RequestPDB.cs

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namespace  ParseData.ParsePDB
{
    using UnityEngine;
    using System.Collections;
    using System.Collections.Generic;
    using System.IO;
    using System.Net;
    using System.Linq;
    using System;
    using Molecule.Model;
    using Molecule.Control;
    using System.Xml;
    using System.Text;  
    using System.Text.RegularExpressions;
    using UI;
    
    public class RequestPDB : MonoBehaviour{
//      private string url="http://www.pdb.org/pdb/downLoad/downLoadFile.do?fileFormat=pdb&compression=NO&structureId=3KX3";
//      private string data="";

        public float progress=0.0f;
        public static bool isDone=false;
        public bool Loading = true;
        //public GUISkin mySkin;
          
            // choice open file
//      bool wantpdb=true;
//      bool wantxgmml=false;
        bool wantobj=false;
        bool wantdx=false;
        bool wantjson =false;
            
        void Start() {
            //mySkin?Resources.Load("MyGUISkin") as GUISkin;
        }
        
        public RequestPDB() {}
        
        
    
        void Update() {
            Loading = !isDone;
        }

        //Move this method to the related class
        public IEnumerator LoadJsonWWW(string file_name, Vector3 Offset) {
            WWW www = new WWW(file_name);
            
            progress = 0;
            isDone = false;
            while(!www.isDone) {    
//              Debug.Log("*** PDB: "+www.progress);
                progress = www.progress;
                yield return new WaitForEndOfFrame();
            }
            
            ReadJson readjson=new ReadJson();
            MoleculeModel.FieldLineList = readjson.ReadFile(www.text,Offset);
            isDone = true;
        }


        


        //TODO put molecule offset here
        public IEnumerator LoadOBJWWW(string file_name) {
            WWW www = new WWW(file_name);
            
            progress = 0;
            isDone = false;
            while(!www.isDone) {    
//              Debug.Log("*** PDB: "+www.progress);
                progress = www.progress;
                yield return new WaitForEndOfFrame();
            }
            
            OBJ obj = new OBJ(new StringReader(www.text));
            obj.Load();
            isDone = true;
        }
        

        public  void LoadXMLRequest(string file_name) {
            XmlReader reader=new XmlTextReader(file_name);
    
//          int i=0;
            while(reader.Read()) {
                if(reader.ReadToFollowing("PDBx:atom_site")) {
                    Vector3 v=new Vector3();
                
                    reader.ReadToDescendant("PDBx:Cartn_x");
                    v.x=reader.ReadElementContentAsFloat();
                    reader.ReadToFollowing("PDBx:Cartn_y");
                    v.y=reader.ReadElementContentAsFloat();
                    reader.ReadToFollowing("PDBx:Cartn_z");
                    v.z=reader.ReadElementContentAsFloat();
                    
    //              print(i%150);
    //              print(i/150);
    //              location1[i%150,i/150]=v;
    //              i++;
                }
            }   
        }


        //Aurélien : initiates the reading of the reaction file
        public void LoadPDBReaction(string resource_name)
        {
            StreamReader sr ;
            
            sr=new StreamReader(resource_name+".txt");
            
            ReadPDBReaction(sr, resource_name);
        }
        
        //Aurélien : initiates the reading of the top animation file
        public void LoadAnimTop(string resource_name)
        {
            StreamReader sr ;
            
            sr=new StreamReader(resource_name+".top");
            
            ReadAnimTop(sr, resource_name);
        }
        
        //Aurélien : initiates the reading of the top animation file
        public void LoadAnimCrd(string resource_name)
        {
            StreamReader sr ;
            
            sr=new StreamReader(resource_name+".mdcrd");
            
            ReadAnimCrd(sr, resource_name);
        }




        public static List<int> sortResIndex(List<string> resChainList){
            // Debug.Log ("sortResIndex :: entering");
            List<String> nbChainStr = new List<string> ();
            List<int> resInOrderByChain = new List<int>();
            Dictionary<string, int> IDofString = new Dictionary<string, int> ();
            //We count the number of different chain
            int stringID = 0;

            for (int i=0; i<resChainList.Count; i++) {
                if (!nbChainStr.Contains (resChainList [i])) {
                    nbChainStr.Add(resChainList[i]);    
                    IDofString.Add (resChainList[i], stringID);
                    stringID++;
                }
            }

            int nbChain = nbChainStr.Count ();

            List<int>[] preSortedList = new List<int>[nbChain];
            //We initialize the preSortedList
            for (int i=0; i<preSortedList.Length; i++) {
                preSortedList[i] = new List<int>();
            }

            //We put the resID in the good chainID

            for (int i=0; i<resChainList.Count; i++){
                preSortedList[IDofString[resChainList[i]]].Add (i);
            }

            //We finaly put all res in order (chain order)
            for (int i=0 ; i<preSortedList.Length; i++){
                resInOrderByChain.AddRange(preSortedList[i]);
            }

            return resInOrderByChain;

        }//End of sortResIndex


        //Aurélien : reads a reaction text file
        private void ReadPDBReaction(TextReader sr, string resource_name)
        {
            ArrayList tmp;
            String s;
//          ControlMolecule.CreateMolecule(sr);//reads the PDB part of the reaction text file
            //sr is closed by ReadPDB, a new StreamReader is required
            StreamReader srdr ;
            srdr = new StreamReader(resource_name+".txt");
            while((s=srdr.ReadLine()).StartsWith("[GEOMETRIES]")==false){}//Skipping the PDB part
            s = srdr.ReadLine();
            while((s = srdr.ReadLine())!=null){
                if(s.StartsWith("END")){//Every reaction step has been treated at this point
                    break;  
                }
                s = srdr.ReadLine();
                tmp = new ArrayList();
                
                while(s!=null){
                    if(s.StartsWith("Coords")){//Every coordinates for the current reaction step has been read at this point
                        break;  
                    }
                    float[] xyz = new float[3];
                    xyz[0] = -float.Parse(s.Substring(7,9));
                    xyz[1] = float.Parse(s.Substring(20,9));
                    xyz[2] = float.Parse(s.Substring(32,9));
                    tmp.Add(xyz);                   
                    s = srdr.ReadLine();
                }
                Reaction.coord.Add(tmp);                
            }
            srdr.Close();
            Reaction.isReaction = true;
            Reaction.current = 0;
            Reaction.affichage = false;
            Reaction.forward = true;
            Reaction.count = Reaction.coord.Count;
            Reaction.acount = ((Reaction.coord)[0] as ArrayList).Count;
            //Applying the Offset defined when the PDB was read to all coordinates
            for(int i=0;i<Reaction.count;i++){
                for(int j=0;j<Reaction.acount;j++){
                    (((Reaction.coord)[i] as ArrayList)[j] as float[])[0] += MoleculeModel.Offset.x;
                    (((Reaction.coord)[i] as ArrayList)[j] as float[])[1] += MoleculeModel.Offset.y;
                    (((Reaction.coord)[i] as ArrayList)[j] as float[])[2] += MoleculeModel.Offset.z;
                }
            }
        }
        
        //Aurélien : reads a top animation text file
        private void ReadAnimTop(TextReader sr, string resource_name)
        {
            
            
            List<float>     BFactorList     =   new List<float>();
            List<int>   calist          =   new List<int>();
            List<string>    resnamelist     =   new List<string>();
            List<string>    atomsNameList   =   new List<string>();
            List<string>    caChainlist     =   new List<string>();
            List<Color> colorList = new List<Color> ();
            
            List<AtomModel> typelist        =   new List<AtomModel>();
            string[] dnaBackboneAtoms = new string[] {"C5'"};
            
            string s;
            s = sr.ReadLine ();
            while(!s.StartsWith("%FORMAT(10I8)"))
            {
                s = sr.ReadLine();  
            }
            s = sr.ReadLine();
            string count = string.Empty;
            int c = 0;
            while(!char.IsDigit(s[c]))
            {
                c++;
            }
            while(char.IsDigit(s[c])){
                count+=s[c];
                c++;
            }
            Reaction.acount = int.Parse(count);
            
            while(!s.StartsWith("%FLAG AMBER_ATOM_TYPE  "))
            {
                s = sr.ReadLine();
            }
            s = sr.ReadLine();
            s = sr.ReadLine();
            while(!s.StartsWith("%"))
            {
                char[] sep = {' '};
                String[] sa = s.Split(sep, 20, StringSplitOptions.RemoveEmptyEntries);
                for(int i = 0; i < sa.Count() ; i++)
                {
                    string typestring = sa[i];
                    atomsNameList.Add(typestring);
                    int bout;
                    bool b = int.TryParse(typestring[0].ToString(), out bout);
                    string type;
                    if(b)
                    {
                        type=typestring[1].ToString();
                    }
                    else
                    {
                        type=typestring[0].ToString();
                        
                    }
                    string resname = "MOL";
                    
                    
                    if(typestring[0].ToString()=="C" && typestring.Length>1)
                    {
                        if(typestring[1].ToString()=="A")
                        {
                            string chaintype = "chain" + "A";
                            calist.Add(i);
                            caChainlist.Add(chaintype);
                        }
                    }
                    if(dnaBackboneAtoms.Contains(typestring))
                    {
                        string chaintype = "chain" + "A";
                        calist.Add(i);
                        caChainlist.Add(chaintype);
                    }
                    float bfactor = 10.00f;
                    BFactorList.Add(bfactor);
                    AtomModel aModel = AtomModel.GetModel(type);
                    if(aModel == null) aModel = AtomModel.GetModel("X");
                    typelist.Add(aModel);

                    if (UIData.ffType == UIData.FFType.atomic)
                    {
                        colorList.Add(MoleculeModel.GetAtomColor(type));
                    }
                    else
                    {
                        colorList.Add(aModel.baseColor);
                    }

                    resnamelist.Add(resname);
                }
                s = sr.ReadLine();  
            }
            sr.Close();
            MoleculeModel.CaSplineChainList     =   caChainlist;
            MoleculeModel.atomsTypelist         =   typelist;
            MoleculeModel.atomsNamelist         =   atomsNameList;
            MoleculeModel.atomsColorList        =   colorList;

            Reaction.CatomsIndList  =   new int[calist.Count];
            for(int i=0;i<calist.Count;i++)
            {
                Reaction.CatomsIndList[i] = calist[i];  
            }
            Reaction.Catomscount = calist.Count;
            MoleculeModel.BFactorList           =   BFactorList;
            MoleculeModel.atomsResnamelist      =   resnamelist;
            Reaction.top = true;

        }
        
        //Aurelien : reads a crd animation file
        private void ReadAnimCrd(TextReader sr, string resource_name)
        {
            int[] caindlist =  new int[Reaction.Catomscount];
            for(int i = 0; i < Reaction.Catomscount; i++)
            {
                caindlist[i] = (int)Reaction.CatomsIndList[i];  
            }
            Reaction.CatomsIndList = null;
            List<float[]>   alist           =   new List<float[]>();
            List<float[]>   calist          =   new List<float[]>();
            int currentcoord = 0;
            int currentatome = 0;
            string s;
            s = sr.ReadLine();
            s = sr.ReadLine();
            string[] tmp;
            char[] sep = {' '};
            float[] xyz = new float[3];
            ArrayList step = new ArrayList();
            while(s != null)
            {
                tmp = s.Split(sep, 10, StringSplitOptions.RemoveEmptyEntries);
                if(tmp.Count () == 0)
                {
                    break;  
                }
                for(int i = 0 ; i < tmp.Count() ; i++)
                {
                    xyz[currentcoord] = float.Parse(tmp[i]);
                    currentcoord++;
                    if(currentcoord == 3)
                    {
                        xyz[0] *= -1;
                        step.Add(xyz);
                        xyz = new float[3];
                        currentcoord = 0;
                        currentatome++;
                        if(currentatome == Reaction.acount)
                        {
                            Reaction.coord.Add(step);
                            currentatome = 0;
                            step = new ArrayList();
                        }
                    }
                }
                s = sr.ReadLine();
            }
            sr.Close();
            float[] xyzi = new float[4];
            for(int i=0;i<Reaction.acount;i++)
            {
                xyzi[0] = ((Reaction.coord[0] as ArrayList)[i] as float[])[0];  
                xyzi[1] = ((Reaction.coord[0] as ArrayList)[i] as float[])[1];
                xyzi[2] = ((Reaction.coord[0] as ArrayList)[i] as float[])[2];
                xyzi[3] = i;
                alist.Add(xyzi);
                xyzi = new float[4];
            }
            MoleculeModel.atomsLocationlist     =   alist;
            
            for (int i =0;i<Reaction.Catomscount;i++)
            {
                calist.Add ((Reaction.coord[0] as ArrayList)[i] as float[]);
            }
            Reaction.Catomscount = 0;
            MoleculeModel.CatomsLocationlist    =   calist;
            
            Molecule.Control.ControlMolecule.BuildMoleculeComponents();
            Molecule.Control.ControlMolecule.CreateSplines();
            
            UIData.isParticlesInitialized = false ; // new file, new particle system needed
            MoleculeModel.networkLoaded = false ; // protein loaded, network removed if present
            
            Reaction.affichage = false;
            Reaction.animation = true;
            Reaction.isReady = false;
            Reaction.forward = true;
            Reaction.top = false;
            Reaction.count = Reaction.coord.Count;
            Reaction.current = 0;
            Reaction.isReaction = true;
            
            //Applying the Offset 
            for(int i=0;i<Reaction.count;i++){
                for(int j=0;j<Reaction.acount;j++){
                    (((Reaction.coord)[i] as ArrayList)[j] as float[])[0] += MoleculeModel.Offset.x;
                    (((Reaction.coord)[i] as ArrayList)[j] as float[])[1] += MoleculeModel.Offset.y;
                    (((Reaction.coord)[i] as ArrayList)[j] as float[])[2] += MoleculeModel.Offset.z;
                }
            }
        }


        public  void LoadXGMML(string file_name)
        {
            WWW www = new WWW(file_name);
            
            progress = 0;
            isDone = false;
            while(!www.isDone){
                progress = www.progress;
            }
            // {    
                // progress = www.progress;
                // yield return new WaitForEndOfFrame();
            // }
            // Debug.Log("read");
            ReadXGMML(www.text);
            isDone = true;
        }

        //TODO: avoid reading the file 3 times
        public void ReadXGMML(String xml_content)   
        {
            List<float[]> alist = new List<float[]>();
            List<float[]> CSRadiusList = new List<float[]>();
            
            List<AtomModel> typelist = new List<AtomModel>();
//          List<string>    chainlist = new List<string>();
            List<int[]> edgelist = new List<int[]>();
            List<string> resnamelist = new List<string>();
            List<string[]> CSSGDList = new List<string[]>();
            List<string[]> CSColorList=new List<string[]>();
            List<string[]> CSLabelList=new List<string[]>();

            List<int[]> CSidList = new List<int[]>();

            
            XmlReader reader=new XmlTextReader(new StringReader(xml_content));
            while(reader.Read())
            {
                if(reader.ReadToFollowing("node"))
                {
                    float[] vect=new float[3];
//                  Vector3 v=new Vector3();
                    float [] intarrayw= new float[1];
                    while (reader.MoveToNextAttribute()) // Read the attributes.
                    {
                        if(reader.Name=="label")
                        {
                            string [] intarray= new string[1];
                            intarray[0]=reader.Value;
                            CSLabelList.Add(intarray);

                        }
                        else if(reader.Name=="id")
                        {
                            int [] intarray= new int[1];
                            intarray[0]=int.Parse(reader.Value);
                            CSidList.Add(intarray);
                        }
    //                      Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
                    }
    //              if(reader.NodeType==XmlNodeType.Element)
    //                {
    //                      Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
    //                  string [] intarray= new string[1];
    //                      intarray[0]=reader.Value;
    //                  if(reader.LocalName=="SGD symbol")CSSGDList.Add(intarray);
    //                  
    //                }
                    reader.ReadToFollowing("graphics");
                    while (reader.MoveToNextAttribute()) // Read the attributes.
                    {
                        if(reader.Name=="type")
                        {
                            
                        }
                        else if(reader.Name=="h")
                        {

                        }
                        else if(reader.Name=="w")
                        {
    //                      Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
                            intarrayw[0]=float.Parse(reader.Value)/60;

                            CSRadiusList.Add(intarrayw);
                        }
                        else if(reader.Name=="x")
                        {
    //                      Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
                            //Take the opposite of y beceause Unity is left-handed
                            vect[0]=float.Parse(reader.Value)/60;
                                
                        }
                        else if(reader.Name=="y")
                        {
    //                      Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
                            //Take the opposite of y beceause screen is directed in -y
                            vect[1]=-float.Parse(reader.Value)/60;
                        }
                        else if(reader.Name=="fill")
                        {
                            string [] intarray= new string[1];
                            intarray[0]=reader.Value;
                            CSColorList.Add(intarray);
                            
                            
                        }
                        else if(reader.Name=="width")
                        {
                            
                        }
                        else if(reader.Name=="outline")
                        {
                            
                        }
    //                      Debug.Log(" " + reader.Name + "='" + reader.Value + "'");

                    }
                    //Take the opposite for z to make the node pop out toward the user
                    vect[2]=-GUIMoleculeController.depthfactor*intarrayw[0];
                    alist.Add(vect);
                    typelist.Add(AtomModel.GetModel("S"));
    //              modellist.Add(model);
                }
                
                                                
            }
            reader.Close();
            XmlReader reader2=new XmlTextReader(new StringReader(xml_content));
            while(reader2.Read())
            {
                if(reader2.ReadToFollowing("edge"))
                {
                    int[] vectint=new int[2];
                    while (reader2.MoveToNextAttribute()) // Read the attributes.
                    {
                        if(reader2.Name=="label")
                        {
                            
                        }
                        else if(reader2.Name=="source")
                        {
    //                      Debug.Log(" " + reader2.Name + "='" + reader2.Value + "'");
                            vectint[0]=int.Parse(reader2.Value);
                        }
                        else if(reader2.Name=="target")
                        {
    //                      Debug.Log(" " + reader2.Name + "='" + reader2.Value + "'");
                            vectint[1]=int.Parse(reader2.Value);
                        }
    //                      Debug.Log(" " + reader.Name + "='" + reader.Value + "'");
                    }
    //                      Debug.Log(" vectint[0]:" + vectint[0]+", vectint[1]:" + vectint[1]);
                    edgelist.Add(vectint);

                }
        
            }
            reader2.Close();
            
            XmlReader reader3=new XmlTextReader(new StringReader(xml_content));
            while(reader3.Read())
            {
                if(reader3.NodeType==XmlNodeType.Element)
                {
                    while (reader3.MoveToNextAttribute()) // Read the attributes.
                    {
                        if(reader3.Name=="name"&& reader3.Value=="SGD symbol")
                        {
                            if(reader3.MoveToNextAttribute())
                            {
    //                          Debug.Log(" " + reader3.Name + "=" + reader3.Value + " ");
                                string [] intarray= new string[1];
                                intarray[0]=reader3.Value;
                                CSSGDList.Add(intarray);
    //                          Debug.Log(" " + reader3.Name + "='" + reader3.Value + "'");
                            }
                            

                        }
                     }
                 }

            }
            reader3.Close();
        
            MoleculeModel.atomsLocationlist=alist;
            MoleculeModel.atomsTypelist=typelist;
            MoleculeModel.atomsResnamelist=resnamelist;
            MoleculeModel.CSidList=CSidList;
            
            MoleculeModel.CSLabelList=CSLabelList;
            MoleculeModel.CSRadiusList=CSRadiusList;
            MoleculeModel.CSColorList=CSColorList;
            MoleculeModel.CSSGDList=CSSGDList;
            //float [] a0=alist[0] as float[];
            
            Vector3 minPoint= new Vector3(float.MaxValue,float.MaxValue,float.MaxValue);
            Vector3 maxPoint= new Vector3(float.MinValue,float.MinValue,float.MinValue);
            
            for(int i=0; i<alist.Count; i++)
            {
                float[] position= alist[i] as float[];
//              Debug.Log(position[0]+","+position[1]+","+position[2]);
                minPoint = Vector3.Min(minPoint, new Vector3(position[0],position[1],position[2]));
                maxPoint = Vector3.Max(maxPoint, new Vector3(position[0],position[1],position[2]));
            }
            Vector3 centerPoint = minPoint + ((maxPoint - minPoint) / 2);
            //MoleculeModel.target = centerPoint;
            
            Camera.main.transform.position=new Vector3(0,0,0);
            
            MoleculeModel.Offset = -centerPoint;
            MoleculeModel.MinValue = minPoint;
            MoleculeModel.MaxValue = maxPoint;
            // Debug.Log("centerPoint="+centerPoint );

        
            
            for(int i=0; i<alist.Count; i++)
            {
                float[] position= alist[i] as float[];
                float[] vectarray=new float[3];
                vectarray[0]=position[0]+MoleculeModel.Offset.x;
                vectarray[1]=position[1]+MoleculeModel.Offset.y;
                vectarray[2]=position[2]+MoleculeModel.Offset.z;
                
                alist[i]=vectarray;
            }
            
            
//          Debug.Log("MoleculeModel.target "+MoleculeModel.target);
            MoleculeModel.cameraLocation.x=MoleculeModel.target.x;
            MoleculeModel.cameraLocation.y=MoleculeModel.target.y;
//          MoleculeModel.cameraLocation.z=MoleculeModel.target.z-((maxPoint - minPoint) ).z;
            MoleculeModel.cameraLocation.z=-80;
//          MoleculeModel.cameraLocation.z=MoleculeModel.target.z;
            
            
//          MoleculeModel.bondList=ControlMolecule.CreateBondsList(alist,typelist);
//          MoleculeModel.bondEPList=ControlMolecule.CreateBondsEPList(alist,typelist);
            MoleculeModel.bondEPList=ControlMolecule.CreateBondsCSList(edgelist);
            MoleculeModel.atomsnumber = alist.Count;
            MoleculeModel.bondsnumber = MoleculeModel.bondEPList.Count;
            
            MoleculeModel.networkLoaded = true ; // there should be a network loaded, if all went well
//          return alist;           
        }
        
    private void LoadChoice(int a)
    {
        FileInfo fieldlinefile=new FileInfo(UI.GUIDisplay.file_base_name+".json");
        if(fieldlinefile.Exists)
            wantjson = GUILayout.Toggle (wantjson, new GUIContent ( "JSON" , "Open the Json file"));
        
        FileInfo Surfacefile=new FileInfo(UI.GUIDisplay.file_base_name+".obj");
        FileInfo Surfacefile0=new FileInfo(UI.GUIDisplay.file_base_name+"0.obj");

        if(Surfacefile.Exists || Surfacefile0.Exists)
            wantobj = GUILayout.Toggle (wantobj, new GUIContent ( "OBJ" , "Open the Obj file"));
            
        FileInfo dxfile=new FileInfo(UI.GUIDisplay.file_base_name+".dx");
        if(dxfile.Exists)
                wantdx = GUILayout.Toggle (wantdx, new GUIContent ( "DX" , "Open the Dx file"));
        if (GUILayout.Button("Confirm")){
//              wantpdb=false;
            }

    }
    
    }
    
}