Position calculations

[RodenLuo]

https://dna.physics.ox.ac.uk/index.php/Documentation#Configuration_file

oxdna-viewer/ts/model/nucleotide.ts

Lines 14 to 124 in b892dd6

	calcPositionsFromConfLine(l: string[], colorUpdate?: boolean) {
	//extract position
	let p = new THREE.Vector3(
	parseFloat(l[0]),
	parseFloat(l[1]),
	parseFloat(l[2])
	);
	// extract axis vector a1 (backbone vector) and a3 (stacking vector)
	let a1 = new THREE.Vector3(
	parseFloat(l[3]),
	parseFloat(l[4]),
	parseFloat(l[5])
	);
	let a3 = new THREE.Vector3(
	parseFloat(l[6]),
	parseFloat(l[7]),
	parseFloat(l[8])
	);
	this.calcPositions(p, a1, a3, colorUpdate)
	};
	calcPositions(p: THREE.Vector3, a1: THREE.Vector3, a3: THREE.Vector3, colorUpdate?: boolean) {
	let sys = this.getSystem(),
	sid = this.sid;
	if (this.dummySys !== null) {
	sys = this.dummySys;
	}
	// according to base.py a2 is the cross of a1 and a3
	let a2 = a1.clone().cross(a3);
	// compute backbone position
	let bb = this.calcBBPos(p, a1, a2, a3);
	// compute nucleoside cm
	let ns = new THREE.Vector3(
	p.x + 0.4 * a1.x,
	p.y + 0.4 * a1.y,
	p.z + 0.4 * a1.z
	)
	// compute nucleoside rotation
	const baseRotation = new THREE.Quaternion().setFromUnitVectors(new THREE.Vector3(0, 1, 0),a3);
	//compute connector position
	const con = bb.clone().add(ns).divideScalar(2);
	// compute connector rotation
	const rotationCon = new THREE.Quaternion().setFromUnitVectors(
	new THREE.Vector3(0, 1, 0),
	con.clone().sub(ns).normalize());
	// compute connector length
	let conLen = this.bbnsDist;
	if (a1.length() == 0 && a2.length() == 0) {
	conLen = 0;
	}
	// compute sugar-phosphate positions/rotations, or set them all to 0 if there is no sugar-phosphate.
	let sp: THREE.Vector3, spLen: number, spRotation;
	if (this.n3) {
	let bbLast = this.n3.getInstanceParameter3('bbOffsets');
	sp = bb.clone().add(bbLast).divideScalar(2);
	spLen = bb.distanceTo(bbLast);
	//introduce distance based cutoff of the backbone connectors
	if (spLen>=box.x*.9 ||spLen>=box.y*.9 || spLen>=box.z*.9 ) spLen = 0;
	spRotation = new THREE.Quaternion().setFromUnitVectors(
	new THREE.Vector3(0, 1, 0), sp.clone().sub(bb).normalize()
	);
	}
	else {
	sp = new THREE.Vector3();
	spLen = 0;
	spRotation = new THREE.Quaternion(0, 0, 0, 0);
	}
	this.handleCircularStrands(sys, sid, bb);
	if (colorUpdate) {
	// determine the mesh color, either from a supplied colormap json or by the strand ID.
	const bbColor = this.strandToColor(this.strand.id);
	sys.fillVec('bbColors', 3, sid, [bbColor.r, bbColor.g, bbColor.b]);
	const nsColor = this.elemToColor(this.type);
	sys.fillVec('nsColors', 3, sid, [nsColor.r, nsColor.g, nsColor.b]);
	let idColor = new THREE.Color();
	idColor.setHex(this.id+1); //has to be +1 or you can't grab nucleotide 0
	sys.fillVec('bbLabels', 3, sid, [idColor.r, idColor.g, idColor.b]);
	}
	//fill the instance matrices with data
	sys.fillVec('cmOffsets', 3, sid, p.toArray());
	sys.fillVec('bbOffsets', 3, sid, bb.toArray());
	sys.fillVec('nsOffsets', 3, sid, ns.toArray());
	sys.fillVec('nsRotation', 4, sid, [baseRotation.w, baseRotation.z, baseRotation.y, baseRotation.x]);
	sys.fillVec('conOffsets', 3, sid, con.toArray());
	sys.fillVec('conRotation', 4, sid, [rotationCon.w, rotationCon.z, rotationCon.y, rotationCon.x]);
	sys.fillVec('bbconOffsets', 3, sid, sp.toArray());
	sys.fillVec('bbconRotation', 4, sid, [spRotation.w, spRotation.z, spRotation.y, spRotation.x]);
	sys.fillVec('scales', 3, sid, [1, 1, 1]);
	sys.fillVec('nsScales', 3, sid, [0.7, 0.3, 0.7]);
	sys.fillVec('conScales', 3, sid, [1, conLen, 1]);
	if(spLen == 0) {
	sys.fillVec('bbconScales', 3, sid, [0, 0, 0]);
	} else {
	sys.fillVec('bbconScales', 3, sid, [1, spLen, 1]);
	}
	sys.fillVec('visibility', 3, sid, [1,1,1]);
	};

oxdna-viewer/ts/model/DNA.ts

Lines 10 to 16 in b892dd6

	calcBBPos(p: THREE.Vector3, a1: THREE.Vector3, a2: THREE.Vector3, a3: THREE.Vector3): THREE.Vector3 {
	return new THREE.Vector3(
	p.x - (0.34 * a1.x + 0.3408 * a2.x),
	p.y - (0.34 * a1.y + 0.3408 * a2.y),
	p.z - (0.34 * a1.z + 0.3408 * a2.z)
	);
	};