package edu.sdsc.mbt.util;

import edu.sdsc.mbt.util.PeriodicTable;
import edu.sdsc.mbt.*;
import edu.sdsc.sirius.util.VectorSet;

public class ElementProperties {
	
	/**
	 * TODO there should be a clear difference between figures for atomic, ionic, covalent
	 * and Van der Walls radii of individual elements
	 */
	private static float elementColors[][];
	private static double atomRadii[];
	private static double ionRadii[];
	private static int elementValencies[][];
	private static int elementCount = 0;
	
	private static double[][] bondLengths;
	
	private static int geometryReference[];
	
	public static final int LINEAR = 0;
	public static final int TRIGONAL = 1;
	public static final int TETRAHEDRAL = 2;
	public static final int TRIGONAL_BIPYRAMIDAL = 3;
	public static final int OCTAHEDRAL = 4;
	
	private static int[] defaultValency = new int[]{ 1 };
	
	
	private static VectorSet bondGeometries[] = new VectorSet[5];//a reference table of different geometries numbered by integers

	static
	{
		elementCount = PeriodicTable.getElementCount( );
		elementValencies = new int[elementCount][];//since each element may have a set of possible valencies
		elementColors = new float[elementCount][3];
		atomRadii = new double[elementCount];
		ionRadii = new double[elementCount];
		geometryReference = new int[elementCount];//values are indices of geometry types

		// Initially set element colors to a medium gray
		for ( int i=0; i<elementCount; i++ )
			setElementColor( i, 0.7f, 0.7f, 0.7f );
		
		// Now, override the default color assignments
		setElementColor(  1, 1.00f, 1.00f, 1.00f );  // Hydrogen
		setElementColor(  2, 0.87f, 1.00f, 1.00f );  // Helium
		setElementColor(  3, 0.81f, 0.48f, 1.00f );  // Lithium
		setElementColor(  4, 0.78f, 1.00f, 0.00f );  // Beryllium
		setElementColor(  5, 1.00f, 0.71f, 0.71f );  // Boron
		setElementColor(  6, 0.60f, 0.60f, 0.60f );  // Carbon
		setElementColor(  7, 0.00f, 0.00f, 1.00f );  // Nitrogen
		setElementColor(  8, 1.00f, 0.00f, 0.00f );  // Oxygen
		setElementColor(  9, 0.71f, 1.00f, 1.00f );  // Flourine
		setElementColor( 10, 0.67f, 0.91f, 0.97f );  // Neon
		setElementColor( 11, 0.67f, 0.35f, 0.97f );  // Sodium
		setElementColor( 12, 0.55f, 1.00f, 0.00f );  // Magnesium
		setElementColor( 13, 0.84f, 0.65f, 0.65f );  // Aluminum
		setElementColor( 14, 0.52f, 0.61f, 0.61f );  // Silicon
		setElementColor( 15, 1.00f, 0.52f, 0.00f );  // Phosphorus
		setElementColor( 16, 1.00f, 0.81f, 0.19f );  // Sulfur
		setElementColor( 17, 0.13f, 0.97f, 0.13f );  // Chlorine
		setElementColor( 18, 0.51f, 0.84f, 0.91f );  // Argon
		setElementColor( 19, 0.55f, 0.26f, 0.84f );  // Potassium
		setElementColor( 20, 0.22f, 1.00f, 0.00f );  // Calcium
		setElementColor( 21, 0.88f, 0.88f, 0.88f );  // Sc
		setElementColor( 22, 0.75f, 0.75f, 0.75f );  // Ti
		setElementColor( 23, 0.63f, 0.63f, 0.66f );  // V
		setElementColor( 24, 0.53f, 0.60f, 0.75f );  // Cr
		setElementColor( 25, 0.60f, 0.47f, 0.75f );  // Mn
		setElementColor( 26, 0.52f, 0.48f, 0.78f );  // Iron
		setElementColor( 27, 0.44f, 0.47f, 0.75f );  // Co
		setElementColor( 28, 0.34f, 0.47f, 0.75f );  // Ni
		setElementColor( 29, 0.97f, 0.47f, 0.37f );  // Cu
		setElementColor( 30, 0.47f, 0.50f, 0.66f );  // Zn
		setElementColor( 31, 0.75f, 0.56f, 0.56f );  // Ga
		setElementColor( 32, 0.37f, 0.56f, 0.56f );  // Ge
		setElementColor( 33, 0.72f, 0.50f, 0.88f );  // As
		setElementColor( 34, 0.97f, 0.63f, 0.00f );  // Se
		setElementColor( 35, 0.63f, 0.16f, 0.16f );  // Br
		setElementColor( 36, 0.35f, 0.72f, 0.82f );  // Kr
		setElementColor( 37, 0.44f, 0.16f, 0.69f );  // Rb
		setElementColor( 38, 0.00f, 0.97f, 0.00f );  // Sr
		setElementColor( 39, 0.56f, 0.97f, 0.97f );  // Y
		setElementColor( 40, 0.56f, 0.88f, 0.88f );  // Zr
		setElementColor( 41, 0.44f, 0.75f, 0.78f );  // Nb
		setElementColor( 42, 0.31f, 0.69f, 0.69f );  // Mo
		setElementColor( 43, 0.22f, 0.60f, 0.66f );  // Tc
		setElementColor( 44, 0.12f, 0.53f, 0.56f );  // Ru
		setElementColor( 45, 0.03f, 0.47f, 0.53f );  // Rh
		setElementColor( 46, 0.00f, 0.40f, 0.50f );  // Pd
		setElementColor( 47, 0.60f, 0.75f, 0.97f );  // Ag
		setElementColor( 48, 0.97f, 0.85f, 0.56f );  // Cd
		setElementColor( 49, 0.67f, 0.44f, 0.44f );  // In
		setElementColor( 50, 0.38f, 0.50f, 0.50f );  // Sn
		setElementColor( 51, 0.60f, 0.38f, 0.69f );  // Sb
		setElementColor( 52, 0.82f, 0.47f, 0.00f );  // Te
		setElementColor( 53, 0.58f, 0.00f, 0.58f );  // Iodine
		setElementColor( 54, 0.25f, 0.60f, 0.69f );  // Xe
		setElementColor( 55, 0.31f, 0.10f, 0.53f );  // Cs
		setElementColor( 56, 0.00f, 0.78f, 0.00f );  // Ba
		setElementColor( 57, 0.44f, 0.85f, 0.97f );  // La
		setElementColor( 58, 0.97f, 0.97f, 0.78f );  // Ce
		setElementColor( 59, 0.85f, 0.97f, 0.78f );  // Pr
		setElementColor( 60, 0.75f, 0.97f, 0.78f );  // Nd
		setElementColor( 61, 0.63f, 0.97f, 0.78f );  // Pm
		setElementColor( 62, 0.56f, 0.97f, 0.78f );  // Sm
		setElementColor( 63, 0.38f, 0.97f, 0.78f );  // Eu
		setElementColor( 64, 0.25f, 0.97f, 0.78f );  // Gd
		setElementColor( 65, 0.19f, 0.97f, 0.78f );  // Tb
		setElementColor( 66, 0.09f, 0.97f, 0.69f );  // Dy
		setElementColor( 67, 0.00f, 0.97f, 0.60f );  // Ho
		setElementColor( 68, 0.00f, 0.88f, 0.44f );  // Er
		setElementColor( 69, 0.00f, 0.82f, 0.31f );  // Tm
		setElementColor( 70, 0.00f, 0.75f, 0.22f );  // Yb
		setElementColor( 71, 0.00f, 0.66f, 0.13f );  // Lu
		setElementColor( 72, 0.28f, 0.75f, 0.97f );  // Hf
		setElementColor( 73, 0.28f, 0.63f, 0.97f );  // Ta
		setElementColor( 74, 0.13f, 0.56f, 0.82f );  // W
		setElementColor( 75, 0.13f, 0.47f, 0.66f );  // Re
		setElementColor( 76, 0.13f, 0.41f, 0.56f );  // Os
		setElementColor( 77, 0.09f, 0.31f, 0.50f );  // Ir
		setElementColor( 78, 0.09f, 0.35f, 0.56f );  // Pt
		setElementColor( 79, 0.97f, 0.82f, 0.13f );  // Au
		setElementColor( 80, 0.69f, 0.69f, 0.76f );  // Hg
		setElementColor( 81, 0.63f, 0.31f, 0.28f );  // Tl
		setElementColor( 82, 0.31f, 0.35f, 0.38f );  // Pb
		setElementColor( 83, 0.60f, 0.28f, 0.69f );  // Bi
		setElementColor( 84, 0.66f, 0.35f, 0.00f );  // Po
		setElementColor( 85, 0.44f, 0.28f, 0.25f );  // At
		setElementColor( 86, 0.25f, 0.50f, 0.56f );  // Rn
		setElementColor( 87, 0.25f, 0.00f, 0.38f );  // Fr
		setElementColor( 88, 0.00f, 0.47f, 0.00f );  // Ra
		setElementColor( 89, 0.44f, 0.66f, 0.97f );  // Ac
		setElementColor( 90, 0.00f, 0.72f, 0.97f );  // Th
		setElementColor( 91, 0.00f, 0.63f, 0.97f );  // Pa
		setElementColor( 92, 0.00f, 0.56f, 0.97f );  // U
		setElementColor( 93, 0.00f, 0.50f, 0.94f );  // Np
		setElementColor( 94, 0.00f, 0.41f, 0.94f );  // Pu
		setElementColor( 95, 0.31f, 0.34f, 0.94f );  // Am
		setElementColor( 96, 0.47f, 0.35f, 0.88f );  // Cm
		setElementColor( 97, 0.53f, 0.28f, 0.88f );  // Bk
		setElementColor( 98, 0.63f, 0.19f, 0.82f );  // Cf
		setElementColor( 99, 0.69f, 0.09f, 0.82f );  // Es
		setElementColor( 100, 0.69f, 0.09f, 0.72f );  // Fm
		setElementColor( 101, 0.69f, 0.03f, 0.63f );  // Md
		setElementColor( 102, 0.72f, 0.03f, 0.50f );  // No
		setElementColor( 103, 0.78f, 0.00f, 0.38f );  // Lr
		setElementColor( 103, 0.78f, 0.00f, 0.38f );  // Lr
		setElementColor( 0, 1.0f, 0.40f, 0.8f );  // EP
	/*
		TODO: Need to complete entry of element colors.
		setElementColor( 104, 0.00f, 0.00f, 0.00f );  // Rf
		setElementColor( 105, 0.00f, 0.00f, 0.00f );  // Db
		setElementColor( 106, 0.00f, 0.00f, 0.00f );  // Sg
		setElementColor( 107, 0.00f, 0.00f, 0.00f );  // Bh
		setElementColor( 108, 0.00f, 0.00f, 0.00f );  // Hs
		setElementColor( 109, 0.00f, 0.00f, 0.00f );  // Mt
		setElementColor( 110, 0.00f, 0.00f, 0.00f );  // Ds
		setElementColor( 111, 0.00f, 0.00f, 0.00f );  // Uuu
		setElementColor( 112, 0.00f, 0.00f, 0.00f );  // Uub
		setElementColor( 113, 0.00f, 0.00f, 0.00f );  // Uut
		setElementColor( 114, 0.00f, 0.00f, 0.00f );  // Uuq
		setElementColor( 115, 0.00f, 0.00f, 0.00f );  // Uup
		setElementColor( 116, 0.00f, 0.00f, 0.00f );  // Uuh
		setElementColor( 117, 0.00f, 0.00f, 0.00f );  // Uus
		setElementColor( 118, 0.00f, 0.00f, 0.00f );  // Uuo
	*/

		//
		// Element Radii
		//

		// Initially set element radii to 2.0
		for ( int i=0; i<elementCount; i++ )
			atomRadii[i] = 2.0;

		// Common elements get set to Van Der Waals Radii
		// http://www.ccdc.cam.ac.uk/prods/mercury/docs/mercury/PortableHTML/mercurydocn122.html
		atomRadii[0]   = 1.00;  // EP
		atomRadii[1]   = 1.20;  // Hydrogen
		atomRadii[2]   = 1.40;  // Helium
		atomRadii[3]   = 1.82;  // Lithium
		atomRadii[4]   = 2.00;  // Beryllium
		atomRadii[5]   = 2.00;  // Boron
		atomRadii[6]   = 1.70;  // Carbon
		atomRadii[7]   = 1.55;  // Nitrogen
		atomRadii[8]   = 1.52;  // Oxygen
		atomRadii[9]   = 1.47;  // Fluorine
		atomRadii[10]  = 1.54;  // Neon
		atomRadii[11]  = 2.27;  // Sodium
		atomRadii[12]  = 1.73;  // Magnesium
		atomRadii[13]  = 2.00;  // Aluminum
		atomRadii[14]  = 2.10;  // Silicon
		atomRadii[15]  = 1.80;  // Phosphorus
		atomRadii[16]  = 1.80;  // Sulfur
		atomRadii[17]  = 1.75;  // Chlorine
		atomRadii[18]  = 1.88;  // Argon
		atomRadii[19]  = 2.75;  // Potassium
		atomRadii[20]  = 2.00;  // Calcium
		// non-contiguous
		atomRadii[26]  = 1.8;	// Iron
		atomRadii[28]  = 1.63;  // Nickel
		atomRadii[29]  = 1.40;  // Copper
		atomRadii[30]  = 1.39;  // Zinc
		atomRadii[31]  = 1.87;  // Gallium
		atomRadii[33]  = 1.85;  // Arsenic
		atomRadii[34]  = 1.90;  // Selenium
		atomRadii[35]  = 1.85;  // Bromine
		atomRadii[36]  = 2.02;  // Krypton
		atomRadii[46]  = 1.63;  // Palladium
		atomRadii[47]  = 1.72;  // Silver
		atomRadii[48]  = 1.58;  // Cadmium
		atomRadii[49]  = 1.93;  // Indium
		atomRadii[50]  = 2.17;  // Tin
		atomRadii[52]  = 2.06;  // Tellurium
		atomRadii[53]  = 1.98;  // Iodine
		atomRadii[54]  = 2.16;  // Xenon
		atomRadii[78]  = 1.72;  // Platinum
		atomRadii[79]  = 1.66;  // Gold
	/*
		TODO: Need to complete entry of element radii.
		atomRadii[80]  = 1.55;  // Mercury
		atomRadii[81]  = 1.96;  // Thallium
		atomRadii[82]  = 2.02;  // Lead
		atomRadii[92]  = 1.86;  // Uranium
	*/

	
		for ( int i=0; i<elementCount; i++ )
			ionRadii[i] = 2.0;
		
			ionRadii[3] = 0.68;
			ionRadii[9] = 1.28;
			ionRadii[11] = 0.97;
			ionRadii[17] = 1.81;
			ionRadii[19] = 1.35;
			ionRadii[35] = 1.97;
			ionRadii[53] = 2.2;
			

	
		
		for (int i = 0; i < elementCount; i++){
			int temp[] = new int[]{ 1 };
			elementValencies[i] = temp;
		}
		
		//for some elements, valencies are known
		elementValencies[0] = new int[]{ 1 };//EP
		elementValencies[4] = new int[]{ 2 };//Be
		elementValencies[6] = new int[]{ 4 };//C
		elementValencies[7] = new int[]{ 3, 5 };//N
		elementValencies[8] = new int[]{ 2 };//O
		elementValencies[12] = new int[]{ 2 };//Mg
		elementValencies[13] = new int[]{ 3 };//Al
		elementValencies[14] = new int[]{ 4 };//Si
		elementValencies[15] = new int[]{ 5 };//P
		elementValencies[16] = new int[]{ 2, 4, 6 };//S
		elementValencies[20] = new int[]{ 2 };//Ca
		elementValencies[21] = new int[]{ 3 };//Sc
		elementValencies[22] = new int[]{ 4 };//Ti
		elementValencies[23] = new int[]{ 3, 5 };//V
		elementValencies[24] = new int[]{ 2, 4, 6, 7 };//Cr
		elementValencies[26] = new int[]{ 2, 3 };//Fe
		
		//bond geometries
		//linear
		VectorSet temp1 = new VectorSet();
		temp1.addVector(new double[]{ 0.0, 0.0, 1.0 });
		temp1.addVector(new double[]{ -1.0, 0.0, 0.0 });
		temp1.addVector(new double[]{ 1.0, 0.0, 0.0 });
		bondGeometries[LINEAR] = temp1;
		
		//trigonal
		VectorSet temp2 = new VectorSet();
		temp2.addVector(new double[]{ 0.0, 0.0, 1.0 });
		temp2.addVector(new double[]{ 1.0, 0.0, 0.0 });
		temp2.addVector(new double[]{ -0.5, 0.866, 0.0 });
		temp2.addVector(new double[]{ -0.5, -0.866, 0.0 });
		bondGeometries[TRIGONAL] = temp2;
		
		//tetrahedron
		VectorSet temp3 = new VectorSet();
		temp3.addVector(new double[]{ 0.7071, 0.7071, 0 });//normal to the first two bonds
		temp3.addVector(new double[]{ -0.57735, 0.57735, 0.57735});
		temp3.addVector(new double[]{ 0.57735, -0.57735, 0.57735});
		temp3.addVector(new double[]{ 0.57735, 0.57735, -0.57735});
		temp3.addVector(new double[]{ -0.57735, -0.57735, -0.57735});
		bondGeometries[TETRAHEDRAL] = temp3;
		
		//trigonal bipyramid
		VectorSet temp4 = new VectorSet();
		temp4.addVector(new double[]{ 0.0, 0.0, 1.0 });
		temp4.addVector(new double[]{ 1.0, 0.0, 0.0 });
		temp4.addVector(new double[]{ -0.5, 0.866, 0.0 });
		temp4.addVector(new double[]{ -0.5, -0.866, 0.0 });
		temp4.addVector(new double[]{ 0.0, 0.0, 1.0 });
		temp4.addVector(new double[]{ 0.0, 0.0, -1.0 });
		bondGeometries[TRIGONAL_BIPYRAMIDAL] = temp4;
		
		//octahedral
		VectorSet temp5 = new VectorSet();
		temp5.addVector(new double[]{ 0.0, 0.0, 1.0 });
		temp5.addVector(new double[]{ 0.57735, 0.57735, 0.0 });
		temp5.addVector(new double[]{ -0.57735, 0.57735, 0.0 });
		temp5.addVector(new double[]{ 0.57735, -0.57735, 0.0 });
		temp5.addVector(new double[]{ -0.57735, -0.57735, 0.0 });
		temp5.addVector(new double[]{ 0.0, 0.0, 1.0 });
		temp5.addVector(new double[]{ 0.0, 0.0, -1.0 });
		bondGeometries[OCTAHEDRAL] = temp5;
		
		//default geometry will be tetrahedron
		for ( int i=0; i<elementCount; i++ )
			geometryReference[i] = TETRAHEDRAL;
		
		
		/**
		 * TODO add specifics that depend on valency, such as N being tetrahedral with 3 ligands
		 * and trigonal bipyramidal with 5.
		 */
		
		//NOTE: bond lengths are given in angstroms
		
		//populate the bond length arrays
		bondLengths = new double[elementCount][elementCount];
		for (int i = 0; i < elementCount; i++){
			for (int j = 0; j < elementCount; j++){
				bondLengths[i][j] = 1.7;//the default
			}
		}
		
		bondLengths[1][1] = 0.74;
		bondLengths[1][5] = 1.19;
		bondLengths[1][6] = 1.09;
		bondLengths[1][14] = 1.48;
		bondLengths[1][32] = 1.53;
		bondLengths[1][50] = 1.7;
		bondLengths[1][7] = 1.01;
		bondLengths[1][15] = 1.44;
		bondLengths[1][33] = 1.52;
		bondLengths[1][8] = 0.96;
		bondLengths[1][16] = 1.34;
		bondLengths[1][34] = 1.46;
		bondLengths[1][9] = 0.92;
		bondLengths[1][17] = 1.27;
		bondLengths[1][35] = 1.41;
		bondLengths[1][52] = 1.61;

		bondLengths[5][1] = 1.19;
		bondLengths[6][1] = 1.09;
		bondLengths[14][1] = 1.48;
		bondLengths[32][1] = 1.53;
		bondLengths[50][1] = 1.7;
		bondLengths[7][1] = 1.01;
		bondLengths[15][1] = 1.44;
		bondLengths[33][1] = 1.52;
		bondLengths[8][1] = 0.96;
		bondLengths[16][1] = 1.34;
		bondLengths[34][1] = 1.46;
		bondLengths[9][1] = 0.92;
		bondLengths[17][1] = 1.27;
		bondLengths[35][1] = 1.41;
		bondLengths[52][1] = 1.61;
		
		

		
		bondLengths[7][7] = 1.45;
		bondLengths[7][8] = 1.4;
		bondLengths[8][7] = 1.4;
		bondLengths[7][9] = 1.36;
		bondLengths[9][7] = 1.36;
		bondLengths[7][17] = 1.75;
		bondLengths[17][7] = 1.75;
		bondLengths[15][15] = 2.21;
		bondLengths[15][8] = 1.63;
		bondLengths[8][15] = 1.63;
		bondLengths[15][9] = 1.54;
		bondLengths[9][15] = 1.54;
		bondLengths[15][17] = 2.03;
		bondLengths[17][15] = 2.03;
		
		bondLengths[6][6] = 1.54;
		bondLengths[6][14] = 1.85;
		bondLengths[14][6] = 1.85;
		bondLengths[6][7] = 1.47;
		bondLengths[7][6] = 1.47;
		bondLengths[6][15] = 1.84;
		bondLengths[15][6] = 1.84;
		bondLengths[6][8] = 1.43;
		bondLengths[8][6] = 1.43;
		bondLengths[6][16] = 1.82;
		bondLengths[16][6] = 1.82;
		bondLengths[6][9] = 1.35;
		bondLengths[9][6] = 1.35;
		bondLengths[6][17] = 1.77;
		bondLengths[17][6] = 1.77;
		bondLengths[6][35] = 1.94;
		bondLengths[35][6] = 1.94;
		bondLengths[6][53] = 2.14;
		bondLengths[53][6] = 2.14;
	
		bondLengths[8][8] = 1.48;
		bondLengths[8][9] = 1.42;
		bondLengths[9][8] = 1.42;
		bondLengths[16][16] = 2.05;
		bondLengths[16][9] = 1.56;
		bondLengths[9][16] = 1.56;
		bondLengths[16][17] = 2.07;
		bondLengths[17][16] = 2.07;
		
		bondLengths[14][8] = 1.63;
		bondLengths[8][14] = 1.63;
	
		bondLengths[9][9] = 1.42;
		bondLengths[17][17] = 1.99;
		bondLengths[35][35] = 2.28;
		bondLengths[53][53] = 2.67;
	
	};
	
	
	/**
	 * Get the number of elements for which style information is
	 * represented by this class.
	 */
	public static int getElementCount( )
	{
		return elementCount;
	}
	
	public static double getBondLength(int e1, int e2){
		return bondLengths[e1][e2];
	}

	public static double getBondLength(short e1, short e2){
		return bondLengths[(int)e1][(int)e2];
	}

	//
	// Color methods
	//

	/**
	 * Set the RGB color of the given element number.
	 * Color components are clamped between 0.0 and 1.0.
	 */
	public static void setElementColor( int number, float r, float g, float b )
	{
		
		if ( r < 0.0f ) r = 0.0f;
		if ( r > 1.0f ) r = 1.0f;
		if ( g < 0.0f ) g = 0.0f;
		if ( g > 1.0f ) g = 1.0f;
		if ( b < 0.0f ) b = 0.0f;
		if ( b > 1.0f ) b = 1.0f;
		
		elementColors[number][0] = r;
		elementColors[number][1] = g;
		elementColors[number][2] = b;
	}

	/**
	 * Set the RGB color of the given element name.
	 * Color components are clamped between 0.0 and 1.0.
	 */
	public static void setElementColor( String name, float r, float g, float b )
	{
		setElementColor( PeriodicTable.getElementNumber(name), r, g, b );
	}

	/**
	 * Get the RGB color of the given element number.
	 * Color components are clamped between 0.0 and 1.0.
	 */
	public static float[] getElementColor( int number )
	{
		if ( number < 0 ) return null;
		if ( number >= elementColors.length ) return null;
		return elementColors[number];
	}

	/**
	 * Get the RGB color of the given element name.
	 * Color components are clamped between 0.0 and 1.0.
	 */
	public static float[] getElementColor( String name )
	{
		int number = PeriodicTable.getElementNumber( name );
		if ( number < 0 ) return null;
		if ( number >= elementColors.length ) return null;
		return elementColors[ number ];
	}

	//
	// Radius methods
	//

	/**
	 * Set the radius of the given element number.
	 * Radius values are constrained to be non-negative.
	 */
	public static void setAtomRadius( int number, double radius )
	{
		if ( radius < 0.0 ) radius = 0.0;
		atomRadii[number] = radius;
	}

	/**
	 * Set the radius of the given element name.
	 * Radius values are constrained to be non-negative.
	 */
	public static void setAtomRadius( String name, double radius )
	{
		setAtomRadius( PeriodicTable.getElementNumber(name), radius );
	}

	/**
	 * Get the radius of the given element number.
	 * Radius values are constrained to be non-negative.
	 */
	public static double getAtomRadius( int number ){
		if (number < 0 || number > atomRadii.length-1) return 1.0;
		return atomRadii[number];
	}
	
	public static double getIonRadius( int number ){
		return ionRadii[number];
	}
	
	public static void setIonRadius( String name, double radius )
	{
		setIonRadius( PeriodicTable.getElementNumber(name), radius );
	}

	public static void setIonRadius( int number, double radius )
	{
		if ( radius < 0.0 ) radius = 0.0;
		ionRadii[number] = radius;
	}


	/**
	 * Get the radius of the given element name.
	 * Radius values are constrained to be non-negative.
	 */
	public static double getAtomRadius( String name )
	{
		return atomRadii[ PeriodicTable.getElementNumber(name) ];
	}
	
	public static double getAtomRadius(short index){
		return atomRadii[index];
	}
	
	/**
	 * Sets element colors to their default values
	 *
	 */
	public static void setDefaultElementColors(){
		// Initially set element colors to a medium gray
		for ( int i=0; i<elementCount; i++ )
			setElementColor( i, 0.7f, 0.7f, 0.7f );
		
		// Now, override the default color assignments
		setElementColor(  1, 1.00f, 1.00f, 1.00f );  // Hydrogen
		setElementColor(  2, 0.87f, 1.00f, 1.00f );  // Helium
		setElementColor(  3, 0.81f, 0.48f, 1.00f );  // Lithium
		setElementColor(  4, 0.78f, 1.00f, 0.00f );  // Beryllium
		setElementColor(  5, 1.00f, 0.71f, 0.71f );  // Boron
		setElementColor(  6, 0.60f, 0.60f, 0.60f );  // Carbon
		setElementColor(  7, 0.00f, 0.00f, 1.00f );  // Nitrogen
		setElementColor(  8, 1.00f, 0.00f, 0.00f );  // Oxygen
		setElementColor(  9, 0.71f, 1.00f, 1.00f );  // Flourine
		setElementColor( 10, 0.67f, 0.91f, 0.97f );  // Neon
		setElementColor( 11, 0.67f, 0.35f, 0.97f );  // Sodium
		setElementColor( 12, 0.55f, 1.00f, 0.00f );  // Magnesium
		setElementColor( 13, 0.84f, 0.65f, 0.65f );  // Aluminum
		setElementColor( 14, 0.52f, 0.61f, 0.61f );  // Silicon
		setElementColor( 15, 1.00f, 0.52f, 0.00f );  // Phosphorus
		setElementColor( 16, 1.00f, 0.81f, 0.19f );  // Sulfur
		setElementColor( 17, 0.13f, 0.97f, 0.13f );  // Chlorine
		setElementColor( 18, 0.51f, 0.84f, 0.91f );  // Argon
		setElementColor( 19, 0.55f, 0.26f, 0.84f );  // Potassium
		setElementColor( 20, 0.22f, 1.00f, 0.00f );  // Calcium
		setElementColor( 21, 0.88f, 0.88f, 0.88f );  // Sc
		setElementColor( 22, 0.75f, 0.75f, 0.75f );  // Ti
		setElementColor( 23, 0.63f, 0.63f, 0.66f );  // V
		setElementColor( 24, 0.53f, 0.60f, 0.75f );  // Cr
		setElementColor( 25, 0.60f, 0.47f, 0.75f );  // Mn
		setElementColor( 26, 0.52f, 0.48f, 0.78f );  // Iron
		setElementColor( 27, 0.44f, 0.47f, 0.75f );  // Co
		setElementColor( 28, 0.34f, 0.47f, 0.75f );  // Ni
		setElementColor( 29, 0.97f, 0.47f, 0.37f );  // Cu
		setElementColor( 30, 0.47f, 0.50f, 0.66f );  // Zn
		setElementColor( 31, 0.75f, 0.56f, 0.56f );  // Ga
		setElementColor( 32, 0.37f, 0.56f, 0.56f );  // Ge
		setElementColor( 33, 0.72f, 0.50f, 0.88f );  // As
		setElementColor( 34, 0.97f, 0.63f, 0.00f );  // Se
		setElementColor( 35, 0.63f, 0.16f, 0.16f );  // Br
		setElementColor( 36, 0.35f, 0.72f, 0.82f );  // Kr
		setElementColor( 37, 0.44f, 0.16f, 0.69f );  // Rb
		setElementColor( 38, 0.00f, 0.97f, 0.00f );  // Sr
		setElementColor( 39, 0.56f, 0.97f, 0.97f );  // Y
		setElementColor( 40, 0.56f, 0.88f, 0.88f );  // Zr
		setElementColor( 41, 0.44f, 0.75f, 0.78f );  // Nb
		setElementColor( 42, 0.31f, 0.69f, 0.69f );  // Mo
		setElementColor( 43, 0.22f, 0.60f, 0.66f );  // Tc
		setElementColor( 44, 0.12f, 0.53f, 0.56f );  // Ru
		setElementColor( 45, 0.03f, 0.47f, 0.53f );  // Rh
		setElementColor( 46, 0.00f, 0.40f, 0.50f );  // Pd
		setElementColor( 47, 0.60f, 0.75f, 0.97f );  // Ag
		setElementColor( 48, 0.97f, 0.85f, 0.56f );  // Cd
		setElementColor( 49, 0.67f, 0.44f, 0.44f );  // In
		setElementColor( 50, 0.38f, 0.50f, 0.50f );  // Sn
		setElementColor( 51, 0.60f, 0.38f, 0.69f );  // Sb
		setElementColor( 52, 0.82f, 0.47f, 0.00f );  // Te
		setElementColor( 53, 0.58f, 0.00f, 0.58f );  // Iodine
		setElementColor( 54, 0.25f, 0.60f, 0.69f );  // Xe
		setElementColor( 55, 0.31f, 0.10f, 0.53f );  // Cs
		setElementColor( 56, 0.00f, 0.78f, 0.00f );  // Ba
		setElementColor( 57, 0.44f, 0.85f, 0.97f );  // La
		setElementColor( 58, 0.97f, 0.97f, 0.78f );  // Ce
		setElementColor( 59, 0.85f, 0.97f, 0.78f );  // Pr
		setElementColor( 60, 0.75f, 0.97f, 0.78f );  // Nd
		setElementColor( 61, 0.63f, 0.97f, 0.78f );  // Pm
		setElementColor( 62, 0.56f, 0.97f, 0.78f );  // Sm
		setElementColor( 63, 0.38f, 0.97f, 0.78f );  // Eu
		setElementColor( 64, 0.25f, 0.97f, 0.78f );  // Gd
		setElementColor( 65, 0.19f, 0.97f, 0.78f );  // Tb
		setElementColor( 66, 0.09f, 0.97f, 0.69f );  // Dy
		setElementColor( 67, 0.00f, 0.97f, 0.60f );  // Ho
		setElementColor( 68, 0.00f, 0.88f, 0.44f );  // Er
		setElementColor( 69, 0.00f, 0.82f, 0.31f );  // Tm
		setElementColor( 70, 0.00f, 0.75f, 0.22f );  // Yb
		setElementColor( 71, 0.00f, 0.66f, 0.13f );  // Lu
		setElementColor( 72, 0.28f, 0.75f, 0.97f );  // Hf
		setElementColor( 73, 0.28f, 0.63f, 0.97f );  // Ta
		setElementColor( 74, 0.13f, 0.56f, 0.82f );  // W
		setElementColor( 75, 0.13f, 0.47f, 0.66f );  // Re
		setElementColor( 76, 0.13f, 0.41f, 0.56f );  // Os
		setElementColor( 77, 0.09f, 0.31f, 0.50f );  // Ir
		setElementColor( 78, 0.09f, 0.35f, 0.56f );  // Pt
		setElementColor( 79, 0.97f, 0.82f, 0.13f );  // Au
		setElementColor( 80, 0.69f, 0.69f, 0.76f );  // Hg
		setElementColor( 81, 0.63f, 0.31f, 0.28f );  // Tl
		setElementColor( 82, 0.31f, 0.35f, 0.38f );  // Pb
		setElementColor( 83, 0.60f, 0.28f, 0.69f );  // Bi
		setElementColor( 84, 0.66f, 0.35f, 0.00f );  // Po
		setElementColor( 85, 0.44f, 0.28f, 0.25f );  // At
		setElementColor( 86, 0.25f, 0.50f, 0.56f );  // Rn
		setElementColor( 87, 0.25f, 0.00f, 0.38f );  // Fr
		setElementColor( 88, 0.00f, 0.47f, 0.00f );  // Ra
		setElementColor( 89, 0.44f, 0.66f, 0.97f );  // Ac
		setElementColor( 90, 0.00f, 0.72f, 0.97f );  // Th
		setElementColor( 91, 0.00f, 0.63f, 0.97f );  // Pa
		setElementColor( 92, 0.00f, 0.56f, 0.97f );  // U
		setElementColor( 93, 0.00f, 0.50f, 0.94f );  // Np
		setElementColor( 94, 0.00f, 0.41f, 0.94f );  // Pu
		setElementColor( 95, 0.31f, 0.34f, 0.94f );  // Am
		setElementColor( 96, 0.47f, 0.35f, 0.88f );  // Cm
		setElementColor( 97, 0.53f, 0.28f, 0.88f );  // Bk
		setElementColor( 98, 0.63f, 0.19f, 0.82f );  // Cf
		setElementColor( 99, 0.69f, 0.09f, 0.82f );  // Es
		setElementColor( 100, 0.69f, 0.09f, 0.72f );  // Fm
		setElementColor( 101, 0.69f, 0.03f, 0.63f );  // Md
		setElementColor( 102, 0.72f, 0.03f, 0.50f );  // No
		setElementColor( 103, 0.78f, 0.00f, 0.38f );  // Lr
		setElementColor( 0, 1.0f, 0.40f, 0.8f );  // EP
	/*
		TODO: Need to complete entry of element colors.
		setElementColor( 104, 0.00f, 0.00f, 0.00f );  // Rf
		setElementColor( 105, 0.00f, 0.00f, 0.00f );  // Db
		setElementColor( 106, 0.00f, 0.00f, 0.00f );  // Sg
		setElementColor( 107, 0.00f, 0.00f, 0.00f );  // Bh
		setElementColor( 108, 0.00f, 0.00f, 0.00f );  // Hs
		setElementColor( 109, 0.00f, 0.00f, 0.00f );  // Mt
		setElementColor( 110, 0.00f, 0.00f, 0.00f );  // Ds
		setElementColor( 111, 0.00f, 0.00f, 0.00f );  // Uuu
		setElementColor( 112, 0.00f, 0.00f, 0.00f );  // Uub
		setElementColor( 113, 0.00f, 0.00f, 0.00f );  // Uut
		setElementColor( 114, 0.00f, 0.00f, 0.00f );  // Uuq
		setElementColor( 115, 0.00f, 0.00f, 0.00f );  // Uup
		setElementColor( 116, 0.00f, 0.00f, 0.00f );  // Uuh
		setElementColor( 117, 0.00f, 0.00f, 0.00f );  // Uus
		setElementColor( 118, 0.00f, 0.00f, 0.00f );  // Uuo
	*/


	}

	public static int[] getElementValency(int number){
		return elementValencies[number];
	}
	
	public static int[] getElementValency(String symbol){
		int n = PeriodicTable.getElementNumber(symbol);
		if (n < 0) return null;
		return elementValencies[ n ];
	}
	
	public static int[] getElementValency(short index){
		
		if (index < 0 || index >= elementValencies.length) return defaultValency;
		return elementValencies[(int)index];
	}

	
	public static VectorSet getBondGeometry(Atom atom){
		
		if (atom.hybridization != Atom.SP3){
			/**
			 * TODO a dirty hack to correctly handle phosphates in nucleic acids.
			 * Will need a more general mechanism for dealing with geometries around
			 * different elements in various hybridization states...
			 */
			if (atom.element == 15)return bondGeometries[TETRAHEDRAL].copy();
			if (atom.hybridization == Atom.SP2){
				return bondGeometries[TRIGONAL].copy();
			}
			else if (atom.hybridization == Atom.SP){
				return bondGeometries[LINEAR].copy();
			}
			return bondGeometries[TETRAHEDRAL].copy();
		}
		else{
			int index = geometryReference[ (int)atom.element ];
			if (index < LINEAR && index > OCTAHEDRAL) return bondGeometries[TETRAHEDRAL].copy();
			return bondGeometries[index].copy();
		}
	}

}