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"
#include "io/basic_ifstrstream.hpp"

#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;
    ifstrstream 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:	3335
Committed:	Thu Jan 24 21:38:53 2008 UTC (16 years, 5 months ago) by chuckv
File size:	8351 byte(s)
Log Message:	Fixed for MPI.
#	User	Rev	Content
1	gezelter	3319	/**********************************************************************
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	chuckv	3335	#include "io/basic_ifstrstream.hpp"
38	gezelter	3319
39			#if !HAVE_STRNCASECMP
40			extern "C" int strncasecmp(const char s1, const char s2, size_t n);
41			#endif
42
43			#ifdef WIN32
44			#define FILE_SEP_CHAR "\\"
45			#else
46			#define FILE_SEP_CHAR "/"
47			#endif
48
49			#ifndef BUFF_SIZE
50			#define BUFF_SIZE 32768
51			#endif
52
53			namespace oopse {
54
55			ElementsTable etab;
56
57			ElementsTable::ElementsTable() {
58			init_ = false;
59			STR_DEFINE(dir_, FRC_PATH );
60			envvar_ = "FORCE_PARAM_PATH";
61			filename_ = "element.txt";
62			}
63
64			ElementsTable::~ElementsTable() {
65			std::vector<Element*>::iterator i;
66			for (i = elements_.begin(); i != elements_.end(); i++)
67			delete *i;
68			}
69
70			void ElementsTable::ParseLine(const char *line) {
71			int num, maxbonds;
72			char symbol[5];
73			char name[256];
74			RealType Rcov,Rvdw,mass, elNeg, ionize, elAffin;
75			RealType red, green, blue;
76
77			// skip comment line (at the top)
78
79			if (line[0] != '#') {
80			sscanf(line,"%d %5s %lf %*f %lf %d %lf %lf %lf %lf %lf %lf %lf %255s",
81			&num,
82			symbol,
83			&Rcov,
84			&Rvdw,
85			&maxbonds,
86			&mass,
87			&elNeg,
88			&ionize,
89			&elAffin,
90			&red,
91			&green,
92			&blue,
93			name);
94
95			Element *ele = new Element(num, symbol, Rcov, Rvdw, maxbonds, mass,
96			elNeg, ionize, elAffin, red, green, blue,
97			name);
98			elements_.push_back(ele);
99			}
100			}
101
102			unsigned int ElementsTable::GetNumberOfElements() {
103			if (!init_)
104			Init();
105
106			return elements_.size();
107			}
108
109			char *ElementsTable::GetSymbol(int atomicnum) {
110			if (!init_)
111			Init();
112
113			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
114			return("\0");
115
116			return(elements_[atomicnum]->GetSymbol());
117			}
118
119			int ElementsTable::GetMaxBonds(int atomicnum) {
120			if (!init_)
121			Init();
122
123			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
124			return(0);
125
126			return(elements_[atomicnum]->GetMaxBonds());
127			}
128
129			RealType ElementsTable::GetElectroNeg(int atomicnum) {
130			if (!init_)
131			Init();
132
133			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
134			return(0.0);
135
136			return(elements_[atomicnum]->GetElectroNeg());
137			}
138
139			RealType ElementsTable::GetIonization(int atomicnum) {
140			if (!init_)
141			Init();
142
143			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
144			return(0.0);
145
146			return(elements_[atomicnum]->GetIonization());
147			}
148
149
150			RealType ElementsTable::GetElectronAffinity(int atomicnum) {
151			if (!init_)
152			Init();
153
154			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
155			return(0.0);
156
157			return(elements_[atomicnum]->GetElectronAffinity());
158			}
159
160			std::vector<RealType> ElementsTable::GetRGB(int atomicnum) {
161			if (!init_)
162			Init();
163
164			std::vector <RealType> colors;
165			colors.reserve(3);
166
167			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size())) {
168			colors.push_back(0.0);
169			colors.push_back(0.0);
170			colors.push_back(0.0);
171			return(colors);
172			}
173
174			colors.push_back(elements_[atomicnum]->GetRed());
175			colors.push_back(elements_[atomicnum]->GetGreen());
176			colors.push_back(elements_[atomicnum]->GetBlue());
177
178			return (colors);
179			}
180
181			std::string ElementsTable::GetName(int atomicnum) {
182			if (!init_)
183			Init();
184
185			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
186			return("Unknown");
187
188			return(elements_[atomicnum]->GetName());
189			}
190
191			RealType ElementsTable::GetVdwRad(int atomicnum) {
192			if (!init_)
193			Init();
194
195			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
196			return(0.0);
197
198			return(elements_[atomicnum]->GetVdwRad());
199			}
200
201			RealType ElementsTable::CorrectedBondRad(int atomicnum, int hyb) {
202			RealType rad;
203			if (!init_)
204			Init();
205
206			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
207			return(1.0);
208
209			rad = elements_[atomicnum]->GetCovalentRad();
210
211			if (hyb == 2)
212			rad *= 0.95;
213			else if (hyb == 1)
214			rad *= 0.90;
215
216			return(rad);
217			}
218
219			RealType ElementsTable::CorrectedVdwRad(int atomicnum, int hyb) {
220			RealType rad;
221			if (!init_)
222			Init();
223
224			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
225			return(1.95);
226
227			rad = elements_[atomicnum]->GetVdwRad();
228
229			if (hyb == 2)
230			rad *= 0.95;
231			else if (hyb == 1)
232			rad *= 0.90;
233
234			return(rad);
235			}
236
237			RealType ElementsTable::GetCovalentRad(int atomicnum) {
238			if (!init_)
239			Init();
240
241			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
242			return(0.0);
243
244			return(elements_[atomicnum]->GetCovalentRad());
245			}
246
247			RealType ElementsTable::GetMass(int atomicnum) {
248			if (!init_)
249			Init();
250
251			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
252			return(0.0);
253
254			return(elements_[atomicnum]->GetMass());
255			}
256
257			int ElementsTable::GetAtomicNum(const char *sym) {
258			int temp;
259			return GetAtomicNum(sym, temp);
260			}
261
262			int ElementsTable::GetAtomicNum(const char *sym, int &iso) {
263			if (!init_)
264			Init();
265
266			std::vector<Element*>::iterator i;
267			for (i = elements_.begin();i != elements_.end();i++)
268			if (!strncasecmp(sym,(*i)->GetSymbol(),2))
269			return((*i)->GetAtomicNum());
270
271			if (strcasecmp(sym, "D") == 0) {
272			iso = 2;
273			return(1);
274			} else if (strcasecmp(sym, "T") == 0) {
275			iso = 3;
276			return(1);
277			} else
278			iso = 0;
279			return(0);
280			}
281
282			void ElementsTable::Init() {
283			if (init_)
284			return;
285			init_ = true;
286
287			std::string buffer, subbuffer;
288	chuckv	3335	ifstrstream ifs1, ifs2, ifs3, ifs4, *ifsP;
289	gezelter	3319	// First, look for an environment variable
290			if (getenv(envvar_.c_str()) != NULL) {
291			buffer = getenv(envvar_.c_str());
292			buffer += FILE_SEP_CHAR;
293
294			if (!subdir_.empty()) {
295			subbuffer = buffer;
296			subbuffer += subdir_;
297			subbuffer += FILE_SEP_CHAR;
298			}
299
300			buffer += filename_;
301			subbuffer += filename_;
302
303			ifs1.open(subbuffer.c_str());
304			ifsP= &ifs1;
305			if (!(*ifsP)) {
306			ifs2.open(buffer.c_str());
307			ifsP = &ifs2;
308			}
309			} else {
310			sprintf( painCave.errMsg,
311			"ElementsTable error.\n"
312			"\tunable to open datafile %s \n", filename_.c_str());
313			painCave.isFatal = 0;
314			simError();
315			}
316
317			char charBuffer[BUFF_SIZE];
318			if ((*ifsP)) {
319			while(ifsP->getline(charBuffer,BUFF_SIZE))
320			ParseLine(charBuffer);
321
322			if (ifs1)
323			ifs1.close();
324			if (ifs2)
325			ifs2.close();
326			if (ifs3)
327			ifs3.close();
328			if (ifs4)
329			ifs4.close();
330
331			if (GetSize() == 0) {
332			sprintf( painCave.errMsg,
333			"ElementsTable error.\n"
334			"\tCannot initialize database %s \n", filename_.c_str());
335			painCave.isFatal = 0;
336			simError();
337			}
338
339			}
340
341			}
342			}