRaw.map(l => [
l[0] - metalCoords[0],
l[1] - metalCoords[1],
l[2] - metalCoords[2]
]);

const SHAPE_REF = {
'HP-6 (Hexagon)': 32.43652,
'PPY-6 (Pentagonal Pyramid)': 29.59348,
'OC-6 (Octahedral)': 0.19694,
'TPR-6 (Trigonal Prism)': 16.60998,
'JPPY-6 (Johnson Pentagonal Pyramid, J2)': 32.84784
};

test('Full CN=6 comparison for user Ni complex', () => {
console.log("\n=== User's Ni Complex: Q-Shape vs SHAPE ===\n");
console.log("Geometry Q-Shape SHAPE Diff RelErr");
console.log("─".repeat(85));

const cn6Geometries = REFERENCE_GEOMETRIES[6];
const results = [];

for (const [name, refCoords] of Object.entries(cn6Geometries)) {
const { measure } = calculateShapeMeasure(ligandCoords, refCoords, 'intensive');
const shapeValue = SHAPE_REF[name];
const diff = measure - shapeValue;
const relErr = Math.abs(diff) / shapeValue * 100;
results.push({ name, measure, shapeValue, diff, relErr });
}

// Sort by Q-Shape measure
results.sort((a, b) => a.measure - b.measure);

for (const r of results) {
console.log(
`${r.name.padEnd(44)} ${r.measure.toFixed(5).padStart(10)} ${r.shapeValue.toFixed(5).padStart(10)} ${r.diff.toFixed(5).padStart(10)} ${r.relErr.toFixed(2).padStart(8)}%`
);
}
console.log("─".repeat(85));

expect(true).toBe(true);
});

test('OC-6 detailed formula analysis', () => {
console.log("\n=== OC-6 Formula Analysis ===\n");

const ocRef = REFERENCE_GEOMETRIES[6]['OC-6 (Octahedral)'];
const { measure, alignedCoords } = calculateShapeMeasure(
ligandCoords, ocRef, 'intensive'
);

console.log("Q-Shape OC-6 CShM:", measure.toFixed(5));
console.log("SHAPE OC-6 CShM: ", SHAPE_REF['OC-6 (Octahedral)'].toFixed(5));
console.log("Difference: ", (measure - SHAPE_REF['OC-6 (Octahedral)']).toFixed(5));
console.log("Relative error: ", ((measure - SHAPE_REF['OC-6 (Octahedral)']) / SHAPE_REF['OC-6 (Octahedral)'] * 100).toFixed(2), "%");

// Centroid-based normalization function
function scaleNormalize(coords) {
const n = coords.length;
const centroid = [0, 0, 0];
for (const c of coords) {
centroid[0] += c[0] / n;
centroid[1] += c[1] / n;
centroid[2] += c[2] / n;
}
const centered = coords.map(c => [
c[0] - centroid[0],
c[1] - centroid[1],
c[2] - centroid[2]
]);
let sumSq = 0;
for (const c of centered) {
sumSq += c[0]*c[0] + c[1]*c[1] + c[2]*c[2];
}
const rms = Math.sqrt(sumSq / n);
const normalized = centered.map(c => [c[0]/rms, c[1]/rms, c[2]/rms]);
return { normalized, centroid, rms };
}

const { normalized: Q_norm } = scaleNormalize(ocRef);
const N = 7;

// Compute using aligned coords
let overlap = 0;
let sumSqDiff = 0;

for (let i = 0; i < N; i++) {
const p = alignedCoords[i];
const q = Q_norm[i];

overlap += p[0]*q[0] + p[1]*q[1] + p[2]*q[2];

const dx = p[0] - q[0];
const dy = p[1] - q[1];
const dz = p[2] - q[2];
sumSqDiff += dx*dx + dy*dy + dz*dz;
}

const overlapNorm = overlap / N;

console.log("\nWith optimal alignment:");
console.log(" Total overlap:", overlap.toFixed(6));
console.log(" Overlap/N:", overlapNorm.toFixed(6));
console.log(" Sum |p-q|²:", sumSqDiff.toFixed(6));

// Formula calculations
const cshm_rmsd = 100 * sumSqDiff / N;
const cshm_overlap = 100 * (1 - overlapNorm * overlapNorm);

console.log("\nFormula comparison:");
console.log(" RMSD-based (100*Σ|p-q|²/N): CShM =", cshm_rmsd.toFixed(5));
console.log(" Overlap-based (100*(1-(o/N)²)): CShM =", cshm_overlap.toFixed(5));
console.log(" SHAPE reference value: CShM =", SHAPE_REF['OC-6 (Octahedral)'].toFixed(5));

console.log("\n=== Key Finding ===");
console.log("RMSD formula matches SHAPE better:", Math.abs(cshm_rmsd - SHAPE_REF['OC-6 (Octahedral)']) < Math.abs(cshm_overlap - SHAPE_REF['OC-6 (Octahedral)']));
console.log("RMSD error:", Math.abs(cshm_rmsd - SHAPE_REF['OC-6 (Octahedral)']).toFixed(5));
console.log("Overlap error:", Math.abs(cshm_overlap - SHAPE_REF['OC-6 (Octahedral)']).toFixed(5));

expect(true).toBe(true);
});

test('Verify normalization', () => {
console.log("\n=== Normalization Verification ===\n");

function scaleNormalize(coords) {
const n = coords.length;
const centroid = [0, 0, 0];
for (const c of coords) {
centroid[0] += c[0] / n;
centroid[1] += c[1] / n;
centroid[2] += c[2] / n;
}
const centered = coords.map(c => [
c[0] - centroid[0],
c[1] - centroid[1],
c[2] - centroid[2]
]);
let sumSq = 0;
for (const c of centered) {
sumSq += c[0]*c[0] + c[1]*c[1] + c[2]*c[2];
}
const rms = Math.sqrt(sumSq / n);
const normalized = centered.map(c => [c[0]/rms, c[1]/rms, c[2]/rms]);
return { normalized, centroid, rms };
}

// Add central atom
const actualWithCentral = [...ligandCoords, [0, 0, 0]];
const ocRef = REFERENCE_GEOMETRIES[6]['OC-6 (Octahedral)'];

const actualNorm = scaleNormalize(actualWithCentral);
const refNorm = scaleNormalize(ocRef);

console.log("Actual structure:");
console.log(" Centroid:", actualNorm.centroid.map(x => x.toFixed(6)));
console.log(" RMS:", actualNorm.rms.toFixed(6));
console.log(" Central atom after norm:", actualNorm.normalized[6].map(x => x.toFixed(6)));

console.log("\nReference OC-6:");
console.log(" Centroid:", refNorm.centroid.map(x => x.toFixed(6)));
console.log(" RMS:", refNorm.rms.toFixed(6));
console.log(" Central atom after norm:", refNorm.normalized[6].map(x => x.toFixed(6)));

// The key difference: actual has y-centroid != 0
console.log("\n=== Key observation ===");
console.log("The actual structure has centroid y =", actualNorm.centroid[1].toFixed(6));
console.log("This shifts the central atom to y =", actualNorm.normalized[6][1].toFixed(6));
console.log("This is a real structural asymmetry that contributes to CShM.");

expect(true).toBe(true);
});
});
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