Reorient.cs

Go to the documentation of this file.

// ------------------------------------------------------------------------------
//  <autogenerated>
//      This code was generated by a tool.
//      Mono Runtime Version: 4.0.30319.1
// 
//      Changes to this file may cause incorrect behavior and will be lost if 
//      the code is regenerated.
//  </autogenerated>
// ------------------------------------------------------------------------------
using System;
using UnityEngine;
using System.Collections;
using Molecule.Model;
using System.Collections.Generic;
using UI;
using Molecule.Control;
using OptimalView;

namespace Reorient
{
    public class Reorient
    {
        public static void LoadSymmetry(float Xorigin, float Yorigin, float Zorigin, float Xdirection, float Ydirection, float Zdirection)
        {
            Debug.Log (MoleculeModel.atomsLocationlist[0][0]+" "+MoleculeModel.atomsLocationlist[0][1]+" "+MoleculeModel.atomsLocationlist[0][2]);
            Debug.Log("REORIENTATION");
            //Vector3 origin = new Vector3 (Xorigin, Yorigin, Zorigin);
            Vector3 direction = new Vector3 (Xdirection, Ydirection, Zdirection);
            direction.Normalize ();
            //float[] position= MoleculeModel.atomsLocationlist[0] as float[];
            
            // Re-orientation of pdb coordinates to be oriented according to the symmetry axis
            //Vector3 orientation = direction;
            //axis = self.symmetry_axes[0].direction
            float angle = Vector3.Angle(direction, -Vector3.up);
            Vector3 rot_axis = Vector3.Cross (direction, -Vector3.up);
            Debug.Log ("Axis: "+rot_axis);
            Debug.Log ("Angle: "+angle);
            Quaternion rotate = Quaternion.AngleAxis (angle, rot_axis);
//              Vector3 test = new Vector3 (2.0f, 2.0f, 2.0f);
//              Vector3 result = rotate * test;
//              Debug.Log ("Result: "+result);
            for (int i=0; i<MoleculeModel.atomsLocationlist.Count; i++) {
                float[] position= MoleculeModel.atomsLocationlist[i] as float[];
                Vector3 vec_pos = new Vector3(position[0], position[1], position[2]);
                Vector3 new_vec = rotate * vec_pos;
                position[0] = new_vec.x;
                position[1] = new_vec.y;
                position[2] = new_vec.z;
                MoleculeModel.atomsLocationlist[i] = position;
            }
            Debug.Log (MoleculeModel.MinValue);
            ControlMolecule.BuildMoleculeComponents ();
            Debug.Log (MoleculeModel.MinValue);
            
            // Switch on the guided navigation mode
            UIData.guided = true;
            
            // Redraw spheres with new atoms positions

            Molecule.View.DisplayMolecule.ChangeRepresentation(UIData.AtomType.sphere,UIData.BondType.nobond);

            BallUpdate.resetColors = true;


//              BallUpdate.resetRadii = true;
            MoleculeModel.newtooltip = GUI.tooltip;
            
            Debug.Log("resname length: "+MoleculeModel.atomsResnamelist.Count);
            Debug.Log("atomtype length: "+MoleculeModel.atomsTypelist.Count);
            Debug.Log("resname length: "+MoleculeModel.atomsChainList.Count);
            Debug.Log("resname length: "+MoleculeModel.atoms.Count);
            
            float x_tot = 0.0f;
            float y_tot = 0.0f;
            float z_tot = 0.0f;
            int count = 0;
            
            for (int i=0; i<MoleculeModel.atomsLocationlist.Count; i++) {
                if(MoleculeModel.atomsChainList[i] == "B" && MoleculeModel.residueIds[i] == 194){
                    float[] position= MoleculeModel.atomsLocationlist[i] as float[];
                    x_tot += position[0];
                    y_tot += position[1];
                    z_tot += position[2];
                    count++;
                }
            }
            float[] target = new float[3];
            target[0] = x_tot/count;
            target[1] = y_tot/count;
            target[2] = z_tot/count;
        
            Debug.Log ("Target coordinates: "+x_tot/count+" "+y_tot/count+" "+z_tot/count);
//              float[] target= MoleculeModel.atomsLocationlist[0] as float[];
            //OptimalView.OptimalView.GetOptimalPosition(target, (float) 15.0);

            //Refilling CA list for CA trace and BF representation

            List<float[]> calist = new List<float[]>();

            for (int i = 0; i<MoleculeModel.atomsNamelist.Count; i++){
                if(MoleculeModel.atomsNamelist[i] == "CA"){
                    float[] vect = new float[3];
                    vect[0] = MoleculeModel.atomsLocationlist[i][0];
                    vect[1] = MoleculeModel.atomsLocationlist[i][1];
                    vect[2] = MoleculeModel.atomsLocationlist[i][2];
                    calist.Add (vect);
                }
            }

            MoleculeModel.CatomsLocationlist = calist;
            MoleculeModel.backupCatomsLocationlist = calist;

            // Refilling residuedictionaries for Ribbons

            List<Dictionary<string, Vector3>>   residueDictList     =   new List<Dictionary<string, Vector3>>();
            Dictionary<string, Vector3>         residueDict         =   new Dictionary<string, Vector3>();
            List<int>                           residueIds          =   MoleculeModel.residueIds;
            Vector3 testVector = Vector3.zero;

            int currResId = int.MinValue+1;
            int prevResId = int.MinValue+1;

            for (int i = 0; i<MoleculeModel.atomsNamelist.Count; i++) {

                currResId = residueIds[i];
                Vector3 currAtom = new Vector3(MoleculeModel.atomsLocationlist[i][0], MoleculeModel.atomsLocationlist[i][1], MoleculeModel.atomsLocationlist[i][2]);

                if(currResId != prevResId) {
                    if(residueDict != null && residueDict.Count > 0){
                        residueDictList.Add(residueDict);
                    }
                    residueDict = new Dictionary<string, Vector3>();
                }
                prevResId = currResId;
                if(!residueDict.TryGetValue(MoleculeModel.atomsNamelist[i], out testVector)){
                    residueDict.Add(MoleculeModel.atomsNamelist[i], currAtom);}
                
            }

            MoleculeModel.residueDictionaries = residueDictList;

            UnityMolMain.getGuidedNavigationManager().CreateAxeAndOrigin();
            
        } // End of LoadSymmetry

    }   
        
}