| 1 |
/********************************************************************** |
| 2 |
|
| 3 |
This basic Periodic Table class was originally taken from the data.cpp |
| 4 |
file in OpenBabel. The code has been modified to match the OOPSE coding style. |
| 5 |
|
| 6 |
We have retained the OpenBabel copyright and GPL license on this class: |
| 7 |
|
| 8 |
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
| 9 |
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
| 10 |
|
| 11 |
This file is part of the Open Babel project. |
| 12 |
For more information, see <http://openbabel.sourceforge.net/> |
| 13 |
|
| 14 |
This program is free software; you can redistribute it and/or modify |
| 15 |
it under the terms of the GNU General Public License as published by |
| 16 |
the Free Software Foundation version 2 of the License. |
| 17 |
|
| 18 |
This program is distributed in the hope that it will be useful, |
| 19 |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 20 |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 21 |
GNU General Public License for more details. |
| 22 |
***********************************************************************/ |
| 23 |
|
| 24 |
/** |
| 25 |
* @file ElementsTable.cpp |
| 26 |
* @author gezelter |
| 27 |
* @date 12/21/2007 |
| 28 |
* @time 11:30am |
| 29 |
* @version 1.0 |
| 30 |
*/ |
| 31 |
|
| 32 |
#include <iostream> |
| 33 |
#include "config.h" |
| 34 |
#include <cstdlib> |
| 35 |
#include <string> |
| 36 |
#include <fstream> |
| 37 |
#include <cstdlib> |
| 38 |
#include "utils/ElementsTable.hpp" |
| 39 |
#include "utils/simError.h" |
| 40 |
#include "io/basic_ifstrstream.hpp" |
| 41 |
|
| 42 |
#if !HAVE_STRNCASECMP |
| 43 |
extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); |
| 44 |
#endif |
| 45 |
|
| 46 |
#ifdef WIN32 |
| 47 |
#define FILE_SEP_CHAR "\\" |
| 48 |
#else |
| 49 |
#define FILE_SEP_CHAR "/" |
| 50 |
#endif |
| 51 |
|
| 52 |
#ifndef BUFF_SIZE |
| 53 |
#define BUFF_SIZE 32768 |
| 54 |
#endif |
| 55 |
|
| 56 |
namespace oopse { |
| 57 |
|
| 58 |
ElementsTable etab; |
| 59 |
|
| 60 |
ElementsTable::ElementsTable() { |
| 61 |
init_ = false; |
| 62 |
STR_DEFINE(dir_, FRC_PATH ); |
| 63 |
envvar_ = "FORCE_PARAM_PATH"; |
| 64 |
filename_ = "element.txt"; |
| 65 |
} |
| 66 |
|
| 67 |
ElementsTable::~ElementsTable() { |
| 68 |
std::vector<Element*>::iterator i; |
| 69 |
for (i = elements_.begin(); i != elements_.end(); i++) |
| 70 |
delete *i; |
| 71 |
} |
| 72 |
|
| 73 |
void ElementsTable::ParseLine(const char *line) { |
| 74 |
int num, maxbonds; |
| 75 |
char symbol[5]; |
| 76 |
char name[256]; |
| 77 |
RealType Rcov,Rvdw,mass, elNeg, ionize, elAffin; |
| 78 |
RealType red, green, blue; |
| 79 |
|
| 80 |
// skip comment line (at the top) |
| 81 |
|
| 82 |
if (line[0] != '#') { |
| 83 |
sscanf(line,"%d %5s %lf %*f %lf %d %lf %lf %lf %lf %lf %lf %lf %255s", |
| 84 |
&num, |
| 85 |
symbol, |
| 86 |
&Rcov, |
| 87 |
&Rvdw, |
| 88 |
&maxbonds, |
| 89 |
&mass, |
| 90 |
&elNeg, |
| 91 |
&ionize, |
| 92 |
&elAffin, |
| 93 |
&red, |
| 94 |
&green, |
| 95 |
&blue, |
| 96 |
name); |
| 97 |
|
| 98 |
Element *ele = new Element(num, symbol, Rcov, Rvdw, maxbonds, mass, |
| 99 |
elNeg, ionize, elAffin, red, green, blue, |
| 100 |
name); |
| 101 |
elements_.push_back(ele); |
| 102 |
|
| 103 |
} |
| 104 |
} |
| 105 |
|
| 106 |
unsigned int ElementsTable::GetNumberOfElements() { |
| 107 |
if (!init_) |
| 108 |
Init(); |
| 109 |
|
| 110 |
return elements_.size(); |
| 111 |
} |
| 112 |
|
| 113 |
char *ElementsTable::GetSymbol(int atomicnum) { |
| 114 |
if (!init_) |
| 115 |
Init(); |
| 116 |
|
| 117 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 118 |
return("\0"); |
| 119 |
|
| 120 |
return(elements_[atomicnum]->GetSymbol()); |
| 121 |
} |
| 122 |
|
| 123 |
int ElementsTable::GetMaxBonds(int atomicnum) { |
| 124 |
if (!init_) |
| 125 |
Init(); |
| 126 |
|
| 127 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 128 |
return(0); |
| 129 |
|
| 130 |
return(elements_[atomicnum]->GetMaxBonds()); |
| 131 |
} |
| 132 |
|
| 133 |
RealType ElementsTable::GetElectroNeg(int atomicnum) { |
| 134 |
if (!init_) |
| 135 |
Init(); |
| 136 |
|
| 137 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 138 |
return(0.0); |
| 139 |
|
| 140 |
return(elements_[atomicnum]->GetElectroNeg()); |
| 141 |
} |
| 142 |
|
| 143 |
RealType ElementsTable::GetIonization(int atomicnum) { |
| 144 |
if (!init_) |
| 145 |
Init(); |
| 146 |
|
| 147 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 148 |
return(0.0); |
| 149 |
|
| 150 |
return(elements_[atomicnum]->GetIonization()); |
| 151 |
} |
| 152 |
|
| 153 |
|
| 154 |
RealType ElementsTable::GetElectronAffinity(int atomicnum) { |
| 155 |
if (!init_) |
| 156 |
Init(); |
| 157 |
|
| 158 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 159 |
return(0.0); |
| 160 |
|
| 161 |
return(elements_[atomicnum]->GetElectronAffinity()); |
| 162 |
} |
| 163 |
|
| 164 |
std::vector<RealType> ElementsTable::GetRGB(int atomicnum) { |
| 165 |
if (!init_) |
| 166 |
Init(); |
| 167 |
|
| 168 |
std::vector <RealType> colors; |
| 169 |
colors.reserve(3); |
| 170 |
|
| 171 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) { |
| 172 |
colors.push_back(0.0); |
| 173 |
colors.push_back(0.0); |
| 174 |
colors.push_back(0.0); |
| 175 |
return(colors); |
| 176 |
} |
| 177 |
|
| 178 |
colors.push_back(elements_[atomicnum]->GetRed()); |
| 179 |
colors.push_back(elements_[atomicnum]->GetGreen()); |
| 180 |
colors.push_back(elements_[atomicnum]->GetBlue()); |
| 181 |
|
| 182 |
return (colors); |
| 183 |
} |
| 184 |
|
| 185 |
std::string ElementsTable::GetName(int atomicnum) { |
| 186 |
if (!init_) |
| 187 |
Init(); |
| 188 |
|
| 189 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 190 |
return("Unknown"); |
| 191 |
|
| 192 |
return(elements_[atomicnum]->GetName()); |
| 193 |
} |
| 194 |
|
| 195 |
RealType ElementsTable::GetVdwRad(int atomicnum) { |
| 196 |
if (!init_) |
| 197 |
Init(); |
| 198 |
|
| 199 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 200 |
return(0.0); |
| 201 |
|
| 202 |
return(elements_[atomicnum]->GetVdwRad()); |
| 203 |
} |
| 204 |
|
| 205 |
RealType ElementsTable::CorrectedBondRad(int atomicnum, int hyb) { |
| 206 |
RealType rad; |
| 207 |
if (!init_) |
| 208 |
Init(); |
| 209 |
|
| 210 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 211 |
return(1.0); |
| 212 |
|
| 213 |
rad = elements_[atomicnum]->GetCovalentRad(); |
| 214 |
|
| 215 |
if (hyb == 2) |
| 216 |
rad *= 0.95; |
| 217 |
else if (hyb == 1) |
| 218 |
rad *= 0.90; |
| 219 |
|
| 220 |
return(rad); |
| 221 |
} |
| 222 |
|
| 223 |
RealType ElementsTable::CorrectedVdwRad(int atomicnum, int hyb) { |
| 224 |
RealType rad; |
| 225 |
if (!init_) |
| 226 |
Init(); |
| 227 |
|
| 228 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 229 |
return(1.95); |
| 230 |
|
| 231 |
rad = elements_[atomicnum]->GetVdwRad(); |
| 232 |
|
| 233 |
if (hyb == 2) |
| 234 |
rad *= 0.95; |
| 235 |
else if (hyb == 1) |
| 236 |
rad *= 0.90; |
| 237 |
|
| 238 |
return(rad); |
| 239 |
} |
| 240 |
|
| 241 |
RealType ElementsTable::GetCovalentRad(int atomicnum) { |
| 242 |
if (!init_) |
| 243 |
Init(); |
| 244 |
|
| 245 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 246 |
return(0.0); |
| 247 |
|
| 248 |
return(elements_[atomicnum]->GetCovalentRad()); |
| 249 |
} |
| 250 |
|
| 251 |
RealType ElementsTable::GetMass(int atomicnum) { |
| 252 |
if (!init_) |
| 253 |
Init(); |
| 254 |
|
| 255 |
if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
| 256 |
return(0.0); |
| 257 |
|
| 258 |
return(elements_[atomicnum]->GetMass()); |
| 259 |
} |
| 260 |
|
| 261 |
int ElementsTable::GetAtomicNum(const char *sym) { |
| 262 |
int temp; |
| 263 |
return GetAtomicNum(sym, temp); |
| 264 |
} |
| 265 |
|
| 266 |
int ElementsTable::GetAtomicNum(const char *sym, int &iso) { |
| 267 |
if (!init_) |
| 268 |
Init(); |
| 269 |
|
| 270 |
std::vector<Element*>::iterator i; |
| 271 |
for (i = elements_.begin();i != elements_.end();i++) |
| 272 |
if (!strncasecmp(sym,(*i)->GetSymbol(),2)) |
| 273 |
return((*i)->GetAtomicNum()); |
| 274 |
|
| 275 |
if (strcasecmp(sym, "D") == 0) { |
| 276 |
iso = 2; |
| 277 |
return(1); |
| 278 |
} else if (strcasecmp(sym, "T") == 0) { |
| 279 |
iso = 3; |
| 280 |
return(1); |
| 281 |
} else |
| 282 |
iso = 0; |
| 283 |
return(0); |
| 284 |
} |
| 285 |
|
| 286 |
void ElementsTable::Init() { |
| 287 |
if (init_) |
| 288 |
return; |
| 289 |
init_ = true; |
| 290 |
|
| 291 |
std::string buffer, subbuffer; |
| 292 |
ifstrstream ifs1, ifs2, ifs3, ifs4, *ifsP; |
| 293 |
// First, look for an environment variable |
| 294 |
if (getenv(envvar_.c_str()) != NULL) { |
| 295 |
buffer = getenv(envvar_.c_str()); |
| 296 |
buffer += FILE_SEP_CHAR; |
| 297 |
|
| 298 |
if (!subdir_.empty()) { |
| 299 |
subbuffer = buffer; |
| 300 |
subbuffer += subdir_; |
| 301 |
subbuffer += FILE_SEP_CHAR; |
| 302 |
} |
| 303 |
|
| 304 |
buffer += filename_; |
| 305 |
subbuffer += filename_; |
| 306 |
|
| 307 |
ifs1.open(subbuffer.c_str()); |
| 308 |
ifsP= &ifs1; |
| 309 |
if (!(*ifsP)) { |
| 310 |
ifs2.open(buffer.c_str()); |
| 311 |
ifsP = &ifs2; |
| 312 |
} |
| 313 |
} else { |
| 314 |
sprintf( painCave.errMsg, |
| 315 |
"ElementsTable error.\n" |
| 316 |
"\tunable to open datafile %s \n", filename_.c_str()); |
| 317 |
painCave.isFatal = 0; |
| 318 |
simError(); |
| 319 |
} |
| 320 |
|
| 321 |
char charBuffer[BUFF_SIZE]; |
| 322 |
if ((*ifsP)) { |
| 323 |
while(ifsP->getline(charBuffer,BUFF_SIZE)) |
| 324 |
ParseLine(charBuffer); |
| 325 |
|
| 326 |
if (ifs1) |
| 327 |
ifs1.close(); |
| 328 |
if (ifs2) |
| 329 |
ifs2.close(); |
| 330 |
if (ifs3) |
| 331 |
ifs3.close(); |
| 332 |
if (ifs4) |
| 333 |
ifs4.close(); |
| 334 |
|
| 335 |
if (GetSize() == 0) { |
| 336 |
sprintf( painCave.errMsg, |
| 337 |
"ElementsTable error.\n" |
| 338 |
"\tCannot initialize database %s \n", filename_.c_str()); |
| 339 |
painCave.isFatal = 0; |
| 340 |
simError(); |
| 341 |
} |
| 342 |
|
| 343 |
} |
| 344 |
|
| 345 |
} |
| 346 |
} |
