MoleculeModel.cs

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namespace Molecule.Model {  
    using UnityEngine;
    using System.Collections;
    using System.Collections.Generic;

    public class MoleculeModel : MonoBehaviour {
        public static string sequence = "";

        //Aurélien : changed the summary to acknowledge the changes I made in RequestPDB.cs

        public static List<float[]> atomsLocationlist = new List<float[]>();
        
        public static List<Vector3> atomsIMDSimulationLocationlist;
        
        public static List<float[]> CatomsLocationlist = new List<float[]>();

        public static List<float[]> backupCatomsLocationlist = new List<float[]>();
        
        public static List<float[]> CaSplineList = new List<float[]>();
        
        public static List<AtomModel> atomsTypelist = new List<AtomModel>();
        
        public static List<string> atomsNamelist = new List<string>();


        public static List<int> atomsNumberList = new List<int>();

        public static List<string> atomsSugarNamelist = new List<string>();
        public static List<string> atomsSugarResnamelist = new List<string>();
        public static List<string> sugarResname = new List<string> {"ABE","ACE","ALT","API","ARA","DHA","FRU","FUC","GAL",
            "GLC","GUL","IDO","DKN","KDO","MAN","NEG","RHA","RIB","SIA","TAG","TAL","XYL",
            "GLA","FUL","GLB","NAG","NDG","BMA","MMA","A2G","AAL","BGC"};
        public static List<float[]> atomsSugarLocationlist = new List<float[]>();
        public static List<string> resSugarChainList = new List<string>();
        public static List<int[]> bondEPSugarList = new List<int[]>(); // Not sure of what EP means btw
        public static List<AtomModel> atomsSugarTypelist = new List<AtomModel>();
        // public static List<int> sortedResIndexByListSugar = new List<int>();

        public static List<int[]> BondListFromPDB = new List<int[]>();

        public static List<string> atomHetTypeList = new List<string>();


        public static List<string> existingName = new List<string>();
        
        public static List<string> atomsResnamelist = new List<string>();
        
        public static List<string> existingRes = new List<string>();
            
        public static List<int> residueIds = new List<int>();
        
        public static Dictionary<int, ArrayList> residues = new Dictionary<int, ArrayList>();
        
        public static List<string> atomsChainList = new List<string>();

        public static List<string> resChainList = new List<string>();

        public static List<string> resChainList2 = new List<string>();

        public static int firstresnb = new int();

        public static List<string> existingChain = new List<string>();
        
        public static List<Color> atomsColorList = new List<Color>();

        public static List<float> atomsLocalScaleList = new List<float>();

        public static List<int> splits = new List<int>();
        
        public static List<int[]> bondList = new List<int[]>();

        public static List<int[]> bondEPList = new List<int[]>(); // Not sure of what EP means btw

        public static Dictionary<int, List<int>> bondEPDict= new Dictionary<int, List<int>>();

        public static List<int[]> CSidList = new List<int[]>(); // List of IDs for networks, or something like that.
        public static List<string[]> CSSGDList = new List<string[]>(); // Dunno
        public static List<float[]> CSRadiusList = new List<float[]>(); // Mystery too.
        public static List<string[]> CSColorList = new List<string[]>(); // List of colors, I guess. Probably for networks.
        public static List<string[]> CSLabelList = new List<string[]>(); // And of labels.
        
        public static List<List<Vector3>> FieldLineList= null;
        //public static ArrayList FieldLineDist= null;// Field lines distance arrays // Apparently not used anywhere
        
        //public static ArrayList CaSplineList=new ArrayList();

        public static List<int[]> bondCAList=new List<int[]>();

        public static List<AtomModel> CaSplineTypeList = new List<AtomModel>();

        public static List<string> CaSplineChainList = new List<string>();

        // public static List<int> sortedResIndexByList = new List<int>();
        //not used!

        public static List<string> backupCaSplineChainList = new List<string>();

        public static List<float> BFactorList = new List<float>();
        
        public static Dictionary<int, int[]> atomsForEllipsoidsPerResidue = new Dictionary<int, int[]>();
        
        public static Dictionary<int, int> atomsForEllipsoidsOrientationPerResidue = new Dictionary<int, int>();
        
        public static List<int> baseIdx = new List<int>();
        
        public static List<float> scale_RNA = new List<float>();
        
        public static List<GameObject> ellipsoids = new List<GameObject>();
        
        public static Dictionary<int, GameObject> ellipsoidsPerResidue = new Dictionary<int, GameObject>();
        
        public static List<GameObject> bondsForReplacedAtoms = new List<GameObject>();

        public static List<Dictionary<string, Vector3>> residueDictionaries;
        public static List<Dictionary<string, Vector3>> residueDictionariesSugar;

        public static List<float[]> ssHelixList    = new List<float[]> ();

        public static List<float[]> ssStrandList   = new List<float[]> ();

        public static List<string> helixChainList  = new List<string>() ;

        public static List<string> strandChainList = new List<string> ();
        
        public static Vector3 target=new Vector3(0f,0f,0f);//
        public static Vector3 cameraLocation=new Vector3(10f,10f,10f);//
        
        public static Vector3 Offset=new Vector3(0f,0f,0f);
        
        public static Vector3 Center=new Vector3(0f,0f,0f);
        
        public static Vector3 MinValue= new Vector3(0f,0f,0f);
        
        public static Vector3 MaxValue= new Vector3(0f,0f,0f);
        
        // NEW PASTEL COLOR THEME
        public static ColorObject oxygenColor = new ColorObject(new Color(0.827f,0.294f,0.333f,1f));
        public static ColorObject carbonColor = new ColorObject(new Color(0.282f,0.6f,0.498f,1f));  
        public static ColorObject nitrogenColor = new ColorObject(new Color(0.443f,0.662f,0.882f,1f));
        public static ColorObject hydrogenColor = new ColorObject(Color.white);                 
        public static ColorObject sulphurColor = new ColorObject(new Color(1f,0.839f,0.325f,1f));
        public static ColorObject phosphorusColor = new ColorObject(new Color(0.960f,0.521f,0.313f,1f));
        public static ColorObject unknownColor = new ColorObject(new Color(1f,0.4f,1f,1f));
//      public static ColorObject selectionColor = new ColorObject(Color.red);
//      public static ColorObject residueColor = new ColorObject(Color.white);
        
        public static Color GetAtomColor(string atomType) {
            switch(atomType) {
            case "O": return oxygenColor.color;
            case "C": return carbonColor.color;
            case "N": return nitrogenColor.color;
            case "H": return hydrogenColor.color;
            case "S": return sulphurColor.color;
            case "P": return phosphorusColor.color; 
            default: return unknownColor.color;
            }
        }
    
        public static string oxygenNumber="0";
        public static string carbonNumber="0";
        public static string nitrogenNumber="0";    
        public static string hydrogenNumber="0";    
        public static string sulphurNumber="0";
        //public static string lodineNumber="0";
        //public static string chlorineNumber="0";      
        public static string phosphorusNumber="0";
        public static string unknownNumber="0";
        
        // public static GameObject [] boxes;
/*
        public static GameObject[] Oes;     
        public static GameObject[] Ces;
        public static GameObject[] Nes;
        public static GameObject[] Hes;     
        public static GameObject[] Ses;
        //public static GameObject[] Les;
        //public static GameObject[] Cles;
        public static GameObject[] Pes;     
        public static GameObject[] NOes;
*/
        
        public static Dictionary<string, GameObject[]> atomsByChar = new Dictionary<string, GameObject[]>();
        public static ArrayList atoms = new ArrayList();
        
        public static GameObject[] clubs;
        
        //public static float []atomsScaleList={1.72f,1.6f,1.32f,2.08f,2.6f,1f};//c\n\o\s\p\n
        
        public static Vector3 vo=new Vector3(0.66f,0.66f,0.66f);        
        public static Vector3 vc=new Vector3(0.86f,0.86f,0.86f);
        public static Vector3 vn=new Vector3(0.80f,0.80f,0.80f);
        public static Vector3 vh=new Vector3(0.78f,0.78f,0.78f);        
        public static Vector3 vs=new Vector3(1.04f,1.04f,1.04f);
        //public static Vector3 vl=new Vector3(1.95f,1.95f,1.95f);
        //public static Vector3 vcl=new Vector3(0.91f,0.91f,0.91f);     
        public static Vector3 vp=new Vector3(1.30f,1.30f,1.30f);
        public static Vector3 vno=new Vector3(1f,1f,1f);
        
        public static   float oxygenScale=100f;
        public static   float carbonScale=100f;
        public static   float nitrogenScale=100f;
        public static   float hydrogenScale=100f;       
        public static   float sulphurScale=100f;
        //public static string lodineScale="100";
        //public static string chlorineScale="100";
        public static   float phosphorusScale=100f;
        public static   float unknownScale=100f;
        
        public static long atomsnumber=0;
        public static long bondsnumber=0;
        
        public static string FPS="";
        
        public static Particle[] p;
        
        public static Particle[] fieldlinep;

        public static string newtooltip;
        
        public static bool fieldLineFileExists=false;
        
        public static bool dxFileExists = false ; // true if a DX file was found

        public static bool surfaceFileExists=false;


        public static bool networkLoaded = false; // set to true when a network is present
        
        public static Vector3[] vertices;

        
        public MoleculeModel() {}

    }
}