GraphVertex.cs

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using UnityEngine;
using System.Collections;
using System.Collections.Generic;

public class GraphVertex
{

    public List<GraphVertex> neighbor = new List<GraphVertex>(); //list of neighboor
    public int idRing = -1 ; //-1 if this atom is not in a ring (only for C or O).
    public char type;
    public int id;
    public string resname;
    public Vector3 coordinate;
    public bool flag=false;
        

    public bool SearchCycle(List<int> vertex,int first, int size=0){
        //we don't want to go to far in checking the size of the cycle.
        if (size>20){
            return false;
        }

        //we search for every neighbor.
        for (int i=0; i<neighbor.Count; i++){
            if (neighbor[i].id==first){
                if (size>3){
                    vertex.Add(id);
                    return true;
                }

            }

            //if we found the first.
            if(neighbor[i].flag==false){
                flag=true;
                if(neighbor[i].SearchCycle(vertex,first, size+1)==true){
                    vertex.Add(id);
                    return true;            
                }
            }
        }
        return false;
    }
        


    public bool AlreadyAdded(Dictionary <int,List<int>>  connectivityList, int key, int atom){
        bool added = false;;
        if (connectivityList.ContainsKey(key)){

            for (int j=0; j<connectivityList[key].Count / 3; j++){
                if (connectivityList[key][0+(3*j)] == atom)
                    added=true;
            }

            if (added)
                return true;
            else
                return false;
        }
        return false;
    }
        
    public void addInDict(Dictionary <int,List<int>>  connectivityList, int ring1, int atom1, int ring2, int atom2){

        if (! AlreadyAdded(connectivityList, ring1, atom1)){
            if (connectivityList.ContainsKey(ring1))
                connectivityList[ring1].AddMany(atom1, ring2, atom2);
            else
                connectivityList[ring1] = new List<int>( new int [] {atom1, ring2, atom2});
        }
    }
        

    public bool SearchConnection(Dictionary <int,List<int>>  connectivityList, List<int> trashlist, int r1=-1, int size=0){

        //we don't want to go to far in checking the size of the cycle.
        if (size>3)
            return false;

        if (size == 0 ){
            r1 = this.idRing;
            if (this.idRing==-1)
                return false;
        }

        if ((size == 1) && (this.idRing != -1))
            return false;



        //we search for every neighbor.
        for (int i=0; i<neighbor.Count; i++){
            if (this.idRing != -1){
                if ((size==2) || (size == 3)){
                    if (this.idRing != r1){
                        trashlist.Add(this.idRing);
                        trashlist.Add(this.id);
                        return true;
                    }
                }
            }




            
            //if we found the first.
            if(neighbor[i].flag==false){
                flag=true;
                if(neighbor[i].SearchConnection(connectivityList,trashlist, r1, size+1)==true){
                    if (size==0){
                        int a1=this.id;
                        int r2 = trashlist[0];
                        int a2 = trashlist[1];
                        if (r1 < r2)
                            addInDict(connectivityList, r1, a1, r2, a2);
                        else
                            addInDict(connectivityList, r2, a2, r1, a1);
                        return true;
                    }else
                        return true;
                }               
            }
        }
        return false;
    }

    
}