BondCubeUpdate.cs

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using UnityEngine;
using System.Collections;
using UI;
using Molecule.Model;

public class BondCubeUpdate : MonoBehaviour {
    
    public static float scale = 1.0f;
    public static float radiusFactor = 1.0f;
    public int atomnumber1 = -1;
    public int atomnumber2 = -1;
    
    public static float oldscale = 1.0f;
    public static float width = RepresentationOldGUI.bondWidth ;
    public static float oldWidth = RepresentationOldGUI.bondWidth ;
//  private float oldrayon1 = 2.0f;
//  private float oldrayon2 = 2.0f;



    //Only check for d3d once
//  private bool d3d= false;
    void  Start () {
//      d3d = SystemInfo.graphicsDeviceVersion.IndexOf("Direct3D") > -1;
//      Debug.Log("BondCubeUpdate: Start()");
        width = RepresentationOldGUI.bondWidth ;

        if(atomnumber1 == -1 || atomnumber2 == -1){
            Debug.LogError("Problem when initializing the bond as a cube");
            return;
        }




        float[] fposAtom1 = MoleculeModel.atomsLocationlist[atomnumber1];
        float[] fposAtom2 = MoleculeModel.atomsLocationlist[atomnumber2];

        Vector3 posAtom1 = new Vector3(fposAtom1[0],fposAtom1[1],fposAtom1[2]);
        Vector3 posAtom2 = new Vector3(fposAtom2[0],fposAtom2[1],fposAtom2[2]);

        Color colorAtom1 = MoleculeModel.atomsColorList[atomnumber1];
        Color colorAtom2 = MoleculeModel.atomsColorList[atomnumber2];


        Vector3 v_dist = posAtom2 - posAtom1 ;
        float length = v_dist.magnitude ;
        Vector3 lscale = new Vector3(transform.localScale.x, transform.localScale.y, length);
        this.transform.localScale = lscale ;


        transform.position = (posAtom1 + posAtom2)/2.0f;
        transform.LookAt(posAtom2);
        
        Renderer rd = GetComponent<Renderer>();
        rd.material.SetVector("_Pos1", posAtom1);
        rd.material.SetVector("_Pos2", posAtom2);
        


        //Debug.Log(color1.ToString());
        rd.material.SetColor("_Color1", colorAtom1);
        
        //Debug.Log(color2.ToString());
        rd.material.SetColor("_Color2", colorAtom2);
        
        Mesh mesh = GetComponent<MeshFilter>().mesh;
        Vector3[] vertices = mesh.vertices;
        Color32[] colors = new Color32[vertices.Length];
        float dist1, dist2;
        Matrix4x4 localToWorld = transform.localToWorldMatrix;
        
        Vector3 pos;
        for(int i=0; i<vertices.Length; i++) {
            pos = localToWorld.MultiplyPoint3x4(vertices[i]);
            dist1 = Vector3.Distance(posAtom1, pos);
            dist2 = Vector3.Distance(posAtom2, pos);
            if( dist1 < dist2 )
                colors[i] = colorAtom1;
            else
                colors[i] = colorAtom2;
        }
        
        mesh.colors32 = colors;
        GetComponent<MeshFilter>().mesh = mesh;
        rd.material.shader = Shader.Find("Custom/Ribbons");
        
    }

}