BridgeHeadFindingRule.java

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package denoptim.fragmenter;
 
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
 
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.isomorphism.Mappings;
 
import denoptim.constants.DENOPTIMConstants;
import denoptim.exception.DENOPTIMException;
import denoptim.graph.APClass;
import denoptim.utils.ManySMARTSQuery;
import denoptim.utils.MoleculeUtils;
 
public class BridgeHeadFindingRule
{
    private String ruleName;
 
    private String smarts;
    
    private int[] bridgeHeadPositions;
    
    private int[] allowedBridgeLength;
    
    private int lengthInAtoms;
 
 
//------------------------------------------------------------------------------
 
    public BridgeHeadFindingRule(String name, String smarts, 
            int[] bridgeHeadPositions, int[] allowedBridgeLength,
            int lengthInAtoms)
    {
        this.ruleName = name;
        this.smarts = smarts;
        this.bridgeHeadPositions = bridgeHeadPositions;
        this.allowedBridgeLength = allowedBridgeLength;
        this.lengthInAtoms = lengthInAtoms;
    }
 
//------------------------------------------------------------------------------
 
    public String getName()
    {
        return ruleName;
    }    
 
//------------------------------------------------------------------------------
    
   public String getSMARTS()
   {
       return smarts;
   }
  
//------------------------------------------------------------------------------
     
    public int[] getBridgeHeadPositions()
    {
        return bridgeHeadPositions;
    }
    
//------------------------------------------------------------------------------
    
   public int[] getAllowedBridgeLength()
   {
       return allowedBridgeLength;
   }
   
 //------------------------------------------------------------------------------
   
  public int[] getAllowedBridgeLength(int maxRingSize)
  {
      if (allowedBridgeLength!=null)
          return allowedBridgeLength;
 
      // Any bridge length is allowed
      int[] anyLength = new int[maxRingSize - lengthInAtoms];
      for (int i=1; i<anyLength.length; i++) {
          anyLength[i-1] = i;
      }
      return anyLength;
  }
   
//------------------------------------------------------------------------------
   
   public int getExistingBridgeLength()
   {
       return lengthInAtoms;
   }
 
//------------------------------------------------------------------------------
 
}