Пример #1
0
//ScaleBond takes a C-H bond and moves the H (in place) so the distance between them is the one given (bond).
//CAUTION: I have only tested it for the case where the original distance>bond, although I expect it to also work in the other case.
func ScaleBond(C, H *v3.Matrix, bond float64) {
	Odist := v3.Zeros(1)
	Odist.Sub(H, C)
	distance := Odist.Norm(0)
	Odist.Scale((distance-bond)/distance, Odist)
	H.Sub(H, Odist)
}
Пример #2
0
//MakeWater Creates a water molecule at distance Angstroms from a2, in a direction that is angle radians from the axis defined by a1 and a2.
//Notice that the exact position of the water is not well defined when angle is not zero. One can always use the RotateAbout
//function to move the molecule to the desired location. If oxygen is true, the oxygen will be pointing to a2. Otherwise,
//one of the hydrogens will.
func MakeWater(a1, a2 *v3.Matrix, distance, angle float64, oxygen bool) *v3.Matrix {
	water := v3.Zeros(3)
	const WaterOHDist = 0.96
	const WaterAngle = 52.25
	const deg2rad = 0.0174533
	w := water.VecView(0) //we first set the O coordinates
	w.Copy(a2)
	w.Sub(w, a1)
	w.Unit(w)
	dist := v3.Zeros(1)
	dist.Sub(a1, a2)
	a1a2dist := dist.Norm(0)
	fmt.Println("ala2dist", a1a2dist, distance) ////////////////7777
	w.Scale(distance+a1a2dist, w)
	w.Add(w, a1)
	for i := 0; i <= 1; i++ {
		o := water.VecView(0)
		w = water.VecView(i + 1)
		w.Copy(o)
		fmt.Println("w1", w) ////////
		w.Sub(w, a2)
		fmt.Println("w12", w) ///////////////
		w.Unit(w)
		fmt.Println("w4", w)
		w.Scale(WaterOHDist+distance, w)
		fmt.Println("w3", w, WaterOHDist, distance)
		o.Sub(o, a2)
		t, _ := v3.NewMatrix([]float64{0, 0, 1})
		upp := v3.Zeros(1)
		upp.Cross(w, t)
		fmt.Println("upp", upp, w, t)
		upp.Add(upp, o)
		upp.Add(upp, a2)
		//water.SetMatrix(3,0,upp)
		w.Add(w, a2)
		o.Add(o, a2)
		sign := 1.0
		if i == 1 {
			sign = -1.0
		}
		temp, _ := RotateAbout(w, o, upp, deg2rad*WaterAngle*sign)
		w.SetMatrix(0, 0, temp)
	}
	var v1, v2 *v3.Matrix
	if angle != 0 {
		v1 = v3.Zeros(1)
		v2 = v3.Zeros(1)
		v1.Sub(a2, a1)
		v2.Copy(v1)
		v2.Set(0, 2, v2.At(0, 2)+1) //a "random" modification. The idea is that its not colinear with v1
		v3 := cross(v1, v2)
		v3.Add(v3, a2)
		water, _ = RotateAbout(water, a2, v3, angle)
	}
	if oxygen {
		return water
	}
	//we move things so an hydrogen points to a2 and modify the distance acordingly.
	e1 := water.VecView(0)
	e2 := water.VecView(1)
	e3 := water.VecView(2)
	if v1 == nil {
		v1 = v3.Zeros(1)
	}
	if v2 == nil {
		v2 = v3.Zeros(1)
	}
	v1.Sub(e2, e1)
	v2.Sub(e3, e1)
	axis := cross(v1, v2)
	axis.Add(axis, e1)
	water, _ = RotateAbout(water, e1, axis, deg2rad*(180-WaterAngle))
	v1.Sub(e1, a2)
	v1.Unit(v1)
	v1.Scale(WaterOHDist, v1)
	water.AddVec(water, v1)
	return water
}