content: package com.actelion.research.chem.forcefield.mmff;
  
  import com.actelion.research.util.DoubleFormat;
  
  public class MMFFExternalPositionConstraint implements EnergyTerm {
  	private final MMFFMolecule mol;
  	private final double[] refPos;
  	private final int constrainedAtom;
  	private final double k;
  	private final double d;
  	
  	
  	public MMFFExternalPositionConstraint(MMFFMolecule mol, int atom, double[] refPos, double k, double d) {
  		this.mol = mol;
  		this.refPos = refPos;
  		this.constrainedAtom = atom;
  		this.k = k;
  		this.d = d;
  	}
  
  	@Override
  	public double getEnergy(double[] pos) {
  		return getEnergy(pos, null, null, false);
  	}
  
  	@Override
  	public double getEnergy(double[] pos, StringBuilder detail, String detailID, boolean skipHydrogen) {
  		if (skipHydrogen && mol.getAtomicNo(constrainedAtom) == 1)
  			return 0.0;
  
  		double dx = pos[3*constrainedAtom]-refPos[0];
  		double dy = pos[3*constrainedAtom+1]-refPos[1];
  		double dz = pos[3*constrainedAtom+2]-refPos[2];
  		double dist = Math.sqrt(dx*dx + dy*dy + dz*dz);
  		double prefactor = 0.0;
  		if(dist>d)
  			prefactor = dist-d;
  		else 
  			prefactor = 0.0;
  
  		double energy = 0.5*k*prefactor*prefactor;
  
  		if (detail != null)
  			detail.append(detailID+"\textPosConstraint\t"+DoubleFormat.toString(dist)+"\t"+DoubleFormat.toString(d)+"\tall\t"+ DoubleFormat.toString(energy)+"\n");
  
  		return energy;
  	}
  
  	@Override
  	public void getGradient(double[] pos, double[] grad) {
  			int a = constrainedAtom;
  			double dx = pos[3*a]-refPos[0];
  			double dy = pos[3*a+1]-refPos[1];
  			double dz = pos[3*a+2]-refPos[2];
  			double dist = Math.sqrt(dx*dx + dy*dy + dz*dz);
  			double prefactor = 0.0;
  			if(dist>d)
  				prefactor = dist-d;
  			else 
  				prefactor = 0.0;
  			grad[a] += prefactor*dx/Math.max(dist, 1E-08);
  			grad[a+1] += prefactor*dy/Math.max(dist, 1E-08);
  			grad[a+2] += prefactor*dz/Math.max(dist, 1E-08);
  	}
  }
  