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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on 29.04.2010
*
*/
package org.biojava.nbio.structure;
import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
/**
* Element is an enumeration of the elements of the periodic table. In addition,
* several attributes of each element are accessible.
* Note: Deuterium and Tritium are treated as separate elements D and T,
* respectively. Sometimes part of a molecule is represented as an R-group, which
* is represented as the element R.
*
*
* @author Peter Rose
* @version %I% %G%
* @since 3.0
*
*/
public enum Element implements Serializable {
// most frequently used elements first
H(1, 1, 39, 1.10f, 0.32f, 1, 1, 1, 1, 1, 1.008f, 0, 1, new int[] {1}, 2.20f, ElementType.OTHER_NONMETAL),
C(6, 2, 0, 1.55f, 0.77f, 4, 4, 4, 4, 4, 12.011f, 2, -4, new int[] {-4,-3,-2,0,-1,1,2,3,4}, 2.55f, ElementType.OTHER_NONMETAL),
N(7, 2, 57, 1.40f, 0.75f, 5, 2, 5, 3, 4, 14.007f, 2, -3, new int[] {-3,-2,-1,0,1,2,3,4,5}, 3.04f, ElementType.OTHER_NONMETAL),
O(8, 2, 65, 1.35f, 0.73f, 6, 1, 2, 2, 2, 16.000f, 2, -2, new int[] {-2,-1,0,1,2}, 3.44f, ElementType.OTHER_NONMETAL),
/**
* Deuterium
*/
D(1, 1, 27, 1.10f, 0.32f, 1, 1, 1, 1, 1, 1.008f, 0, 1, new int[] {0,1}, 2.20f, ElementType.OTHER_NONMETAL), // need to edit properties!
/**
* Tritium
*/
T(1, 1, 90, 1.10f, 0.32f, 1, 1, 1, 1, 1, 1.008f, 0, 1, new int[] {0,1}, 2.20f, ElementType.OTHER_NONMETAL), // need to edit properties!
He(2, 1, 40, 2.20f, 1.60f, 2, 0, 12, 0, 0, 4.003f, 2, 0, new int[] {0}, 0.0f, ElementType.NOBLE_GAS), // electroneg not reported
Li(3, 2, 50, 1.22f, 1.34f, 1, 0, 12, 0, 1, 6.940f, 2, 1, new int[] {0,1}, 0.98f, ElementType.ALKALI_METAL),
Be(4, 2, 12, 0.63f, 0.90f, 2, 0, 12, 2, 2, 9.012f, 2, 2, new int[] {0,1,2}, 1.57f, ElementType.TRANSITION_METAL),
B(5, 2, 10, 1.55f, 0.82f, 3, 3, 5, 3, 4, 10.810f, 2, 3, new int[] {0,1,2,3}, 2.04f, ElementType.METALLOID),
F(9, 2, 32, 1.30f, 0.72f, 7, 0, 1, 1, 1, 18.998f, 2, -1, new int[] {-1,0,1}, 3.98f, ElementType.HALOGEN),
Ne(10, 2, 61, 2.02f, 1.12f, 8, 0, 12, 0, 0, 20.170f, 10, 0, new int[] {}, 0.00f, ElementType.NOBLE_GAS), // electroneg not reported
Na(11, 3, 58, 2.20f, 1.54f, 1, 0, 1, 0, 0, 22.990f, 10, 1, new int[] {-1,0,1}, 0.93f, ElementType.ALKALI_METAL),
Mg(12, 3, 54, 1.50f, 1.30f, 2, 0, 2, 0, 2, 24.305f, 10, 2, new int[] {0,1,2}, 1.31f, ElementType.ALKALINE_EARTH_METAL),
Al(13, 3, 4, 1.50f, 1.18f, 3, 0, 5, 0, 4, 26.982f, 10, 3, new int[] {0,1,2,3}, 1.61f, ElementType.POST_TRANSITION_METAL),
Si(14, 3, 86, 2.20f, 1.11f, 4, 4, 4, 4, 4, 28.086f, 10, 4, new int[] {-4,-3,-2,-1,0,1,2,3,4}, 1.90f, ElementType.METALLOID),
P(15, 3, 67, 1.88f, 1.06f, 5, 3, 5, 3, 5, 30.974f, 10, 5, new int[] {-3,-2,-1,0,1,2,3,4,5}, 2.19f, ElementType.OTHER_NONMETAL),
S(16, 3, 82, 1.81f, 1.02f, 6, 2, 6, 2, 6, 32.060f, 10, -2, new int[] {-2,-1,0,1,2,3,4,5,6}, 2.58f, ElementType.OTHER_NONMETAL),
Cl(17, 3, 21, 1.75f, 0.99f, 7, 0, 1, 1, 1, 35.453f, 10, -1, new int[] {-1,0,1,2,3,4,5,6,7}, 3.16f, ElementType.HALOGEN),
Ar(18, 4, 6, 2.77f, 1.54f, 8, 0, 12, 0, 0, 39.948f, 18, 0, new int[] {0}, 0.00f, ElementType.NOBLE_GAS), // electroneg not reported
K(19, 4, 47, 2.39f, 1.96f, 1, 0, 12, 0, 0, 39.102f, 18, 1, new int[] {-1,0,1}, 0.82f, ElementType.ALKALI_METAL),
Ca(20, 4, 17, 1.95f, 1.74f, 2, 0, 2, 0, 0, 40.080f, 18, 2, new int[] {0,1,2}, 1.00f, ElementType.ALKALINE_EARTH_METAL),
Sc(21, 4, 84, 1.32f, 1.44f, 3, 0, 12, 3, 0, 44.956f, 18, 3, new int[] {0,1,2,3}, 1.36f, ElementType.TRANSITION_METAL),
Ti(22, 4, 96, 1.95f, 1.36f, 4, 2, 4, 3, 4, 47.880f, 18, 4, new int[] {-1,0,1,2,3,4}, 1.54f, ElementType.TRANSITION_METAL),
V(23, 4, 100, 1.06f, 1.25f, 5, 0, 12, 3, 0, 50.040f, 18, 5, new int[] {-1,0,1,2,3,4,5}, 1.63f, ElementType.TRANSITION_METAL),
Cr(24, 4, 24, 1.13f, 1.27f, 6, 0, 12, 2, 0, 51.996f, 18, 3, new int[] {-2,-1,0,1,2,3,4,5,6}, 1.66f, ElementType.TRANSITION_METAL),
Mn(25, 4, 55, 1.19f, 1.39f, 7, 0, 12, 0, 0, 54.938f, 18, 2, new int[] {-3,-2,-1,0,1,2,3,4,5,6,7}, 1.55f, ElementType.TRANSITION_METAL),
Fe(26, 4, 33, 1.95f, 1.25f, 3, 0, 8, 0, 0, 55.847f, 18, 3, new int[] {-2,-1,0,1,2,3,4,5,6}, 1.83f, ElementType.TRANSITION_METAL),
Co(27, 4, 23, 1.13f, 1.26f, 3, 0, 12, 0, 0, 58.933f, 18, 2, new int[] {-1,0,1,2,3,4,5}, 1.88f, ElementType.TRANSITION_METAL),
Ni(28, 4, 62, 1.24f, 1.21f, 3, 0, 12, 0, 0, 58.710f, 18, 2, new int[] {-1,0,1,2,3,4}, 1.91f, ElementType.TRANSITION_METAL),
Cu(29, 4, 26, 1.15f, 1.38f, 2, 0, 4, 0, 0, 63.546f, 18, 2, new int[] {0,1,2,3,4}, 1.90f, ElementType.TRANSITION_METAL),
Zn(30, 4, 106, 1.15f, 1.31f, 2, 0, 2, 0, 0, 65.380f, 18, 2, new int[] {0,1,2}, 1.65f, ElementType.TRANSITION_METAL),
Ga(31, 4, 36, 1.55f, 1.26f, 3, 1, 4, 2, 4, 69.720f, 28, 3, new int[] {0,1,2,3}, 1.81f, ElementType.POST_TRANSITION_METAL),
Ge(32, 4, 38, 2.72f, 1.22f, 4, 0, 12, 4, 4, 72.590f, 28, 4, new int[] {-4,-3,-2,-1,0,1,2,3,4}, 2.01f, ElementType.METALLOID),
As(33, 4, 7, 0.83f, 1.19f, 5, 0, 12, 3, 5, 74.922f, 28, -3, new int[] {-3,0,1,2,3,5}, 2.18f, ElementType.METALLOID),
Se(34, 4, 85, 0.90f, 1.16f, 6, 0, 12, 2, 6, 78.960f, 28, 4, new int[] {-2,0,1,2,4,6}, 2.55f, ElementType.OTHER_NONMETAL),
Br(35, 4, 15, 1.95f, 1.14f, 7, 0, 1, 1, 1, 79.904f, 28, -1, new int[] {-1,0,1,2,3,4,5,7}, 2.96f, ElementType.HALOGEN),
Kr(36, 4, 48, 1.90f, 1.60f, 8, 0, 12, 0, 0, 83.800f, 28, 0, new int[] {0,2}, 3.00f, ElementType.NOBLE_GAS),
Rb(37, 5, 77, 2.65f, 2.11f, 1, 0, 12, 0, 0, 85.467f, 36, 1, new int[] {-1,0,1}, 0.82f, ElementType.ALKALI_METAL),
Sr(38, 5, 89, 2.02f, 1.92f, 2, 0, 12, 2, 0, 87.620f, 36, 2, new int[] {0,1,2}, 0.95f, ElementType.ALKALINE_EARTH_METAL),
Y(39, 5, 103, 1.61f, 1.62f, 3, 0, 12, 3, 0, 88.806f, 36, 3, new int[] {0,1,2,3}, 1.22f, ElementType.TRANSITION_METAL),
Zr(40, 5, 105, 1.42f, 1.48f, 4, 0, 12, 4, 0, 91.220f, 36, 4, new int[] {0,1,2,3,4}, 1.33f, ElementType.TRANSITION_METAL),
Nb(41, 5, 59, 1.33f, 1.37f, 5, 0, 12, 3, 0, 92.906f, 36, 5, new int[] {-1,0,1,2,3,4,5}, 1.60f, ElementType.TRANSITION_METAL),
Mo(42, 5, 56, 1.75f, 1.45f, 6, 1, 6, 3, 0, 95.940f, 36, 6, new int[] {-2,-1,0,1,2,3,4,5,6}, 2.16f, ElementType.TRANSITION_METAL),
Tc(43, 5, 93, 1.80f, 1.56f, 7, 0, 12, 6, 0, 98.910f, 36, 7, new int[] {-3,-1,0,1,2,3,4,5,6,7}, 1.90f, ElementType.TRANSITION_METAL),
Ru(44, 5, 81, 1.20f, 1.26f, 8, 0, 12, 3, 0, 101.070f, 36, 4, new int[] {-2,0,1,2,3,4,5,6,7,8}, 2.20f, ElementType.TRANSITION_METAL),
Rh(45, 5, 79, 1.22f, 1.35f, 4, 0, 12, 3, 0, 102.906f, 36, 3, new int[] {-1,0,1,2,3,4,5,6}, 2.28f, ElementType.TRANSITION_METAL),
Pd(46, 5, 70, 1.44f, 1.31f, 4, 0, 12, 2, 0, 106.400f, 36, 2, new int[] {0,1,2,4}, 2.20f, ElementType.TRANSITION_METAL),
Ag(47, 5, 3, 1.55f, 1.53f, 1, 0, 6, 0, 0, 107.868f, 36, 1, new int[] {0,1,2,3,4}, 1.93f, ElementType.TRANSITION_METAL),
Cd(48, 5, 18, 1.75f, 1.48f, 2, 0, 12, 0, 0, 112.400f, 36, 2, new int[] {0,1,2}, 1.69f, ElementType.TRANSITION_METAL),
In(49, 5, 45, 1.46f, 1.44f, 3, 0, 12, 3, 0, 114.820f, 46, 3, new int[] {0,1,2,3}, 1.78f, ElementType.POST_TRANSITION_METAL),
Sn(50, 5, 88, 1.67f, 1.41f, 4, 0, 12, 2, 4, 118.690f, 46, 4, new int[] {-4,0,2,4}, 1.96f, ElementType.POST_TRANSITION_METAL),
Sb(51, 5, 83, 1.12f, 1.38f, 5, 0, 12, 4, 5, 121.750f, 46, -3, new int[] {-3,0,3,5}, 2.05f, ElementType.METALLOID),
Te(52, 5, 94, 1.26f, 1.35f, 6, 0, 12, 2, 6, 127.600f, 46, 4, new int[] {-2,0,2,4,5,6}, 2.10f, ElementType.METALLOID),
I(53, 5, 44, 2.15f, 1.33f, 7, 1, 1, 1, 1, 126.905f, 46, -1, new int[] {-1,0,1,3,4,5,7}, 2.66f, ElementType.HALOGEN),
Xe(54, 5, 102, 2.10f, 1.70f, 8, 0, 12, 0, 0, 131.300f, 46, 0, new int[] {0,1,2,4,6,8}, 2.60f, ElementType.NOBLE_GAS),
Cs(55, 6, 25, 3.01f, 2.25f, 1, 0, 12, 0, 0, 132.905f, 54, 1, new int[] {-1,0,1}, 0.79f, ElementType.ALKALI_METAL),
Ba(56, 6, 11, 2.41f, 1.98f, 2, 0, 12, 0, 0, 137.340f, 54, 2, new int[] {0,2}, 0.89f, ElementType.ALKALINE_EARTH_METAL),
La(57, 6, 49, 1.83f, 1.95f, 3, 0, 12, 3, 0, 138.905f, 54, 3, new int[] {0,2,3}, 1.10f, ElementType.LANTHANOID),
Ce(58, 6, 19, 1.86f, 1.03f, 4, 0, 12, 3, 0, 140.120f, 54, 3, new int[] {0,2,3,4}, 1.12f, ElementType.LANTHANOID),
Pr(59, 6, 73, 1.62f, 0.90f, 4, 0, 12, 3, 0, 140.908f, 55, 3, new int[] {0,2,3,4}, 1.13f, ElementType.LANTHANOID),
Nd(60, 6, 60, 1.79f, 0.99f, 3, 0, 12, 3, 0, 144.240f, 56, 3, new int[] {0,2,3,4}, 1.14f, ElementType.LANTHANOID),
Pm(61, 6, 71, 1.76f, 0.98f, 3, 0, 12, 3, 0, 145.000f, 58, 3, new int[] {0,2,3}, 1.13f, ElementType.LANTHANOID),
Sm(62, 6, 87, 1.74f, 0.96f, 3, 0, 12, 2, 0, 150.400f, 59, 3, new int[] {0,2,3}, 1.17f, ElementType.LANTHANOID),
Eu(63, 6, 31, 1.96f, 1.09f, 3, 0, 12, 2, 0, 151.960f, 60, 3, new int[] {0,2,3}, 1.20f, ElementType.LANTHANOID),
Gd(64, 6, 37, 1.69f, 0.94f, 3, 0, 12, 3, 0, 157.250f, 61, 3, new int[] {0,1,2,3}, 1.20f, ElementType.LANTHANOID),
Tb(65, 6, 92, 1.66f, 0.92f, 4, 0, 12, 3, 0, 158.925f, 61, 3, new int[] {0,1,2,3,4}, 1.10f, ElementType.LANTHANOID),
Dy(66, 6, 28, 1.63f, 0.91f, 3, 0, 12, 3, 0, 162.500f, 62, 3, new int[] {0,2,3,4}, 1.22f, ElementType.LANTHANOID),
Ho(67, 6, 43, 1.61f, 0.89f, 3, 0, 12, 3, 0, 164.930f, 64, 3, new int[] {0,2,3}, 1.23f, ElementType.LANTHANOID),
Er(68, 6, 29, 1.59f, 0.88f, 3, 0, 12, 3, 0, 167.260f, 65, 3, new int[] {0,2,3}, 1.24f, ElementType.LANTHANOID),
Tm(69, 6, 98, 1.57f, 0.87f, 3, 0, 12, 3, 0, 168.934f, 66, 3, new int[] {0,2,3,4}, 1.25f, ElementType.LANTHANOID),
Yb(70, 6, 104, 1.54f, 0.86f, 3, 0, 12, 2, 0, 173.040f, 67, 3, new int[] {0,2,3}, 1.10f, ElementType.LANTHANOID),
Lu(71, 6, 52, 1.53f, 0.85f, 3, 0, 12, 3, 0, 174.970f, 68, 3, new int[] {0,3}, 1.27f, ElementType.LANTHANOID),
Hf(72, 6, 41, 1.40f, 1.58f, 4, 0, 12, 4, 0, 178.490f, 68, 4, new int[] {0,2,3,4}, 1.30f, ElementType.TRANSITION_METAL),
Ta(73, 6, 91, 1.22f, 1.38f, 5, 0, 12, 5, 0, 180.850f, 68, 5, new int[] {-1,0,2,3,4,5}, 1.50f, ElementType.TRANSITION_METAL),
W(74, 6, 101, 1.26f, 1.46f, 6, 0, 12, 6, 0, 183.850f, 68, 6, new int[] {-2,-1,0,1,2,3,4,5,6}, 2.36f, ElementType.TRANSITION_METAL),
Re(75, 6, 78, 1.30f, 1.59f, 7, 0, 12, 4, 0, 186.200f, 68, 7, new int[] {-3,-1,0,1,2,3,4,5,6,7}, 1.90f, ElementType.TRANSITION_METAL),
Os(76, 6, 66, 1.58f, 1.28f, 8, 0, 12, 2, 0, 190.200f, 68, 4, new int[] {-2,-1,0,1,2,3,4,5,6,7,8}, 2.20f, ElementType.TRANSITION_METAL),
Ir(77, 6, 46, 1.22f, 1.37f, 6, 0, 12, 3, 0, 192.220f, 68, 4, new int[] {-3,-1,0,1,2,3,4,5,6,8}, 2.20f, ElementType.TRANSITION_METAL),
Pt(78, 6, 74, 1.55f, 1.28f, 4, 0, 6, 0, 0, 195.090f, 68, 4, new int[] {-2,-1,0,1,2,3,4,5,6}, 2.28f, ElementType.TRANSITION_METAL),
Au(79, 6, 9, 1.45f, 1.44f, 3, 0, 6, 0, 0, 196.967f, 68, 3, new int[] {-1,0,1,2,3,5}, 2.54f, ElementType.TRANSITION_METAL),
Hg(80, 6, 42, 1.55f, 1.32f, 2, 0, 12, 1, 2, 200.59f, 78, 1, new int[] {0,1,2,4}, 2.00f, ElementType.TRANSITION_METAL),
Tl(81, 6, 97, 1.96f, 1.45f, 3, 0, 12, 1, 3, 204.3833f, 78, 1, new int[] {-1,0,1,3}, 1.62f, ElementType.POST_TRANSITION_METAL),
Pb(82, 6, 69, 2.16f, 1.47f, 4, 0, 12, 2, 4, 207.200f, 78, 2, new int[] {-4,0,2,4}, 2.33f, ElementType.POST_TRANSITION_METAL),
Bi(83, 6, 13, 1.73f, 1.46f, 5, 0, 12, 3, 3, 208.981f, 78, 3, new int[] {-3,0,1,3,5}, 2.20f, ElementType.POST_TRANSITION_METAL),
Po(84, 6, 72, 1.21f, 0.67f, 6, 0, 12, 4, 2, 209.000f, 78, 4, new int[] {-2,0,2,4,5,6}, 2.0f, ElementType.METALLOID),
At(85, 6, 8, 1.12f, 0.62f, 7, 0, 12, 1, 1, 210.000f, 78, -1, new int[] {-1,0,1,3,5,7}, 2.20f, ElementType.HALOGEN),
Rn(86, 6, 80, 2.30f, 1.90f, 8, 0, 12, 0, 0, 222.000f, 78, 0, new int[] {0,2,6}, 0.0f, ElementType.NOBLE_GAS), // electroneg not reported
Fr(87, 7, 35, 3.24f, 1.80f, 1, 0, 12, 0, 0, 223.000f, -1, 1, new int[] {0,1}, 0.70f, ElementType.ALKALI_METAL),
Ra(88, 7, 76, 2.57f, 1.43f, 2, 0, 12, 2, 0, 226.000f, -1, 2, new int[] {0,2}, 0.9f, ElementType.ALKALINE_EARTH_METAL),
Ac(89, 7, 2, 2.12f, 1.18f, 3, 0, 12, 4, 0, 227.000f, -1, 3, new int[] {0,2,3}, 1.1f, ElementType.ACTINOID),
Th(90, 7, 95, 1.84f, 1.02f, 4, 0, 12, 1, 0, 232.038f, -1, 4, new int[] {0,2,3,4}, 1.30f, ElementType.ACTINOID),
Pa(91, 7, 68, 1.60f, 0.89f, 5, 0, 12, 4, 0, 231.036f, -1, 5, new int[] {0,2,3,4,5}, 1.50f, ElementType.ACTINOID),
U(92, 7, 99, 1.75f, 0.97f, 6, 0, 12, 4, 0, 238.029f, -1, 6, new int[] {0,2,3,4,5,6}, 1.38f, ElementType.ACTINOID),
Np(93, 7, 64, 1.71f, 0.95f, 6, 0, 12, 4, 0, 237.048f, -1, 5, new int[] {0,3,4,5,6,7}, 1.36f, ElementType.ACTINOID),
Pu(94, 7, 75, 1.67f, 0.93f, 6, 0, 12, 3, 0, 244.000f, -1, 4, new int[] {0,3,4,5,6,7,8}, 1.28f, ElementType.ACTINOID),
Am(95, 7, 5, 1.66f, 0.92f, 6, 0, 12, 3, 0, 243.000f, -1, 3, new int[] {0,2,3,4,5,6,7}, 1.13f, ElementType.ACTINOID),
Cm(96, 7, 22, 1.65f, 0.91f, 3, 0, 12, 3, 0, 248.000f, -1, 3, new int[] {0,3,4}, 1.28f, ElementType.ACTINOID),
Bk(97, 7, 14, 1.64f, 0.90f, 4, 0, 12, 3, 0, 247.000f, -1, 3, new int[] {0,2,3,4}, 1.30f, ElementType.ACTINOID),
Cf(98, 7, 20, 1.63f, 0.89f, 3, 0, 12, 4, 0, 251.000f, -1, 3, new int[] {0,2,3,4}, 1.30f, ElementType.ACTINOID),
Es(99, 7, 30, 1.62f, 0.88f, -1, 0, 12, 4, 0, 254.000f, -1, 3, new int[] {0,2,3}, 1.30f, ElementType.ACTINOID),
Fm(100, 7, 34, 1.61f, 0.87f, -1, 0, 12, 4, 0, 257.000f, -1, 3, new int[] {0,2,3}, 1.30f, ElementType.ACTINOID),
Md(101, 7, 53, 1.60f, 0.86f, -1, 0, 12, 4, 0, 256.000f, -1, 3, new int[] {0,2,3}, 1.30f, ElementType.ACTINOID),
No(102, 7, 63, 1.59f, 0.85f, -1, 0, 12, 4, 0, 254.000f, -1, 3, new int[] {0,2,3}, 1.30f, ElementType.ACTINOID),
Lr(103, 7, 51, 1.58f, 0.84f, -1, 0, 12, 4, 0, 257.000f, -1, 3, new int[] {0,3}, 0.00f, ElementType.ACTINOID), // electroneg not reported
/**
* R-group to represent generic groups that are sometimes present in MDL .sdf
* files.
*/
R(104, 0, 105, 0.0f, 0.0f, 0, 0, 4, 1, 0, 0.000f, -1, 3, null, 0.00f, ElementType.UNKNOWN); // this is an R-group
// should these be declared final?
private int atomicNumber;
private int period;
//private int hillOrder;
private float VDWRadius; // in Angstroms
private float covalentRadius; // in Angstroms
private int valenceElectronCount;
private int minimumValence;
private int maximumValence;
private int commonValence;
private int maximumCovalentValence;
private float atomicMass;
private int coreElectronCount;
private int oxidationState;
private int[] allOxidationStates;
// Pauling electronegativity: http://en.wikipedia.org/wiki/Electronegativity
private float paulingElectronegativity;
// Element type: http://www.ptable.com/
private ElementType elementType;
//private static final Element[] hillOrderIndex;
//
// static {
// hillOrderIndex = new Element[Element.values().length + 1];
// for (Element e : Element.values()) {
// hillOrderIndex[e.getHillOrder()] = e;
// }
// hillOrderIndex[Element.H.getHillOrder()] = Element.H; // special case for hydrogen
// }
private static final Map allElements ;
static {
allElements = new HashMap();
for (Element e : Element.values()){
allElements.put(e.toString().toLowerCase(), e);
}
}
private Element(int atomicNumber,
int period,
int hillOrder,
float VDWRadius,
float covalentRadius,
int valenceElectronCount,
int minimumValence,
int maximumValence,
int commonValence,
int maximumCovalentValence,
float atomicMass,
int coreElectronCount,
int oxidationState,
int[] allOxidationStates,
float paulingElectronegativity,
ElementType elementType) {
this.atomicNumber = atomicNumber;
this.period = period;
//this.hillOrder = hillOrder;
this.VDWRadius = VDWRadius;
this.covalentRadius = covalentRadius;
this.valenceElectronCount = valenceElectronCount;
this.minimumValence = minimumValence;
this.maximumValence = maximumValence;
this.commonValence = commonValence;
this.maximumCovalentValence = maximumCovalentValence;
this.atomicMass = atomicMass;
this.coreElectronCount = coreElectronCount;
this.oxidationState = oxidationState;
this.allOxidationStates = allOxidationStates;
this.paulingElectronegativity = paulingElectronegativity;
this.elementType = elementType;
}
/**
* Returns a list of all oxidation states the element is found in.
* The set is by Greenwood and Norman in "Chemistry of the Elements (ISBN:0080379419).
* @return An array of oxidation states sorted from most negative to most positive.
*/
public int[] getAllOxidationStates() {
return allOxidationStates;
}
/**
* Returns the atomic number of this Element.
* @return the atomic number of this Element.
*/
public int getAtomicNumber() {
return atomicNumber;
}
/**
* Returns the period in the periodic table of this Element.
* @return the period in the periodic table of this Element.
*/
public int getPeriod() {
return period;
}
/**
* Returns the Hill Order of this Element. The Hill Order represents the
* priority by which elements are sorted in molecular formulas.
* The Hill system is a system of writing chemical formulas such that the
* number of carbon atoms in a molecule is indicated first, the number of
* hydrogen atoms next, and then the number of all other chemical elements
* subsequently, in alphabetical order. When the formula contains no carbon,
* all the elements, including hydrogen, are listed alphabetically.
*
* Edwin A. Hill, "On A System Of Indexing Chemical Literature;
* Adopted By The Classification Division Of The U. S. Patent Office".
* J. Am. Chem. Soc. 1900, 22(8), 478-494.
*
*
* http://en.wikipedia.org/wiki/Hill_system
*
* @return the Hill Order of this Element.
*/
public int getHillOrder() {
throw new RuntimeException("Not implemented, yet!");
//throw new NotImplementedYetException();
//return hillOrder;
}
/**
* Returns the van der Waals radius of this Element.
* @return the van der Waals radius of this Element, measured in Angstroms.
*/
public float getVDWRadius() {
return VDWRadius;
}
/**
* Returns the covalent radius of this Element.
* @return covalent radius, measured in Angstroms.
*/
public float getCovalentRadius() {
return covalentRadius;
}
/**
* Returns the number of valence electrons for this Element.
* @return the number of valence electrons for this Element.
*/
public int getValenceElectronCount() {
return valenceElectronCount;
}
/**
* Returns the minimum valence for this Element.
* @return the minimum valence of this atom.
*/
public int getMinimumValence() {
return minimumValence;
}
/**
* Returns the maximum valence for this Element.
* @return the maximum valence for this Element.
*/
public int getMaximumValence() {
return maximumValence;
}
/**
* Returns the common valence for this Element.
* @return the common valence for this Element.
*/
public int getCommonValence() {
return commonValence;
}
/**
* Returns the maximum valence for this Element.
* @return the maximum valence of this element.
*/
public int getMaximumCovalentValence() {
return maximumCovalentValence;
}
/**
* Returns the atomic mass for this Element.
* @return the atomic mass for this Element, measured in g/mol.
*/
public float getAtomicMass() {
return atomicMass;
}
/**
* Returns the number of core electrons for this Element.
* @return number of core electrons for this Element.
*/
public int getCoreElectronCount() {
return coreElectronCount;
}
/**
* Returns a typical oxidation state for this Element. This information is mostly
* useful for metals.
* @return a typical oxidation state for this Element.
*/
public int getOxidationState() {
return oxidationState;
}
/**
* Returns the Pauling electronegativity for this Element.
* @return the Pauling electronegativity for this Element.
*/
public float getPaulingElectronegativity() {
return paulingElectronegativity;
}
/**
* Returns the Element Type for this Element.
* @return the Element Type for this Element.
*/
public ElementType getElementType() {
return elementType;
}
/**
* Returns the Element that corresponds to the specified element symbol. The case
* of the element symbol is ignored. Example: FE, fe, Fe represent iron.
* @param elementSymbol element symbol to specify Element.
* @return the Element specified by the element symbol.
*/
public static Element valueOfIgnoreCase(String elementSymbol) throws IllegalArgumentException {
Element e = allElements.get(elementSymbol.toLowerCase());
if ( e != null)
return e;
throw new IllegalArgumentException("Invalid element symbol: " + elementSymbol);
}
/**
* Returns true if this Element is Hydrogen.
*
* Note: Deuterium ({@link #D}) and Tritium ({@link Element#T}) will return
* true to this method.
*
*
* @return true if the Element is Hydrogen.
*/
public boolean isHydrogen() {
return this == H || this == D || this == T;
}
/**
* Returns true is the Element is an not Hydrogen (or an
* isotope of Hydrogen).
*
* This method is the exact opposite of {@link #isHydrogen()}.
*
*
* @return true is Element is not Hydrogen.
*/
public boolean isHeavyAtom() {
return !isHydrogen();
}
/**
* Returns true if Element is not Hydrogen and not Carbon.
* @return true if Element is not Hydrogen and not Carbon.
*/
public boolean isHeteroAtom() {
return !(this == C || this == H);
}
/**
* Returns true if ElementType is a metal.
* @return true if ElementType is a metal.
*/
public boolean isMetal() {
return elementType.isMetal();
}
/**
* Returns true if ElementType is a metalloid.
* @return true if ElementType is a metalloid.
*/
public boolean isMetalloid() {
return elementType.isMetalloid();
}
/**
* Returns true if ElementType is a non-metal.
* @return true if ElementType is a non-metal.
*/
public boolean isNonMetal() {
return elementType.isNonMetal();
}
/**
* Returns true if Element is a halogen (F, Cl, Br, I, At).
* @return true if Element is a halogen.
*/
public boolean isHalogen() {
return elementType.equals(ElementType.HALOGEN);
}
/**
* Returns true if Element is a chalcogen (O, S, Se, Te, Po).
* @return true if Element is a chalcogen.
*/
public boolean isChalcogen() {
return (this == O || this == S || this == Se || this == Te ||
this == Po);
}
/**
* Returns the Element that corresponds to the specified Hill Order.
* @param index the Hill Order.
* @return the Element that corresponds to the specified Hill Order.
* @see #getHillOrder()
*/
public static Element getElementFromHillIndex(int index) {
throw new UnsupportedOperationException("Not implemented, yet!");
//return hillOrderIndex[index];
}
}
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