Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : University of Illinois Open Source License
3 : Copyright 2003 Theoretical and Computational Biophysics Group,
4 : All rights reserved.
5 :
6 : Developed by: Theoretical and Computational Biophysics Group
7 : University of Illinois at Urbana-Champaign
8 : http://www.ks.uiuc.edu/
9 :
10 : Permission is hereby granted, free of charge, to any person obtaining a copy of
11 : this software and associated documentation files (the Software), to deal with
12 : the Software without restriction, including without limitation the rights to
13 : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
14 : of the Software, and to permit persons to whom the Software is furnished to
15 : do so, subject to the following conditions:
16 :
17 : Redistributions of source code must retain the above copyright notice,
18 : this list of conditions and the following disclaimers.
19 :
20 : Redistributions in binary form must reproduce the above copyright notice,
21 : this list of conditions and the following disclaimers in the documentation
22 : and/or other materials provided with the distribution.
23 :
24 : Neither the names of Theoretical and Computational Biophysics Group,
25 : University of Illinois at Urbana-Champaign, nor the names of its contributors
26 : may be used to endorse or promote products derived from this Software without
27 : specific prior written permission.
28 :
29 : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
30 : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
31 : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
32 : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
33 : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
34 : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
35 : OTHER DEALINGS WITH THE SOFTWARE.
36 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
37 : #ifndef __PLUMED_molfile_periodic_table_h
38 : #define __PLUMED_molfile_periodic_table_h
39 : /***************************************************************************
40 : * RCS INFORMATION:
41 : *
42 : * $RCSfile: periodic_table.h,v $
43 : * $Author: johns $ $Locker: $ $State: Exp $
44 : * $Revision: 1.12 $ $Date: 2009/01/21 17:45:41 $
45 : *
46 : ***************************************************************************/
47 :
48 : /*
49 : * periodic table of elements and helper functions to convert
50 : * ordinal numbers to labels and back.
51 : * all tables and functions are declared static, so that it
52 : * can be safely included by all plugins that may need it.
53 : *
54 : * 2002-2009 akohlmey@cmm.chem.upenn.edu, vmd@ks.uiuc.edu
55 : */
56 :
57 : #include <string.h>
58 : #include <ctype.h>
59 :
60 : namespace PLMD{
61 : namespace molfile{
62 : /* periodic table of elements for translation of ordinal to atom type */
63 : static const char *pte_label[] = {
64 : "X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne",
65 : "Na", "Mg", "Al", "Si", "P" , "S", "Cl", "Ar", "K", "Ca", "Sc",
66 : "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge",
67 : "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc",
68 : "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe",
69 : "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", "Tb",
70 : "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os",
71 : "Ir", "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr",
72 : "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf",
73 : "Es", "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt",
74 : "Ds", "Rg"
75 : };
76 : static const int nr_pte_entries = sizeof(pte_label) / sizeof(char *);
77 :
78 : /* corresponding table of masses. */
79 : static const float pte_mass[] = {
80 : /* X */ 0.00000, 1.00794, 4.00260, 6.941, 9.012182, 10.811,
81 : /* C */ 12.0107, 14.0067, 15.9994, 18.9984032, 20.1797,
82 : /* Na */ 22.989770, 24.3050, 26.981538, 28.0855, 30.973761,
83 : /* S */ 32.065, 35.453, 39.948, 39.0983, 40.078, 44.955910,
84 : /* Ti */ 47.867, 50.9415, 51.9961, 54.938049, 55.845, 58.9332,
85 : /* Ni */ 58.6934, 63.546, 65.409, 69.723, 72.64, 74.92160,
86 : /* Se */ 78.96, 79.904, 83.798, 85.4678, 87.62, 88.90585,
87 : /* Zr */ 91.224, 92.90638, 95.94, 98.0, 101.07, 102.90550,
88 : /* Pd */ 106.42, 107.8682, 112.411, 114.818, 118.710, 121.760,
89 : /* Te */ 127.60, 126.90447, 131.293, 132.90545, 137.327,
90 : /* La */ 138.9055, 140.116, 140.90765, 144.24, 145.0, 150.36,
91 : /* Eu */ 151.964, 157.25, 158.92534, 162.500, 164.93032,
92 : /* Er */ 167.259, 168.93421, 173.04, 174.967, 178.49, 180.9479,
93 : /* W */ 183.84, 186.207, 190.23, 192.217, 195.078, 196.96655,
94 : /* Hg */ 200.59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0,
95 : /* Fr */ 223.0, 226.0, 227.0, 232.0381, 231.03588, 238.02891,
96 : /* Np */ 237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0,
97 : /* Md */ 258.0, 259.0, 262.0, 261.0, 262.0, 266.0, 264.0, 269.0,
98 : /* Mt */ 268.0, 271.0, 272.0
99 : };
100 :
101 : /*
102 : * corresponding table of VDW radii.
103 : * van der Waals radii are taken from A. Bondi,
104 : * J. Phys. Chem., 68, 441 - 452, 1964,
105 : * except the value for H, which is taken from R.S. Rowland & R. Taylor,
106 : * J.Phys.Chem., 100, 7384 - 7391, 1996. Radii that are not available in
107 : * either of these publications have RvdW = 2.00 Å.
108 : * The radii for Ions (Na, K, Cl, Ca, Mg, and Cs are based on the CHARMM27
109 : * Rmin/2 parameters for (SOD, POT, CLA, CAL, MG, CES) by default.
110 : */
111 : static const float pte_vdw_radius[] = {
112 : /* X */ 1.5, 1.2, 1.4, 1.82, 2.0, 2.0,
113 : /* C */ 1.7, 1.55, 1.52, 1.47, 1.54,
114 : /* Na */ 1.36, 1.18, 2.0, 2.1, 1.8,
115 : /* S */ 1.8, 2.27, 1.88, 1.76, 1.37, 2.0,
116 : /* Ti */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
117 : /* Ni */ 1.63, 1.4, 1.39, 1.07, 2.0, 1.85,
118 : /* Se */ 1.9, 1.85, 2.02, 2.0, 2.0, 2.0,
119 : /* Zr */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
120 : /* Pd */ 1.63, 1.72, 1.58, 1.93, 2.17, 2.0,
121 : /* Te */ 2.06, 1.98, 2.16, 2.1, 2.0,
122 : /* La */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
123 : /* Eu */ 2.0, 2.0, 2.0, 2.0, 2.0,
124 : /* Er */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
125 : /* W */ 2.0, 2.0, 2.0, 2.0, 1.72, 1.66,
126 : /* Hg */ 1.55, 1.96, 2.02, 2.0, 2.0, 2.0, 2.0,
127 : /* Fr */ 2.0, 2.0, 2.0, 2.0, 2.0, 1.86,
128 : /* Np */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
129 : /* Md */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
130 : /* Mt */ 2.0, 2.0, 2.0
131 : };
132 :
133 : /* lookup functions */
134 :
135 0 : static const char *get_pte_label(const int idx)
136 : {
137 0 : if ((idx < 1) || (idx >= nr_pte_entries)) return pte_label[0];
138 :
139 0 : return pte_label[idx];
140 : }
141 :
142 0 : static float get_pte_mass(const int idx)
143 : {
144 0 : if ((idx < 1) || (idx >= nr_pte_entries)) return pte_mass[0];
145 :
146 0 : return pte_mass[idx];
147 : }
148 :
149 0 : static float get_pte_vdw_radius(const int idx)
150 : {
151 0 : if ((idx < 1) || (idx >= nr_pte_entries)) return pte_vdw_radius[0];
152 :
153 : #if 1
154 : /* Replace with Hydrogen radius with an "all-atom" radius */
155 0 : if (idx == 1)
156 : return 1.0; /* H */
157 : #else
158 : /* Replace with old VMD atom radii values */
159 : switch (idx) {
160 : case 1: return 1.0; /* H */
161 : case 6: return 1.5; /* C */
162 : case 7: return 1.4; /* N */
163 : case 8: return 1.3; /* O */
164 : case 9: return 1.2; /* F */
165 : case 15: return 1.5; /* P */
166 : case 16: return 1.9; /* S */
167 : }
168 : #endif
169 :
170 0 : return pte_vdw_radius[idx];
171 : }
172 :
173 : static int get_pte_idx(const char *label)
174 : {
175 : int i;
176 : char atom[3];
177 :
178 : /* zap string */
179 : atom[0] = (char) 0;
180 : atom[1] = (char) 0;
181 : atom[2] = (char) 0;
182 : /* if we don't have a null-pointer, there must be at least two
183 : * chars, which is all we need. we convert to the capitalization
184 : * convention of the table above during assignment. */
185 : if (label != NULL) {
186 : atom[0] = (char) toupper((int) label[0]);
187 : atom[1] = (char) tolower((int) label[1]);
188 : }
189 : /* discard numbers in atom label */
190 : if (isdigit(atom[1])) atom[1] = (char) 0;
191 :
192 : for (i=0; i < nr_pte_entries; ++i) {
193 : if ( (pte_label[i][0] == atom[0])
194 : && (pte_label[i][1] == atom[1]) ) return i;
195 : }
196 :
197 : return 0;
198 : }
199 :
200 0 : static int get_pte_idx_from_string(const char *label) {
201 : int i, ind;
202 : char atom[3];
203 :
204 0 : if (label != NULL) {
205 : /* zap string */
206 0 : atom[0] = atom[1] = atom[2] = '\0';
207 :
208 0 : for (ind=0,i=0; (ind<2) && (label[i]!='\0'); i++) {
209 0 : if (label[i] != ' ') {
210 0 : atom[ind] = toupper(label[i]);
211 0 : ind++;
212 : }
213 : }
214 :
215 0 : if (ind < 1)
216 : return 0; /* no non-whitespace characters */
217 :
218 0 : for (i=0; i < nr_pte_entries; ++i) {
219 0 : if ((toupper(pte_label[i][0]) == atom[0]) && (toupper(pte_label[i][1]) == atom[1]))
220 : return i;
221 : }
222 : }
223 :
224 : return 0;
225 : }
226 :
227 : #if 0
228 : #include <stdio.h>
229 :
230 : int main() {
231 : int i;
232 :
233 : printf("Periodic table check/dump\n");
234 : printf(" Table contains data for %d elements\n", nr_pte_entries);
235 : printf(" Mass table size check: %d\n", sizeof(pte_mass) / sizeof(float));
236 : printf(" VDW table size check: %d\n", sizeof(pte_vdw_radius) / sizeof(float));
237 : printf("\n");
238 : printf("Symbol Num Mass rVDW\n");
239 : for (i=0; i<nr_pte_entries; i++) {
240 : printf(" %-2s %3d %6.2f %4.2f\n",
241 : get_pte_label(i), i, get_pte_mass(i), get_pte_vdw_radius(i));
242 : }
243 : return 0;
244 : }
245 : #endif
246 : }
247 : }
248 : #endif
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