Index: src/Element/elements_db.cpp
===================================================================
--- src/Element/elements_db.cpp	(revision 3bdb6de29d0b7776bda5bfd425ac0a815e8a8d88)
+++ src/Element/elements_db.cpp	(revision 3bdb6de29d0b7776bda5bfd425ac0a815e8a8d88)
@@ -0,0 +1,549 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
+/*
+ * elements_db.cpp
+ *
+ *  Created on: 17.05.2010
+ *      Author: heber
+ */
+
+// include config.h
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "CodePatterns/MemDebug.hpp"
+
+const char *elementsDB =\
+"#	Covalent	radius	of	each	element	in	Angstroem	from	CSD	(binding	is:	[Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t]	with	t	=	0.4A\n\
+#Element	Name	Symbol	Period	Group	Block	Atomic	Number	AtomicWeight	Covalent	Radius	vdW	Radius\n\
+Hydrogen	H	1	1	s	1	1.008	0.23	1.09\n\
+Helium	He	1	18	p	2	4.003	1.50	1.40\n\
+Lithium	Li	2	1	s	3	6.941	0.68	1.82\n\
+Beryllium	Be	2	2	s	4	9.012	0.35	2.00\n\
+Boron	B	2	13	p	5	10.811	0.83	2.00\n\
+Carbon	C	2	14	p	6	12.011	0.68	1.70\n\
+Nitrogen	N	2	15	p	7	14.007	0.68	1.55\n\
+Oxygen	O	2	16	p	8	15.999	0.68	1.52\n\
+Fluorine	F	2	17	p	9	18.998	0.64	1.47\n\
+Neon	Ne	2	18	p	10	20.180	1.50	1.54\n\
+Sodium	Na	3	1	s	11	22.991	0.97	2.27\n\
+Magnesium	Mg	3	2	s	12	24.305	1.10	1.73\n\
+Aluminium	Al	3	13	p	13	26.982	1.35	2.00\n\
+Silicon	Si	3	14	p	14	28.086	1.20	2.10\n\
+Phosphorus	P	3	15	p	15	30.974	1.05	1.80\n\
+Sulphur	S	3	16	p	16	32.066	1.02	1.80\n\
+Chlorine	Cl	3	17	p	17	35.453	0.99	1.75\n\
+Argon	Ar	3	18	p	18	39.948	1.51	1.88\n\
+Potassium	K	4	1	s	19	39.098	1.33	2.75\n\
+Calcium	Ca	4	2	s	20	40.078	0.99	2.00\n\
+Scandium	Sc	4	3	d	21	44.956	1.44	2.00\n\
+Titanium	Ti	4	4	d	22	47.867	1.47	2.00\n\
+Vanadium	V	4	5	d	23	50.942	1.33	2.00\n\
+Chromium	Cr	4	6	d	24	51.996	1.35	2.00\n\
+Manganese	Mn	4	7	d	25	54.938	1.35	2.00\n\
+Iron	Fe	4	8	d	26	55.845	1.34	2.00\n\
+Cobalt	Co	4	9	d	27	58.933	1.33	2.00\n\
+Nickel	Ni	4	10	d	28	58.693	1.50	1.63\n\
+Copper	Cu	4	11	d	29	63.546	1.52	1.40\n\
+Zinc	Zn	4	12	d	30	65.390	1.45	1.39\n\
+Gallium	Ga	4	13	p	31	69.723	1.22	1.87\n\
+Germanium	Ge	4	14	p	32	72.610	1.17	2.00\n\
+Arsenic	As	4	15	p	33	74.922	1.21	1.85\n\
+Selenium	Se	4	16	p	34	78.960	1.22	1.90\n\
+Bromine	Br	4	17	p	35	79.904	1.21	1.85\n\
+Krypton	Kr	4	18	p	36	83.800	1.50	2.02\n\
+Rubidium	Rb	5	1	s	37	85.468	1.47	2.00\n\
+Strontium	Sr	5	2	s	38	87.620	1.12	2.00\n\
+Yttrium	Y	5	3	d	39	88.906	1.78	2.00\n\
+Zirconium	Zr	5	4	d	40	91.224	1.56	2.00\n\
+Niobium	Nb	5	5	d	41	92.906	1.48	2.00\n\
+Molybdenum	Mo	5	6	d	42	95.940	1.47	2.00\n\
+Technetium	Tc	5	7	d	43	98	1.35	2.00\n\
+Ruthenium	Ru	5	8	d	44	101.070	1.40	2.00\n\
+Rhodium	Rh	5	9	d	45	102.906	1.45	2.00\n\
+Palladium	Pd	5	10	d	46	106.420	1.50	1.63\n\
+Silver	Ag	5	11	d	47	107.868	1.59	1.72\n\
+Cadmium	Cd	5	12	d	48	112.411	1.69	1.58\n\
+Indium	In	5	13	p	49	114.818	1.63	1.93\n\
+Tin	Sn	5	14	p	50	118.71	1.46	2.17\n\
+Antimony	Sb	5	15	p	51	121.760	1.46	2.00\n\
+Tellurium	Te	5	16	p	52	127.600	1.47	2.06\n\
+Iodine	I	5	17	p	53	126.904	1.40	1.98\n\
+Xenon	Xe	5	18	p	54	131.290	1.50	2.16\n\
+Caesium	Cs	6	1	s	55	132.905	1.67	2.00\n\
+Barium	Ba	6	2	s	56	137.327	1.34	2.00\n\
+Lutetium	Lu	6	3	d	71	174.967	1.72	2.00\n\
+Hafnium	Hf	6	4	d	72	178.490	1.57	2.00\n\
+Tantalum	Ta	6	5	d	73	180.948	1.43	2.00\n\
+Tungsten	W	6	6	d	74	183.840	1.37	2.00\n\
+Rhenium	Re	6	7	d	75	186.207	1.35	2.00\n\
+Osmium	Os	6	8	d	76	190.230	1.37	2.00\n\
+Iridium	Ir	6	9	d	77	192.217	1.32	2.00\n\
+Platinum	Pt	6	10	d	78	195.078	1.50	1.72\n\
+Gold	Au	6	11	d	79	196.967	1.50	1.66\n\
+Mercury	Hg	6	12	d	80	200.590	1.70	1.55\n\
+Thallium	Tl	6	13	p	81	204.383	1.55	1.96\n\
+Lead	Pb	6	14	p	82	207.200	1.54	2.02\n\
+Bismuth	Bi	6	15	p	83	208.980	1.54	2.00\n\
+Polonium	Po	6	16	p	84	210	1.68	2.00\n\
+Astatine	At	6	17	p	85	210	1.21	2.00\n\
+Radon	Rn	6	18	p	86	222	1.50	2.00\n\
+Cerium	Ce	6Lan	19	f	58	140.116	1.83	2.00\n\
+Dysprosium	Dy	6Lan	19	f	66	162.500	1.75	2.00\n\
+Erbium	Er	6Lan	19	f	68	167.260	1.73	2.00\n\
+Europium	Eu	6Lan	19	f	63	151.964	1.99	2.00\n\
+Gadolinium	Gd	6Lan	19	f	64	157.250	1.79	2.00\n\
+Holmium	Ho	6Lan	19	f	67	164.930	1.74	2.00\n\
+Lanthanum	La	6Lan	19	f	57	138.906	1.87	2.00\n\
+Neodymium	Nd	6Lan	19	f	60	144.240	1.81	2.00\n\
+Promethium	Pm	6Lan	19	f	61	145	1.80	2.00\n\
+Praseodymium	Pr	6Lan	19	f	59	140.908	1.82	2.00\n\
+Samarium	Sm	6Lan	19	f	62	150.360	1.80	2.00\n\
+Terbium	Tb	6Lan	19	f	65	158.925	1.76	2.00\n\
+Thulium	Tm	6Lan	19	f	69	168.934	1.72	2.00\n\
+Ytterbium	Yb	6Lan	19	f	70	173.040	1.94	2.00\n\
+Francium	Fr	7	1	s	87	223	1.50	2.00\n\
+Radium	Ra	7	2	s	88	226	1.90	2.00\n\
+Lawrencium	Lr	7	3	d	103	262	1.50	2.00\n\
+Rutherfordium	Rf	7	4	d	104	261	1.50	2.00\n\
+Dubnium	Db	7	5	d	105	262	1.50	2.00\n\
+Seaborgium	Sg	7	6	d	106	266	1.50	2.00\n\
+Bohrium	Bh	7	7	d	107	264	1.50	2.00\n\
+Hassium	Hs	7	8	d	108	269	1.50	2.00\n\
+Meitnerium	Mt	7	9	d	109	268	1.50	2.00\n\
+Darmstadtium	Ds	7	10	d	110	271	1.50	2.00\n\
+Actinium	Ac	7Act	20	f	89	227	1.88	2.00\n\
+Americium	Am	7Act	20	f	95	243	1.51	2.00\n\
+Berkelium	Bk	7Act	20	f	97	247	1.54	2.00\n\
+Californium	Cf	7Act	20	f	98	251	1.83	2.00\n\
+Curium	Cm	7Act	20	f	96	247	0.99	2.00\n\
+Einsteinium	Es	7Act	20	f	99	252	1.50	2.00\n\
+Fermium	Fm	7Act	20	f	100	257	1.50	2.00\n\
+Mendelevium	Md	7Act	20	f	101	258	1.50	2.00\n\
+Nobelium	No	7Act	20	f	102	259	1.50	2.00\n\
+Neptunium	Np	7Act	20	f	93	237	1.55	2.00\n\
+Protactinium	Pa	7Act	20	f	91	231.036	1.61	2.00\n\
+Plutonium	Pu	7Act	20	f	94	244	1.53	2.00\n\
+Thorium	Th	7Act	20	f	90	232.038	1.79	2.00\n\
+Uranium	U	7Act	20	f	92	238.029	1.58	1.86\n\
+";
+
+const char *ElectronegativitiesDB =\
+"#atomic number\tEN [Pauling units], taken from http://en.wikipedia.org/wiki/Electronegativities_of_the_elements_%28data_page%29\n\
+1 2.2\n\
+2 -1\n\
+3 0.98\n\
+4 1.57\n\
+5 2.04\n\
+6 2.55\n\
+7 3.04\n\
+8 3.44\n\
+9  3.98\n\
+10  -1\n\
+11  0.93\n\
+12  1.31\n\
+13  1.61\n\
+14  1.90\n\
+15  2.19\n\
+16  2.58\n\
+17  3.16\n\
+18  -1\n\
+19  0.82\n\
+20  1.00\n\
+21  1.36\n\
+22  1.54\n\
+23  1.63\n\
+24  1.66\n\
+25  1.55\n\
+26  1.83\n\
+27  1.88\n\
+28  1.91\n\
+29  1.90\n\
+30  1.65\n\
+31  1.81\n\
+32  2.01\n\
+33  2.18\n\
+34  2.55\n\
+35  2.96\n\
+36  3.00\n\
+37  0.82\n\
+38  0.95\n\
+39  1.22\n\
+40  1.33\n\
+41  1.6\n\
+42  2.16\n\
+43  1.9\n\
+44  2.2\n\
+45  2.28\n\
+46  2.20\n\
+47  1.93\n\
+48  1.69\n\
+49  1.78\n\
+50  1.96\n\
+51  2.05\n\
+52  2.1\n\
+53  2.66\n\
+54  2.6\n\
+55  0.79\n\
+56  0.89\n\
+57  1.10\n\
+58  1.12\n\
+59  1.13\n\
+60  1.14\n\
+61  -1\n\
+62  1.17\n\
+63  -1\n\
+64  1.20\n\
+65  -1\n\
+66  1.22\n\
+67  1.23\n\
+68  1.24\n\
+69  1.25\n\
+70  -1\n\
+71  1.27\n\
+72  1.3\n\
+73  1.5\n\
+74  2.36\n\
+75  1.9\n\
+76  2.2\n\
+77  2.20\n\
+78  2.28\n\
+79  2.54\n\
+80  2.00\n\
+81  1.62\n\
+82  2.33\n\
+83  2.02\n\
+84  2.0\n\
+85  2.2\n\
+86  -1\n\
+87  0.7\n\
+88  0.9\n\
+89  1.1\n\
+90  1.3\n\
+91  1.5\n\
+92  1.38\n\
+93  1.36\n\
+94  1.28\n\
+95  1.3\n\
+96  1.3\n\
+97  1.3\n\
+98  1.3\n\
+99  1.3\n\
+100 1.3\n\
+101 1.3\n\
+102 1.3\n\
+";
+
+const char *HbonddistanceDB =\
+"#atomic number bond distances for single, double and triple bond (-1 no bond)\n\
+1	0.74	-1	-1\n\
+2	0.77429209	-1	-1\n\
+5	1.23	1.19	1.18\n\
+6	1.09	1.076	1.06\n\
+7	1.04	1.02	1.01\n\
+8	0.96	0.957	-1\n\
+14	1.48	1.48	1.48\n\
+15	1.42	-1	-1\n\
+16	1.35	-1	-1\n\
+17	1.29	-1	-1\n\
+20	1.09	1.09	-1\n\
+34	1.47	-1	-1\n\
+35	1.44	-1	-1\n\
+";
+
+const char *HbondangleDB =\
+"# atomicnumber angles for single, double and triple bond (-1 no angle)\n\
+1	180	-1	-1\n\
+5	180	131.0	109.2\n\
+6	180	120	109.47\n\
+7	180	110	106.67\n\
+8	180	104.5	-1\n\
+14	180	120	109.47\n\
+15	180	-1	-1\n\
+16	180	-1	-1\n\
+17	180 -1 -1\n\
+20	180	120	109.47\n\
+34	180 -1 -1\n\
+35	180 -1 -1\n\
+";
+
+const char *orbitalsDB =\
+"# atomicnumber	numberoforbitals\n\
+1	1\n\
+2	0\n\
+3	1\n\
+4	2\n\
+5	3\n\
+6	4\n\
+7	3\n\
+8	2\n\
+9	1\n\
+10	0\n\
+11	1\n\
+12	2\n\
+13	3\n\
+14	4\n\
+15	3\n\
+16	2\n\
+17	1\n\
+18	0\n\
+19	1\n\
+20	4\n\
+21	3\n\
+22	4\n\
+23	5\n\
+24	6\n\
+25	4\n\
+26	3\n\
+27	3\n\
+28	2\n\
+29	2\n\
+30	2\n\
+31	3\n\
+32	4\n\
+33	3\n\
+34	2\n\
+35	1\n\
+36	0\n\
+37	1\n\
+38	2\n\
+39	3\n\
+40	4\n\
+41	5\n\
+42	6\n\
+43	6\n\
+44	8\n\
+45	4\n\
+46	4\n\
+47	1\n\
+48	2\n\
+49	3\n\
+50	4\n\
+51	3\n\
+52	2\n\
+53	1\n\
+54	0\n\
+55	1\n\
+56	2\n\
+57	3\n\
+58	4\n\
+59	3\n\
+60	4\n\
+61	3\n\
+62	3\n\
+63	3\n\
+64	3\n\
+65	4\n\
+66	3\n\
+67	3\n\
+68	3\n\
+69	3	\n\
+70	3\n\
+71	3\n\
+72	4\n\
+73	5\n\
+74	6\n\
+75	7\n\
+76	8\n\
+77	6\n\
+78	6\n\
+79	3\n\
+80	2\n\
+81	3\n\
+82	4\n\
+83	3\n\
+84	4\n\
+86	0\n\
+88	2\n\
+89	3\n\
+90	4\n\
+91	5\n\
+92	6\n\
+";
+
+const char *valenceDB =\
+"#atomicnumber numberofvalenceorbitals\n\
+1	0.10000000000000E+01\n\
+2	0.20000000000000E+01\n\
+3	0.10000000000000E+01\n\
+4	0.20000000000000E+01\n\
+5	0.30000000000000E+01\n\
+6	0.40000000000000E+01\n\
+7	0.50000000000000E+01\n\
+8	0.60000000000000E+01\n\
+9	0.70000000000000E+01\n\
+10	0.80000000000000E+01\n\
+11	0.10000000000000E+01\n\
+12	0.40000000000000E+01\n\
+13	.3000000000000000E+01\n\
+14	0.40000000000000E+01\n\
+15	0.50000000000000E+01\n\
+16	0.60000000000000E+01\n\
+17	0.70000000000000E+01\n\
+18	0.80000000000000E+01\n\
+19	0.30000000000000E+01\n\
+20	0.40000000000000E+01\n\
+21	0.30000000000000E+01\n\
+22	0.40000000000000E+01\n\
+23	0.50000000000000E+01\n\
+24	0.60000000000000E+01\n\
+25	0.70000000000000E+01\n\
+26	0.80000000000000E+01\n\
+27	0.90000000000000E+01\n\
+28	0.10000000000000E+02\n\
+29	0.11000000000000E+02\n\
+30	0.12000000000000E+02\n\
+31	3.00000000000000000\n\
+32	0.40000000000000E+01\n\
+33	5.00000000000000000\n\
+34	0.60000000000000E+01\n\
+35	0.70000000000000E+01\n\
+36	0.80000000000000E+01\n\
+37	0.10000000000000E+01\n\
+38	0.20000000000000E+01\n\
+39	0.30000000000000E+01\n\
+40	0.40000000000000E+01\n\
+41	0.50000000000000E+01\n\
+42	0.60000000000000E+01\n\
+43	0.70000000000000E+01\n\
+44	0.80000000000000E+01\n\
+45	0.90000000000000E+01\n\
+46	0.10000000000000E+02\n\
+47	0.11000000000000E+02\n\
+48	0.12000000000000E+02\n\
+49	0.30000000000000E+01\n\
+50	0.40000000000000E+01\n\
+51	0.50000000000000E+01\n\
+52	0.60000000000000E+01\n\
+53	0.70000000000000E+01\n\
+54	0.80000000000000E+01\n\
+55	0.10000000000000E+01\n\
+56	0.20000000000000E+01\n\
+72	0.40000000000000E+01\n\
+73	0.50000000000000E+01\n\
+74	0.60000000000000E+01\n\
+75	0.70000000000000E+01\n\
+76	0.80000000000000E+01\n\
+77	0.90000000000000E+01\n\
+78	0.10000000000000E+02\n\
+79	0.11000000000000E+02\n\
+80	0.12000000000000E+02\n\
+";
+
+const char *ColorDB =\
+"# AtomicNumber, symbol, [red, green, blue] component, hex value\n\
+1\tH\t255\t255\t255\n\
+2\tHe\t217\t255\t255\n\
+3\tLi\t204\t128\t255\n\
+4\tBe\t194\t255\t0\n\
+5\tB\t255\t181\t181\n\
+6\tC\t144\t144\t144\n\
+7\tN\t48\t80\t248\n\
+8\tO\t255\t13\t13\n\
+9\tF\t144\t224\t80\n\
+10\tNe\t179\t227\t245\n\
+11\tNa\t171\t92\t242\n\
+12\tMg\t138\t255\t0\n\
+13\tAl\t191\t166\t166\n\
+14\tSi\t240\t200\t160\n\
+15\tP\t255\t128\t0\n\
+16\tS\t255\t255\t48\n\
+17\tCl\t31\t240\t31\n\
+18\tAr\t128\t209\t227\n\
+19\tK\t143\t64\t212\n\
+20\tCa\t61\t255\t0\n\
+21\tSc\t230\t230\t230\n\
+22\tTi\t191\t194\t199\n\
+23\tV\t166\t166\t171\n\
+24\tCr\t138\t153\t199\n\
+25\tMn\t156\t122\t199\n\
+26\tFe\t224\t102\t51\n\
+27\tCo\t240\t144\t160\n\
+28\tNi\t80\t208\t80\n\
+29\tCu\t200\t128\t51\n\
+30\tZn\t125\t128\t176\n\
+31\tGa\t194\t143\t143\n\
+32\tGe\t102\t143\t143\n\
+33\tAs\t189\t128\t227\n\
+34\tSe\t255\t161\t0\n\
+35\tBr\t166\t41\t41\n\
+36\tKr\t92\t184\t209\n\
+37\tRb\t112\t46\t176\n\
+38\tSr\t0\t255\t0\n\
+39\tY\t148\t255\t255\n\
+40\tZr\t148\t224\t224\n\
+41\tNb\t115\t194\t201\n\
+42\tMo\t84\t181\t181\n\
+43\tTc\t59\t158\t158\n\
+44\tRu\t36\t143\t143\n\
+45\tRh\t10\t125\t140\n\
+46\tPd\t0\t105\t133\n\
+47\tAg\t192\t192\t192\n\
+48\tCd\t255\t217\t143\n\
+49\tIn\t166\t117\t115\n\
+50\tSn\t102\t128\t128\n\
+51\tSb\t158\t99\t181\n\
+52\tTe\t212\t122\t0\n\
+53\tI\t148\t0\t148\n\
+54\tXe\t66\t158\t176\n\
+55\tCs\t87\t23\t143\n\
+56\tBa\t0\t201\t0\n\
+57\tLa\t112\t212\t255\n\
+58\tCe\t255\t255\t199\n\
+59\tPr\t217\t255\t199\n\
+60\tNd\t199\t255\t199\n\
+61\tPm\t163\t255\t199\n\
+62\tSm\t143\t255\t199\n\
+63\tEu\t97\t255\t199\n\
+64\tGd\t69\t255\t199\n\
+65\tTb\t48\t255\t199\n\
+66\tDy\t31\t255\t199\n\
+67\tHo\t0\t255\t156\n\
+68\tEr\t0\t230\t117\n\
+69\tTm\t0\t212\t82\n\
+70\tYb\t0\t191\t56\n\
+71\tLu\t0\t171\t36\n\
+72\tHf\t77\t194\t255\n\
+73\tTa\t77\t166\t255\n\
+74\tW\t33\t148\t214\n\
+75\tRe\t38\t125\t171\n\
+76\tOs\t38\t102\t150\n\
+77\tIr\t23\t84\t135\n\
+78\tPt\t208\t208\t224\n\
+79\tAu\t255\t209\t35\n\
+80\tHg\t184\t184\t208\n\
+81\tTl\t166\t84\t77\n\
+82\tPb\t87\t89\t97\n\
+83\tBi\t158\t79\t181\n\
+84\tPo\t171\t92\t0\n\
+85\tAt\t117\t79\t69\n\
+86\tRn\t66\t130\t150\n\
+87\tFr\t66\t0\t102\n\
+88\tRa\t0\t125\t0\n\
+89\tAc\t112\t171\t250\n\
+90\tTh\t0\t186\t255\n\
+91\tPa\t0\t161\t255\n\
+92\tU\t0\t143\t255\n\
+93\tNp\t0\t128\t255\n\
+94\tPu\t0\t107\t255\n\
+95\tAm\t84\t92\t242\n\
+96\tCm\t120\t92\t227\n\
+97\tBk\t138\t79\t227\n\
+98\tCf\t161\t54\t212\n\
+99\tEs\t179\t31\t212\n\
+100\tFm\t179\t31\t186\n\
+101\tMd\t179\t13\t166\n\
+102\tNo\t189\t13\t135\n\
+103\tLr\t199\t0\t102\n\
+104\tRf\t204\t0\t89\n\
+105\tDb\t209\t0\t79\n\
+106\tSg\t217\t0\t69\n\
+107\tBh\t224\t0\t56\n\
+108\tHs\t230\t0\t46\n\
+";
