ParsePDB.cs

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using UnityEngine;
using System.Collections;
using System.Collections.Generic;
using System.IO;
using Molecule.Model;
using Molecule.Control;
using System.Net;
using UI;
using System.Linq;

public class ParsePDB   {

    public static void FetchPDB2(string url,string id, string proxyserver = "", int proxyport = 0) {
        StreamReader sr ;
        Stream dataStream=null;
        HttpWebResponse response=null;

        if (UIData.loadHireRNA == false) {
            UIData.ffType = UIData.FFType.atomic;
            AtomModel.InitAtomic();
        }
        else
        {
            UIData.ffType = UIData.FFType.HiRERNA;
            AtomModel.InitHiRERNA();
        }
        
        HttpWebRequest request =(HttpWebRequest) WebRequest.Create (url+id+".pdb");
        
        // If required by the server, set the credentials.
        request.Credentials = CredentialCache.DefaultCredentials;
        
        //Set proxy information if needed
        // Debug.Log("LoadPDB: " + proxyserver + " " + proxyport);
        if(proxyserver != "")
            request.Proxy = new WebProxy(proxyserver,proxyport);
        
        // Get the response.
        response = (HttpWebResponse)request.GetResponse ();
        // Display the status.
        Debug.Log("LoadPDB Status :: " + response.StatusDescription);
        
        // Get the stream containing content returned by the server.
        dataStream = response.GetResponseStream ();
        // Open the stream using a StreamReader for easy access.
        sr = new StreamReader (dataStream);
        
        ReadPDB2(sr);
        //ReadPDB(sr);
        
        if(dataStream!=null&& response!=null) {
            dataStream.Close ();
            response.Close ();
        }
    }
    public static void LoadPDBRequest2(string file_base_name,bool withData = true) {
        StreamReader sr ;
            
//          FileInfo file=new FileInfo(file_base_name+".pdb");
        sr=new StreamReader(file_base_name+".pdb");

        if (UIData.loadHireRNA == false) {
            UIData.ffType = UIData.FFType.atomic;
            AtomModel.InitAtomic();
        }
        else
        {
            UIData.ffType = UIData.FFType.HiRERNA;
            AtomModel.InitHiRERNA();
        }
        
        ReadPDB2(sr);

        if(withData) {
            FileInfo fieldlinefile=new FileInfo(file_base_name+".json");
            FileInfo apffile=new FileInfo(file_base_name+".apf");
            if(fieldlinefile.Exists) {
                LoadJsonRequest(file_base_name+".json",MoleculeModel.Offset);
                MoleculeModel.fieldLineFileExists=true;
            } else if(apffile.Exists) {
                LoadJsonRequest(file_base_name+".apf",MoleculeModel.Offset);
                MoleculeModel.fieldLineFileExists=true;
            } else {
                MoleculeModel.fieldLineFileExists=false;
                MoleculeModel.FieldLineList=null;
            }
                
            FileInfo Surfacefile=new FileInfo(file_base_name+".obj");
            FileInfo Surfacefile0=new FileInfo(file_base_name+"0.obj");

            if(Surfacefile.Exists || Surfacefile0.Exists) {
                LoadOBJRequest(file_base_name);
                MoleculeModel.surfaceFileExists=true;
                ElectrostaticOldGUI.showFieldLines = true;
            } else {
                MoleculeModel.surfaceFileExists=false;
            }
                
            FileInfo dxfile=new FileInfo(file_base_name+".dx");
            MoleculeModel.dxFileExists = false ; // otherwise a molecule might load dx data from a previous molecule
            if(dxfile.Exists) {
                MoleculeModel.dxFileExists = true ;
                LoadDxRequest(file_base_name+".dx",MoleculeModel.Offset);
            }
        }
    }     


    public static void ReadPDB2(TextReader sr){


        List<float[]>   alist           =   new List<float[]>();
        List<float[]>   calist          =   new List<float[]>();
        
        List<float>     BFactorList     =   new List<float>();
        
        List<string>    resnamelist     =   new List<string>();
        List<string>    atomsNameList   =   new List<string>();
        List<string>    caChainlist     =   new List<string>();
        
        List<AtomModel> typelist        =   new List<AtomModel>();
        List<string>    chainList       =   new List<string>();
        
        List<Color>     colorList       = new List<Color>();
        
        List<float[]>   sshelixlist     = new List<float[]> ();
        List<float[]>   sssheetlist     = new List<float[]> ();


        string[] dnaBackboneAtoms = new string[] {"C5'"};
        List<int> residueIds = new List<int>();
        List<int> splits = new List<int>();
        List<int> atomsNumberList = new List<int>();
        
        int resNb = 0;
        int prevRes = int.MinValue;
        int currentRes = int.MinValue+1;
        
        int nowline=0;
        int nbAtoms = 0;
        int nbTers = 0;
        
        string s;
        string[] lines = sr.ReadToEnd().Split(new [] { '\r', '\n' });
        int idl = 0;
        int prevresnb = 0;
        
        // while((s=sr.ReadLine())!=null) {
        while(idl < lines.Length){
            s = lines[idl];
            idl++;
            if(s.StartsWith("ENDMDL"))
                break;
            
            if(s.Length>4) {
                bool isAtomLine = s.StartsWith("ATOM");
                //                  bool isHetAtm = s.StartsWith("HETATM");
                bool isHelixLine = s.StartsWith ("HELIX");
                bool isSheetLine = s.StartsWith("SHEET");
                bool isConnectLine = s.StartsWith("CONECT");
                if(s.StartsWith("TER")) {
                    splits.Add(resNb);
                    nbTers++;
                }
                
                if(isHelixLine){
                    string chainh = s.Substring (19,2).Trim ();
                    string initr = s.Substring(22,4);
                    string termr = s.Substring (34,4);
                    string classH = s.Substring(39,2);
                    
                    string len = s.Substring(72,5);
                    float[] vect = new float[4];
                    float initres = float.Parse (initr);
                    float termres = float.Parse (termr);
                    float length = float.Parse (len);
                    float classhelix = 1f;
                    try{
                        classhelix = float.Parse (classH);
                    }catch{
                        classhelix = float.Parse (s.Substring(38,2));
                    }
                    vect[0] = initres;
                    vect[1] = termres;
                    vect[2] = length;
                    vect[3] = classhelix;
                    sshelixlist.Add (vect);
                    MoleculeModel.helixChainList.Add (chainh);
                }
                
                if(isSheetLine){
                    string chainS = s.Substring (21, 2).Trim ();
                    string initr = s.Substring (23, 4);
                    string termr = s.Substring (34, 4);
                    float[] vect = new float[2];
                    vect[0] = float.Parse (initr);
                    vect[1] = float.Parse (termr);
                    sssheetlist.Add (vect);
                    MoleculeModel.strandChainList.Add (chainS);
                }
                
                if(UIData.readHetAtom)
                    isAtomLine = isAtomLine || s.StartsWith("HETATM");
                
                if(!UIData.readWater){
                    try{
                        if ((string) s.Substring(17,3).Trim() == "HOH")
                            isAtomLine = false;
                    }catch{
                        isAtomLine = false;
                    }
                }
                
                if(isAtomLine) {
                    float[] vect=new float[4];
                    //Aurélien : reading the atom's index
                    string sind = s.Substring(7,5);
                    MoleculeModel.atomHetTypeList.Add(s.Split(' ')[0]);
                    string sx=s.Substring(30,8);
                    string sy=s.Substring(38,8);
                    string sz=s.Substring(46,8);
                    string sbfactor = null;
                    bool parseBFactor = false;
                    if (s.Length > 60) {
                        sbfactor = s.Substring(60,6);
                        parseBFactor = true;
                    }
                    string atomsNumber = s.Substring(6,5);
                    string typestring=s.Substring(12,4).Trim();
                    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=s.Substring(17,3).Trim();
                    int resid = int.Parse(s.Substring(22,4));
                    residueIds.Add(resid);
                    currentRes = resid;
                    atomsNumberList.Add (int.Parse(atomsNumber));
                    
                    
                    //Unity has a left-handed coordinates system while PDBs are right-handed
                    //So we have to reverse the X coordinates
                    float x=-float.Parse(sx);
                    float y=float.Parse(sy);
                    float z=float.Parse(sz);
                    //Aurélien : parsing the atom's index
                    float ind = float.Parse(sind);
                    float bfactor = 0.0f;
                    if (parseBFactor == true)
                    {
                        bfactor= float.Parse(sbfactor);
                    }
                    vect[0]=x;
                    vect[1]=y;
                    vect[2]=z;
                    //Aurélien : stocking the atom's index
                    vect[3]=ind;
                    
                    //CA case
                    if(typestring[0].ToString()=="C" && typestring.Length>1) {
                        if(typestring[1].ToString()=="A") {
                            string chaintype = s.Substring(21,1);
                            calist.Add(vect);
                            caChainlist.Add(chaintype);
                        }
                    }
                    
                    
                    //??
                    if(dnaBackboneAtoms.Contains(typestring)) {
                        string chaintype = s.Substring(21,1);
                        calist.Add(vect);
                        caChainlist.Add(chaintype);
                    }
                    
                    if(s.Substring(21,1) != " "){
                        string chain = s.Substring(21,1);
                        chainList.Add(chain);
                        
                    }
                    
                    if (parseBFactor == true)
                    {
                        BFactorList.Add(bfactor);
                    }
                    alist.Add(vect);
                    AtomModel aModel;
                    if (UIData.ffType == UIData.FFType.atomic)
                    {
                        aModel = AtomModel.GetModel(type);
                    }
                    else
                    {
                        aModel = AtomModel.GetModel (typestring);
                    }
                    
                    if(aModel == null) aModel = AtomModel.GetModel("X");
                    typelist.Add(aModel);
                    if (MoleculeModel.sugarResname.Contains(resname))
                        MoleculeModel.atomsSugarTypelist.Add(aModel);
                    
                    
                    if (UIData.ffType == UIData.FFType.atomic)
                    {
                        //                          Debug.Log ("%%%%%% FFType atomic");
                        colorList.Add(MoleculeModel.GetAtomColor(type));
                    }
                    else
                    {
                        //                          Debug.Log ("%%%%%% FFType not atomic");
                        colorList.Add(aModel.baseColor);
                    }
                    
                    resnamelist.Add(resname);
                    
                    if(MoleculeModel.residues.ContainsKey(resid) == false){
                        MoleculeModel.residues.Add(resid, new ArrayList());
                        //add the chain name for each residu
                        MoleculeModel.resChainList.Add (s.Substring(21,1));
                        //If we have a sugar, we add theses informations in some special list
                        if (MoleculeModel.sugarResname.Contains(resname))
                            MoleculeModel.resSugarChainList.Add (s.Substring(21,1));
                    }
                    
                    int curresnb = int.Parse (s.Substring(22,4));
                    if(prevresnb == 0 && curresnb != 0)
                        MoleculeModel.firstresnb = curresnb;
                    if(curresnb != prevresnb){
                        MoleculeModel.resChainList2.Add (s.Substring (21,1));
                        prevresnb = curresnb;
                    }
                    
                    MoleculeModel.residues[resid].Add(nbAtoms);
                    
                    if(prevRes != currentRes)
                        resNb++;
                    
                    prevRes = currentRes;
                    
                    nbAtoms ++;
                    
                    //If we have a sugar, we add theses informations in some special list
                    if (MoleculeModel.sugarResname.Contains(resname)){
                        MoleculeModel.atomsSugarLocationlist.Add (vect);
                        MoleculeModel.atomsSugarResnamelist.Add (resname);
                        MoleculeModel.atomsSugarNamelist.Add(typestring);
                    }
                    
                }
                
                if (isConnectLine){
                    if (UIData.connectivity_PDB){
                        string[] splitedStringTemp = s.Split(' '); //0 is Connect, 1 is the atom, 2,3..... is the bounded atoms
                        List<string> splitedString = new List<string>();
                        for (int j=0; j<splitedStringTemp.Length; j++){
                            if (splitedStringTemp[j]!="")
                                splitedString.Add(splitedStringTemp[j]);
                        }
                        for (int j=2; j<splitedString.Count; j++){
                            MoleculeModel.BondListFromPDB.Add(new int[2]{int.Parse(splitedString[1])-1, int.Parse(splitedString[j])-1});
                        }
                    }
                }

                nowline++;
            }
        }

        Ribbons.mustSplitDictList = (nbTers > 1);
        
        for(int i = 0; i < typelist.Count; i++)
            MoleculeModel.atomsLocalScaleList.Add(100.0f);
        
        foreach(string name in atomsNameList)
            if(!MoleculeModel.existingName.Contains(name))
                MoleculeModel.existingName.Add(name);
        
        // existingRes is created in DisplayMolecule.CheckResidues after looking for protonated HIS
        
        foreach(string chain in chainList)
            if(!MoleculeModel.existingChain.Contains(chain))
                MoleculeModel.existingChain.Add(chain);
        
        MoleculeModel.existingName.Sort();
        MoleculeModel.existingChain.Sort();
        
        sr.Close ();
        // Debug.Log("typelist:"+typelist.Count);
        // Debug.Log("resnameList:"+resnamelist.Count);
        // Debug.Log("caChainlist:"+caChainlist.Count);
        // Debug.Log("chainlist:"+chainList.Count);
        // Debug.Log("colorList:"+colorList.Count);
        // Debug.Log ("atomsLocalScaleList:" + MoleculeModel.atomsLocalScaleList.Count);
        // Debug.Log ("BfactorList: " + BFactorList.Count);
        if(resnamelist.Count == typelist.Count)
            UIData.hasResidues = true;
        if(chainList.Count == typelist.Count)
            UIData.hasChains = true;
        
        MoleculeModel.atomsLocationlist     =   alist;
        MoleculeModel.CatomsLocationlist    =   calist;
        MoleculeModel.CaSplineChainList     =   caChainlist;
        MoleculeModel.atomsTypelist         =   typelist;
        MoleculeModel.atomsNamelist         =   atomsNameList;
        MoleculeModel.atomsNumberList       =   atomsNumberList;
        MoleculeModel.BFactorList           =   BFactorList;
        MoleculeModel.atomsResnamelist      =   resnamelist;
        MoleculeModel.residueIds            =   residueIds;
        MoleculeModel.splits                =   splits;
        MoleculeModel.atomsChainList        =   chainList;
        MoleculeModel.atomsColorList        =   colorList;
        MoleculeModel.ssHelixList           =   sshelixlist;
        MoleculeModel.ssStrandList          =   sssheetlist;
        //MoleculeModel.residueDictionaries =   residueDictList;
        
        //Here we will fill the sortedIndex residue by the Chain ID
        // MoleculeModel.sortedResIndexByList = sortResIndex (MoleculeModel.resChainList);
        // MoleculeModel.sortedResIndexByListSugar = sortResIndex (MoleculeModel.resSugarChainList);

        UIData.isFileLoaded = true;


    }
    public static void LoadJsonRequest(string file_name, Vector3 Offset) {
        StreamReader sr = new StreamReader(file_name);
        string text;
        using (sr)
        {              
            text = sr.ReadToEnd();                 
        }
        
        ParseData.ParsePDB.ReadJson readjson=new ParseData.ParsePDB.ReadJson();
        MoleculeModel.FieldLineList = readjson.ReadFile(text,Offset);

    } 

    //Move this method to the related class
    public static void LoadDxRequest(string file_name, Vector3 Offset) {  // function Loading DX file
    
//          ReadDX readdx = new ReadDX();
//          Debug.Log("time avant: "+ DateTime.Now);
//          DateTime temp = DateTime.Now;
//          readdx.getDX(file_name);
//          Debug.Log("time : apres"+ (DateTime.Now-temp));
//          temp = DateTime.Now;
//
//          
//          // Calcul et affichage des ligne de champs7
//          
//          
//          readdx.isoSurface(10f);
//          Debug.Log("time : surface "+ (DateTime.Now-temp));
        // lancement de la transformation du pdb en density
//          temp = DateTime.Now;

    }
    //TODO put molecule offset here
    public static void LoadOBJRequest(string file_base_name){
        
        Debug.Log("name:"+file_base_name+".obj");
        
                    
        string path = file_base_name+".obj";
//          path = "file:/"+path;
        // Debug.Log("file complet :"+ path);
//          string path = "http://www.everyday3d/unity3d/obj/monkey.obj";
        
        
        FileInfo file=new FileInfo(file_base_name+".obj");

        if ( file.Exists){
//          ReadOBJ readObj =new ReadOBJ();
//          readObj.GetOBJ(url,id);
//          OBJ obj = Camera.main.GetComponent<OBJ>(path);
//              var go = new GameObject("Your Script Container");
//              var obj = go.AddComponent<OBJ>();
            // THIS PRODUCES A WARNING:: You are trying to create a MonoBehaviour using the 'new' keyword.  This is not allowed.  MonoBehaviours can only be added using AddComponent().  Alternatively, your script can inherit from ScriptableObject or no base class at all
            OBJ obj = new OBJ(path);
            Debug.Log("Generate new OBJ from "+path);
            obj.Load();
//          Debug.Log("Coroutine Started");$
        } 
        else {
            for (int i =0;i< 6;i++){
                file=new FileInfo(file_base_name+i+".obj");
                if (file.Exists){
                    path = file_base_name+i+".obj";
                    OBJ obj = new OBJ(path);
                    Debug.Log("new OBJ");
                    obj.Load();
                }
            }
        }
    }
        

}