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Updated the algo for SP3D2 #12

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Updated the algo for SP3D2 #12

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6 changes: 5 additions & 1 deletion molecule-visulaiser/src/App.js
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,8 @@ const MoleculeVisualizer = () => {
H: 0,
O: 0,
N: 0,
S: 0,
F: 0,
});

const [compoundFormula, setCompoundFormula] = useState("");
Expand Down Expand Up @@ -297,6 +299,8 @@ const MoleculeVisualizer = () => {
{ value: "H", label: "H" },
{ value: "O", label: "O" },
{ value: "N", label: "N" },
{ value: "S", label: "S" },
{ value: "F", label: "F" },
];

const getBondMenuItems = () => {
Expand All @@ -315,7 +319,7 @@ const MoleculeVisualizer = () => {
return bondMenuItems;
};

const sampleMolecules = ["CH4", "C2H6", "C6H6", "H2O"];
const sampleMolecules = ["CH4", "C2H6", "C6H6", "H2O", "SF6"];

return (
<div className="flex flex-col h-screen bg-[#141414] font-inter">
Expand Down
24 changes: 24 additions & 0 deletions molecule-visulaiser/src/components/EditMolecule.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -144,6 +144,29 @@ export default function EditMolecule({
getCoordinates(water);
setMolecule(water);
break;
case "SF6":
const sulphurHexaFluoride = new Molecule();

addAtoms(sulphurHexaFluoride, createAtomNode("S0", "sp3d2", "S"));
addAtoms(sulphurHexaFluoride, createAtomNode("F0", "sp", "F"));
addAtoms(sulphurHexaFluoride, createAtomNode("F1", "sp", "F"));
addAtoms(sulphurHexaFluoride, createAtomNode("F2", "sp", "F"));
addAtoms(sulphurHexaFluoride, createAtomNode("F3", "sp", "F"));
addAtoms(sulphurHexaFluoride, createAtomNode("F4", "sp", "F"));
addAtoms(sulphurHexaFluoride, createAtomNode("F5", "sp", "F"));

addBonds(sulphurHexaFluoride, "S0", "F0", true, false, false); //consider only the sngle bond
addBonds(sulphurHexaFluoride, "S0", "F1", true, false, false);
addBonds(sulphurHexaFluoride, "S0", "F2", true, false, false);
addBonds(sulphurHexaFluoride, "S0", "F3", true, false, false);
addBonds(sulphurHexaFluoride, "S0", "F4", true, false, false);
addBonds(sulphurHexaFluoride, "S0", "F5", true, false, false);

setAtomCounters({ C: 0, H: 0, O: 0, N: 0, S: 1, F: 6 });
getCoordinates(sulphurHexaFluoride);
setMolecule(sulphurHexaFluoride);
break;

default:
break;
}
Expand Down Expand Up @@ -237,6 +260,7 @@ export default function EditMolecule({
<FormControlLabel value="sp" control={<Radio />} label="sp" />
<FormControlLabel value="sp2" control={<Radio />} label="sp2" />
<FormControlLabel value="sp3" control={<Radio />} label="sp3" />
<FormControlLabel value="sp3d2" control={<Radio />} label="sp3d2" />
</RadioGroup>
<Button
type="submit"
Expand Down
132 changes: 111 additions & 21 deletions molecule-visulaiser/src/components/GraphADT.js
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Expand Up @@ -5,38 +5,111 @@ export class atomNode {
this.atomSymbol = atomSymbol;
this.coordinates = [0, 0, 0];
this.connections = [];
this.bondAngles = new Map(); // Store bond angles for each connected atom
}
}

export class Molecule {
constructor() {
this.adjacencyList = {};
this.atomList = [];
this.bondAngles = new Map(); // Store all bond angles in the molecule
}

getNeighbours(atom) {
if (atom && this.adjacencyList[atom.atomName]) {
return this.adjacencyList[atom.atomName].map(({ atomName }) =>
this.atomList.find((a) => a.atomName === atomName)
);
calculateBondAngle(atom1, atom2, atom3) {
if (!atom1.coordinates || !atom2.coordinates || !atom3.coordinates) {
return null;
}

// Calculate vectors
const vector1 = [
atom1.coordinates[0] - atom2.coordinates[0],
atom1.coordinates[1] - atom2.coordinates[1],
atom1.coordinates[2] - atom2.coordinates[2]
];

const vector2 = [
atom3.coordinates[0] - atom2.coordinates[0],
atom3.coordinates[1] - atom2.coordinates[1],
atom3.coordinates[2] - atom2.coordinates[2]
];

const mag1 = Math.sqrt(vector1.reduce((sum, val) => sum + val * val, 0));
const mag2 = Math.sqrt(vector2.reduce((sum, val) => sum + val * val, 0));

// dot product
const dotProduct = vector1.reduce((sum, val, i) => sum + val * vector2[i], 0);

// Calculate angle in radians and convert
const angle = Math.acos(dotProduct / (mag1 * mag2)) * (180 / Math.PI);

return angle;
}

//Store bond angle
storeBondAngle(centralAtom, atom1, atom2) {
const angle = this.calculateBondAngle(atom1, centralAtom, atom2);
if (angle !== null) {
//created keys
const angleKey = `${atom1.atomName}-${centralAtom.atomName}-${atom2.atomName}`;
this.bondAngles.set(angleKey, angle);

// Store in the central atom's
centralAtom.bondAngles.set(angleKey, angle);
}
}

// Get bond angle between specific atoms
getBondAngle(centralAtom, atom1, atom2) {
const angleKey = `${atom1.atomName}-${centralAtom.atomName}-${atom2.atomName}`;
return this.bondAngles.get(angleKey);
}

// Get all bond angles for a specific atom
getAtomBondAngles(centralAtom) {
const angles = {};
if (!centralAtom.bondAngles) return angles;

for (const [key, angle] of centralAtom.bondAngles) {
angles[key] = angle;
}
return angles;
}
return [];
}

//stroitng
storeExpectedAngles(atom) {
const hybridAngles = {
'sp': 180,
'sp2': 120,
'sp3': 109.5,
'sp3d2': 90 // Octahedral geometry
};

if (hybridAngles[atom.hybridisation]) {
atom.expectedAngle = hybridAngles[atom.hybridisation];
}
}

// Existing methods...
getNeighbours(atom) {
if (atom && this.adjacencyList[atom.atomName]) {
return this.adjacencyList[atom.atomName].map(({ atomName }) =>
this.atomList.find((a) => a.atomName === atomName)
);
}
return [];
}

addAtoms(atom) {
if (!this.adjacencyList[atom.atomName]) {
this.adjacencyList[atom.atomName] = [];
this.atomList.push(atom);
} else {
this.storeExpectedAngles(atom); // Store expected angles when adding atom
}
}

addBond(atom1, atom2, isSingleBond = false, isDoubleBond = false, isTripleBond = false) {
if (
this.adjacencyList[atom1.atomName] &&
this.adjacencyList[atom2.atomName]
) {
if (this.adjacencyList[atom1.atomName] && this.adjacencyList[atom2.atomName]) {
let flag1 = 0;
for (let i = 0; i < this.adjacencyList[atom1.atomName].length; i++) {
if (this.adjacencyList[atom1.atomName][i].atomName === atom2.atomName) {
Expand All @@ -47,12 +120,12 @@ export class Molecule {
if (!flag1) {
this.adjacencyList[atom1.atomName].push({
atomName: atom2.atomName,
isSingleBond: isSingleBond && !isDoubleBond && !isTripleBond,
isDoubleBond: !isSingleBond && isDoubleBond && !isTripleBond,
isTripleBond: !isSingleBond && !isDoubleBond && isTripleBond
isSingleBond,
isDoubleBond,
isTripleBond
});
}

let flag2 = 0;
for (let i = 0; i < this.adjacencyList[atom2.atomName].length; i++) {
if (this.adjacencyList[atom2.atomName][i].atomName === atom1.atomName) {
Expand All @@ -63,12 +136,29 @@ export class Molecule {
if (!flag2) {
this.adjacencyList[atom2.atomName].push({
atomName: atom1.atomName,
isSingleBond: isSingleBond && !isDoubleBond && !isTripleBond,
isDoubleBond: !isSingleBond && isDoubleBond && !isTripleBond,
isTripleBond: !isSingleBond && !isDoubleBond && isTripleBond
isSingleBond,
isDoubleBond,
isTripleBond
});
}

// Calculate and store bond angles after adding new bond
const neighbours1 = this.getNeighbours(atom1);
const neighbours2 = this.getNeighbours(atom2);

// Store angles for atom1's bonds
for (let i = 0; i < neighbours1.length - 1; i++) {
for (let j = i + 1; j < neighbours1.length; j++) {
this.storeBondAngle(atom1, neighbours1[i], neighbours1[j]);
}
}

// Store angles for atom2's bonds
for (let i = 0; i < neighbours2.length - 1; i++) {
for (let j = i + 1; j < neighbours2.length; j++) {
this.storeBondAngle(atom2, neighbours2[i], neighbours2[j]);
}
}
}
}

}
}
106 changes: 103 additions & 3 deletions molecule-visulaiser/src/components/Molecule.js
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Expand Up @@ -8,7 +8,14 @@ export function addAtoms(molecule, atom) {
molecule.addAtoms(atom);
}

export function addBonds(molecule, atom1Name, atom2Name, isSingleBond, isDoubleBond, isTripleBond) {
export function addBonds(
molecule,
atom1Name,
atom2Name,
isSingleBond,
isDoubleBond,
isTripleBond
) {
const atom1 = molecule.atomList.find((atom) => atom.atomName === atom1Name);
const atom2 = molecule.atomList.find((atom) => atom.atomName === atom2Name);

Expand Down Expand Up @@ -39,9 +46,83 @@ export function findCentralAtoms(molecule) {
return centralAtoms;
}

// Calculate Coordiantes of the atoms in 3D Plane.
export function getCoordinates(molecule) {


function calcSp3d2bondDirection(parentAtom, currentAtom) {
if (!parentAtom || !parentAtom.coordinates) {
console.error("Invalid parent atom");
return [1, 0, 0];
}

const existingBonds = (parentAtom.bonds || [])
.filter(bond => bond.atomEnd && bond.atomEnd !== currentAtom)
.map(bond => {
if (!bond.atomEnd.coordinates) return null;
// Calculate direction using existing coordinates
return normalizeVector([
bond.atomEnd.coordinates[0] - parentAtom.coordinates[0],
bond.atomEnd.coordinates[1] - parentAtom.coordinates[1],
bond.atomEnd.coordinates[2] - parentAtom.coordinates[2]
]);
})
.filter(dir => dir !== null);

if (existingBonds.length === 0) {
return [1, 0, 0];
}

if (existingBonds.length === 1) {
return [-1, 0, 0];
}

if (existingBonds.length === 2) {
return [0, 1, 0];
}
if (existingBonds.length === 3) {
return [0, -1, 0];
}

if (existingBonds.length === 4) {
return [0, 0, 1];
}
if (existingBonds.length === 5) {
return [0, 0, -1];
}

return [1, 0, 0];
}

// Helper function for vector normalization
function normalizeVector(vector) {
const magnitude = Math.sqrt(vector[0] * vector[0] + vector[1] * vector[1] + vector[2] * vector[2]);
return magnitude === 0 ? vector : vector.map(component => component / magnitude);
}

function validatePlanarArrangement(bonds) {
if (bonds.length < 4) return false;

const planarBonds = bonds.slice(0, 4);
return planarBonds.every(bond => Math.abs(bond[2]) < 0.1);
}

function getPlaneNormal(bonds) {
if (bonds.length < 2) return [0, 0, 1];

const v1 = bonds[0];
const v2 = bonds[1];

return normalizeVector([
v1[1] * v2[2] - v1[2] * v2[1],
v1[2] * v2[0] - v1[0] * v2[2],
v1[0] * v2[1] - v1[1] * v2[0]
]);
}

export function getCoordinates(molecule) {
if (!molecule || !molecule.coordinates || molecule.coordinates.length < 3) {
console.error("Invalid molecule or coordinates:", molecule);
return null; // or a default value, e.g., [0, 0, 0]
}
// Constant Angles defined for respective hybridisations.
const angles = {
sp: { angleX: Math.PI, angleY: 0, angleZ: 0 },
Expand All @@ -51,6 +132,12 @@ export function getCoordinates(molecule) {
angleY: 0.955 * Math.PI,
angleZ: 0.615 * Math.PI,
},
//octahedral geometry.
sp3d2: {
angleX: Math.PI / 2,
angleY: Math.PI / 2,
angleZ: Math.PI / 2,
},
};

// Get Central Atoms of the Molecule.
Expand Down Expand Up @@ -176,6 +263,19 @@ export function getCoordinates(molecule) {
firstCoordinate,
secondCoordinate
);
if (parentAtom.hybridisation === "sp3d2") {
newDirection = calcSp3d2bondDirection(parentAtom, currentAtom);
directionVectorStack.push(newDirection);

// i implemented the new coordinatess inside the sp3d2 section
const newCoordinates = [
parentCoordinates[0] + bondlength * newDirection[0],
parentCoordinates[1] + bondlength * newDirection[1],
parentCoordinates[2] + bondlength * newDirection[2],
];
currentAtom.coordinates = newCoordinates;
continue;
}
directionVectorStack.push(newDirection);

console.log("New Direction:", newDirection);
Expand Down