src/utils/ElementsTable.cpp

/**********************************************************************

This basic Periodic Table class was originally taken from the data.cpp
file in OpenBabel. The code has been modified to match the OOPSE coding style.

We have retained the OpenBabel copyright and GPL license on this class:  

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

/**
 * @file ElementsTable.cpp
 * @author gezelter
 * @date 12/21/2007
 * @time 11:30am
 * @version 1.0
 */

#include "config.h"
#include <string>
#include <fstream>
#include "utils/ElementsTable.hpp"
#include "utils/simError.h"

#if !HAVE_STRNCASECMP
extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
#endif

#ifdef WIN32
#define FILE_SEP_CHAR "\\"
#else
#define FILE_SEP_CHAR "/"
#endif

#ifndef BUFF_SIZE
#define BUFF_SIZE 32768
#endif

namespace oopse {

  ElementsTable etab;

  ElementsTable::ElementsTable() {
    init_ = false;
    STR_DEFINE(dir_, FRC_PATH );
    envvar_ = "FORCE_PARAM_PATH";
    filename_ = "element.txt";
  }
  
  ElementsTable::~ElementsTable() {
    std::vector<Element*>::iterator i;
    for (i = elements_.begin(); i != elements_.end(); i++)
      delete *i;
  }
  
  void ElementsTable::ParseLine(const char *line) {
    int num, maxbonds;
    char symbol[5];
    char name[256];
    RealType Rcov,Rvdw,mass, elNeg, ionize, elAffin;
    RealType red, green, blue;

    // skip comment line (at the top)
    
    if (line[0] != '#')  {
      sscanf(line,"%d %5s %lf %*f %lf %d %lf %lf %lf %lf %lf %lf %lf %255s",
             &num,
             symbol,
             &Rcov,
             &Rvdw,
             &maxbonds,
             &mass,
             &elNeg,
             &ionize,
             &elAffin,
             &red,
             &green,
             &blue,
             name);
    
      Element *ele = new Element(num, symbol, Rcov, Rvdw, maxbonds, mass, 
                                 elNeg, ionize, elAffin, red, green, blue, 
                                 name);
      elements_.push_back(ele);
    }
  }

  unsigned int ElementsTable::GetNumberOfElements() { 
    if (!init_)
      Init();
    
    return elements_.size();
  }

  char *ElementsTable::GetSymbol(int atomicnum) {
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return("\0");
    
    return(elements_[atomicnum]->GetSymbol());
  }

  int ElementsTable::GetMaxBonds(int atomicnum) {
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(0);
    
    return(elements_[atomicnum]->GetMaxBonds());
  }
  
  RealType ElementsTable::GetElectroNeg(int atomicnum) {
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(0.0);
    
    return(elements_[atomicnum]->GetElectroNeg());
  }
  
  RealType ElementsTable::GetIonization(int atomicnum) {
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(0.0);
    
    return(elements_[atomicnum]->GetIonization());
  }
  

  RealType ElementsTable::GetElectronAffinity(int atomicnum) {
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(0.0);

    return(elements_[atomicnum]->GetElectronAffinity());
  }
  
  std::vector<RealType> ElementsTable::GetRGB(int atomicnum) {
    if (!init_)
      Init();
    
    std::vector <RealType> colors;
    colors.reserve(3);
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) {
      colors.push_back(0.0);
      colors.push_back(0.0);
      colors.push_back(0.0);
      return(colors);
    }

    colors.push_back(elements_[atomicnum]->GetRed());
    colors.push_back(elements_[atomicnum]->GetGreen());
    colors.push_back(elements_[atomicnum]->GetBlue());
    
    return (colors);
  }
  
  std::string ElementsTable::GetName(int atomicnum) {
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return("Unknown");
    
    return(elements_[atomicnum]->GetName());
  }

  RealType ElementsTable::GetVdwRad(int atomicnum) {
    if (!init_)
      Init();

    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(0.0);

    return(elements_[atomicnum]->GetVdwRad());
  }
  
  RealType ElementsTable::CorrectedBondRad(int atomicnum, int hyb) {
    RealType rad;
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(1.0);
    
    rad = elements_[atomicnum]->GetCovalentRad();
    
    if (hyb == 2)
      rad *= 0.95;
    else if (hyb == 1)
      rad *= 0.90;

    return(rad);
  }

  RealType ElementsTable::CorrectedVdwRad(int atomicnum, int hyb) {
    RealType rad;
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(1.95);
    
    rad = elements_[atomicnum]->GetVdwRad();
    
    if (hyb == 2)
      rad *= 0.95;
    else if (hyb == 1)
      rad *= 0.90;
    
    return(rad);
  }

  RealType ElementsTable::GetCovalentRad(int atomicnum) {
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(0.0);
    
    return(elements_[atomicnum]->GetCovalentRad());
  }
  
  RealType ElementsTable::GetMass(int atomicnum) {
    if (!init_)
      Init();
    
    if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size()))
      return(0.0);
    
    return(elements_[atomicnum]->GetMass());
  }
  
  int ElementsTable::GetAtomicNum(const char *sym) {
    int temp;
    return GetAtomicNum(sym, temp);
  }

  int ElementsTable::GetAtomicNum(const char *sym, int &iso) {
    if (!init_)
      Init();
    
    std::vector<Element*>::iterator i;
    for (i = elements_.begin();i != elements_.end();i++)
      if (!strncasecmp(sym,(*i)->GetSymbol(),2))
        return((*i)->GetAtomicNum());

    if (strcasecmp(sym, "D") == 0) {
      iso = 2;
      return(1);
    } else if (strcasecmp(sym, "T") == 0) {
      iso = 3;
      return(1);
    } else 
      iso = 0;
    return(0);
  }

  void ElementsTable::Init() {
    if (init_)
      return;
    init_ = true;
    
    std::string buffer, subbuffer;
    std::ifstream ifs1, ifs2, ifs3, ifs4, *ifsP;
    // First, look for an environment variable
    if (getenv(envvar_.c_str()) != NULL) {
      buffer = getenv(envvar_.c_str());
      buffer += FILE_SEP_CHAR;
      
      if (!subdir_.empty()) {
        subbuffer = buffer;
        subbuffer += subdir_;
        subbuffer += FILE_SEP_CHAR;
      }
      
      buffer += filename_;
      subbuffer += filename_;
      
      ifs1.open(subbuffer.c_str());
      ifsP= &ifs1;
      if (!(*ifsP)) {
        ifs2.open(buffer.c_str());
        ifsP = &ifs2;
      }
    } else {
      sprintf( painCave.errMsg,
               "ElementsTable error.\n"
               "\tunable to open datafile %s \n", filename_.c_str());
      painCave.isFatal = 0;
      simError();
    }
      
    char charBuffer[BUFF_SIZE];
    if ((*ifsP)) {
      while(ifsP->getline(charBuffer,BUFF_SIZE))
        ParseLine(charBuffer);
          
    if (ifs1)
      ifs1.close();
    if (ifs2)
      ifs2.close();
    if (ifs3)
      ifs3.close();
    if (ifs4)
      ifs4.close();
    
    if (GetSize() == 0) {
      sprintf( painCave.errMsg,
               "ElementsTable error.\n"
               "\tCannot initialize database %s \n", filename_.c_str());
      painCave.isFatal = 0;
      simError();
    }
    
    }
  
  }
}
Revision:	1210
Committed:	Wed Jan 23 03:45:33 2008 UTC (17 years, 3 months ago) by gezelter
File size:	8317 byte(s)
Log Message:	Removed older version of openbabel from our code. We now have a configure check to see if openbabel is installed and then we link to the stuff we need. Conversion to OOPSE's md format is handled by only one application (atom2md), so most of the work went on there. ElementsTable still needs some work to function in parallel.
#	User	Rev	Content
1	gezelter	1210	/**********************************************************************
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 "config.h"
33			#include <string>
34			#include <fstream>
35			#include "utils/ElementsTable.hpp"
36			#include "utils/simError.h"
37
38			#if !HAVE_STRNCASECMP
39			extern "C" int strncasecmp(const char s1, const char s2, size_t n);
40			#endif
41
42			#ifdef WIN32
43			#define FILE_SEP_CHAR "\\"
44			#else
45			#define FILE_SEP_CHAR "/"
46			#endif
47
48			#ifndef BUFF_SIZE
49			#define BUFF_SIZE 32768
50			#endif
51
52			namespace oopse {
53
54			ElementsTable etab;
55
56			ElementsTable::ElementsTable() {
57			init_ = false;
58			STR_DEFINE(dir_, FRC_PATH );
59			envvar_ = "FORCE_PARAM_PATH";
60			filename_ = "element.txt";
61			}
62
63			ElementsTable::~ElementsTable() {
64			std::vector<Element*>::iterator i;
65			for (i = elements_.begin(); i != elements_.end(); i++)
66			delete *i;
67			}
68
69			void ElementsTable::ParseLine(const char *line) {
70			int num, maxbonds;
71			char symbol[5];
72			char name[256];
73			RealType Rcov,Rvdw,mass, elNeg, ionize, elAffin;
74			RealType red, green, blue;
75
76			// skip comment line (at the top)
77
78			if (line[0] != '#') {
79			sscanf(line,"%d %5s %lf %*f %lf %d %lf %lf %lf %lf %lf %lf %lf %255s",
80			&num,
81			symbol,
82			&Rcov,
83			&Rvdw,
84			&maxbonds,
85			&mass,
86			&elNeg,
87			&ionize,
88			&elAffin,
89			&red,
90			&green,
91			&blue,
92			name);
93
94			Element *ele = new Element(num, symbol, Rcov, Rvdw, maxbonds, mass,
95			elNeg, ionize, elAffin, red, green, blue,
96			name);
97			elements_.push_back(ele);
98			}
99			}
100
101			unsigned int ElementsTable::GetNumberOfElements() {
102			if (!init_)
103			Init();
104
105			return elements_.size();
106			}
107
108			char *ElementsTable::GetSymbol(int atomicnum) {
109			if (!init_)
110			Init();
111
112			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
113			return("\0");
114
115			return(elements_[atomicnum]->GetSymbol());
116			}
117
118			int ElementsTable::GetMaxBonds(int atomicnum) {
119			if (!init_)
120			Init();
121
122			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
123			return(0);
124
125			return(elements_[atomicnum]->GetMaxBonds());
126			}
127
128			RealType ElementsTable::GetElectroNeg(int atomicnum) {
129			if (!init_)
130			Init();
131
132			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
133			return(0.0);
134
135			return(elements_[atomicnum]->GetElectroNeg());
136			}
137
138			RealType ElementsTable::GetIonization(int atomicnum) {
139			if (!init_)
140			Init();
141
142			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
143			return(0.0);
144
145			return(elements_[atomicnum]->GetIonization());
146			}
147
148
149			RealType ElementsTable::GetElectronAffinity(int atomicnum) {
150			if (!init_)
151			Init();
152
153			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
154			return(0.0);
155
156			return(elements_[atomicnum]->GetElectronAffinity());
157			}
158
159			std::vector<RealType> ElementsTable::GetRGB(int atomicnum) {
160			if (!init_)
161			Init();
162
163			std::vector <RealType> colors;
164			colors.reserve(3);
165
166			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size())) {
167			colors.push_back(0.0);
168			colors.push_back(0.0);
169			colors.push_back(0.0);
170			return(colors);
171			}
172
173			colors.push_back(elements_[atomicnum]->GetRed());
174			colors.push_back(elements_[atomicnum]->GetGreen());
175			colors.push_back(elements_[atomicnum]->GetBlue());
176
177			return (colors);
178			}
179
180			std::string ElementsTable::GetName(int atomicnum) {
181			if (!init_)
182			Init();
183
184			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
185			return("Unknown");
186
187			return(elements_[atomicnum]->GetName());
188			}
189
190			RealType ElementsTable::GetVdwRad(int atomicnum) {
191			if (!init_)
192			Init();
193
194			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
195			return(0.0);
196
197			return(elements_[atomicnum]->GetVdwRad());
198			}
199
200			RealType ElementsTable::CorrectedBondRad(int atomicnum, int hyb) {
201			RealType rad;
202			if (!init_)
203			Init();
204
205			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
206			return(1.0);
207
208			rad = elements_[atomicnum]->GetCovalentRad();
209
210			if (hyb == 2)
211			rad *= 0.95;
212			else if (hyb == 1)
213			rad *= 0.90;
214
215			return(rad);
216			}
217
218			RealType ElementsTable::CorrectedVdwRad(int atomicnum, int hyb) {
219			RealType rad;
220			if (!init_)
221			Init();
222
223			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
224			return(1.95);
225
226			rad = elements_[atomicnum]->GetVdwRad();
227
228			if (hyb == 2)
229			rad *= 0.95;
230			else if (hyb == 1)
231			rad *= 0.90;
232
233			return(rad);
234			}
235
236			RealType ElementsTable::GetCovalentRad(int atomicnum) {
237			if (!init_)
238			Init();
239
240			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
241			return(0.0);
242
243			return(elements_[atomicnum]->GetCovalentRad());
244			}
245
246			RealType ElementsTable::GetMass(int atomicnum) {
247			if (!init_)
248			Init();
249
250			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
251			return(0.0);
252
253			return(elements_[atomicnum]->GetMass());
254			}
255
256			int ElementsTable::GetAtomicNum(const char *sym) {
257			int temp;
258			return GetAtomicNum(sym, temp);
259			}
260
261			int ElementsTable::GetAtomicNum(const char *sym, int &iso) {
262			if (!init_)
263			Init();
264
265			std::vector<Element*>::iterator i;
266			for (i = elements_.begin();i != elements_.end();i++)
267			if (!strncasecmp(sym,(*i)->GetSymbol(),2))
268			return((*i)->GetAtomicNum());
269
270			if (strcasecmp(sym, "D") == 0) {
271			iso = 2;
272			return(1);
273			} else if (strcasecmp(sym, "T") == 0) {
274			iso = 3;
275			return(1);
276			} else
277			iso = 0;
278			return(0);
279			}
280
281			void ElementsTable::Init() {
282			if (init_)
283			return;
284			init_ = true;
285
286			std::string buffer, subbuffer;
287			std::ifstream ifs1, ifs2, ifs3, ifs4, *ifsP;
288			// First, look for an environment variable
289			if (getenv(envvar_.c_str()) != NULL) {
290			buffer = getenv(envvar_.c_str());
291			buffer += FILE_SEP_CHAR;
292
293			if (!subdir_.empty()) {
294			subbuffer = buffer;
295			subbuffer += subdir_;
296			subbuffer += FILE_SEP_CHAR;
297			}
298
299			buffer += filename_;
300			subbuffer += filename_;
301
302			ifs1.open(subbuffer.c_str());
303			ifsP= &ifs1;
304			if (!(*ifsP)) {
305			ifs2.open(buffer.c_str());
306			ifsP = &ifs2;
307			}
308			} else {
309			sprintf( painCave.errMsg,
310			"ElementsTable error.\n"
311			"\tunable to open datafile %s \n", filename_.c_str());
312			painCave.isFatal = 0;
313			simError();
314			}
315
316			char charBuffer[BUFF_SIZE];
317			if ((*ifsP)) {
318			while(ifsP->getline(charBuffer,BUFF_SIZE))
319			ParseLine(charBuffer);
320
321			if (ifs1)
322			ifs1.close();
323			if (ifs2)
324			ifs2.close();
325			if (ifs3)
326			ifs3.close();
327			if (ifs4)
328			ifs4.close();
329
330			if (GetSize() == 0) {
331			sprintf( painCave.errMsg,
332			"ElementsTable error.\n"
333			"\tCannot initialize database %s \n", filename_.c_str());
334			painCave.isFatal = 0;
335			simError();
336			}
337
338			}
339
340			}
341			}