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 <iostream>
#include "config.h"
#include <cstdlib>
#include <string>
#include <fstream>
#include <cstdlib>
#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->is_open())) {
        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:	3453
Committed:	Thu Sep 18 21:51:20 2008 UTC (17 years, 1 month ago) by chuckv
File size:	8379 byte(s)
Log Message:	Fixed MPI bug in opening elements.txt.
#	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	chuckv	3450	#include <iostream>
33	gezelter	3319	#include "config.h"
34	cli2	3446	#include <cstdlib>
35	gezelter	3319	#include <string>
36			#include <fstream>
37	gezelter	3448	#include <cstdlib>
38	gezelter	3319	#include "utils/ElementsTable.hpp"
39			#include "utils/simError.h"
40	chuckv	3335	#include "io/basic_ifstrstream.hpp"
41	gezelter	3319
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			if (line[0] != '#') {
82			sscanf(line,"%d %5s %lf %*f %lf %d %lf %lf %lf %lf %lf %lf %lf %255s",
83			&num,
84			symbol,
85			&Rcov,
86			&Rvdw,
87			&maxbonds,
88			&mass,
89			&elNeg,
90			&ionize,
91			&elAffin,
92			&red,
93			&green,
94			&blue,
95			name);
96
97			Element *ele = new Element(num, symbol, Rcov, Rvdw, maxbonds, mass,
98			elNeg, ionize, elAffin, red, green, blue,
99			name);
100			elements_.push_back(ele);
101	chuckv	3450
102	gezelter	3319	}
103			}
104
105			unsigned int ElementsTable::GetNumberOfElements() {
106			if (!init_)
107			Init();
108
109			return elements_.size();
110			}
111
112			char *ElementsTable::GetSymbol(int atomicnum) {
113			if (!init_)
114			Init();
115
116			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
117			return("\0");
118
119			return(elements_[atomicnum]->GetSymbol());
120			}
121
122			int ElementsTable::GetMaxBonds(int atomicnum) {
123			if (!init_)
124			Init();
125
126			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
127			return(0);
128
129			return(elements_[atomicnum]->GetMaxBonds());
130			}
131
132			RealType ElementsTable::GetElectroNeg(int atomicnum) {
133			if (!init_)
134			Init();
135
136			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
137			return(0.0);
138
139			return(elements_[atomicnum]->GetElectroNeg());
140			}
141
142			RealType ElementsTable::GetIonization(int atomicnum) {
143			if (!init_)
144			Init();
145
146			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
147			return(0.0);
148
149			return(elements_[atomicnum]->GetIonization());
150			}
151
152
153			RealType ElementsTable::GetElectronAffinity(int atomicnum) {
154			if (!init_)
155			Init();
156
157			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
158			return(0.0);
159
160			return(elements_[atomicnum]->GetElectronAffinity());
161			}
162
163			std::vector<RealType> ElementsTable::GetRGB(int atomicnum) {
164			if (!init_)
165			Init();
166
167			std::vector <RealType> colors;
168			colors.reserve(3);
169
170			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size())) {
171			colors.push_back(0.0);
172			colors.push_back(0.0);
173			colors.push_back(0.0);
174			return(colors);
175			}
176
177			colors.push_back(elements_[atomicnum]->GetRed());
178			colors.push_back(elements_[atomicnum]->GetGreen());
179			colors.push_back(elements_[atomicnum]->GetBlue());
180
181			return (colors);
182			}
183
184			std::string ElementsTable::GetName(int atomicnum) {
185			if (!init_)
186			Init();
187
188			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
189			return("Unknown");
190
191			return(elements_[atomicnum]->GetName());
192			}
193
194			RealType ElementsTable::GetVdwRad(int atomicnum) {
195			if (!init_)
196			Init();
197
198			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
199			return(0.0);
200
201			return(elements_[atomicnum]->GetVdwRad());
202			}
203
204			RealType ElementsTable::CorrectedBondRad(int atomicnum, int hyb) {
205			RealType rad;
206			if (!init_)
207			Init();
208
209			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
210			return(1.0);
211
212			rad = elements_[atomicnum]->GetCovalentRad();
213
214			if (hyb == 2)
215			rad *= 0.95;
216			else if (hyb == 1)
217			rad *= 0.90;
218
219			return(rad);
220			}
221
222			RealType ElementsTable::CorrectedVdwRad(int atomicnum, int hyb) {
223			RealType rad;
224			if (!init_)
225			Init();
226
227			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
228			return(1.95);
229
230			rad = elements_[atomicnum]->GetVdwRad();
231
232			if (hyb == 2)
233			rad *= 0.95;
234			else if (hyb == 1)
235			rad *= 0.90;
236
237			return(rad);
238			}
239
240			RealType ElementsTable::GetCovalentRad(int atomicnum) {
241			if (!init_)
242			Init();
243
244			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
245			return(0.0);
246
247			return(elements_[atomicnum]->GetCovalentRad());
248			}
249
250			RealType ElementsTable::GetMass(int atomicnum) {
251			if (!init_)
252			Init();
253
254			if (atomicnum < 0 \|\| atomicnum > static_cast<int>(elements_.size()))
255			return(0.0);
256
257			return(elements_[atomicnum]->GetMass());
258			}
259
260			int ElementsTable::GetAtomicNum(const char *sym) {
261			int temp;
262			return GetAtomicNum(sym, temp);
263			}
264
265			int ElementsTable::GetAtomicNum(const char *sym, int &iso) {
266			if (!init_)
267			Init();
268
269			std::vector<Element*>::iterator i;
270			for (i = elements_.begin();i != elements_.end();i++)
271			if (!strncasecmp(sym,(*i)->GetSymbol(),2))
272			return((*i)->GetAtomicNum());
273
274			if (strcasecmp(sym, "D") == 0) {
275			iso = 2;
276			return(1);
277			} else if (strcasecmp(sym, "T") == 0) {
278			iso = 3;
279			return(1);
280			} else
281			iso = 0;
282			return(0);
283			}
284
285			void ElementsTable::Init() {
286			if (init_)
287			return;
288			init_ = true;
289
290			std::string buffer, subbuffer;
291	chuckv	3335	ifstrstream ifs1, ifs2, ifs3, ifs4, *ifsP;
292	gezelter	3319	// First, look for an environment variable
293			if (getenv(envvar_.c_str()) != NULL) {
294			buffer = getenv(envvar_.c_str());
295			buffer += FILE_SEP_CHAR;
296
297	chuckv	3453
298
299
300	gezelter	3319	if (!subdir_.empty()) {
301			subbuffer = buffer;
302			subbuffer += subdir_;
303			subbuffer += FILE_SEP_CHAR;
304			}
305
306	chuckv	3453
307
308	gezelter	3319	buffer += filename_;
309			subbuffer += filename_;
310	chuckv	3453
311	gezelter	3319
312			ifs1.open(subbuffer.c_str());
313			ifsP= &ifs1;
314	chuckv	3453	if (!(ifsP->is_open())) {
315	gezelter	3319	ifs2.open(buffer.c_str());
316			ifsP = &ifs2;
317			}
318	chuckv	3453
319	gezelter	3319	} else {
320			sprintf( painCave.errMsg,
321			"ElementsTable error.\n"
322			"\tunable to open datafile %s \n", filename_.c_str());
323			painCave.isFatal = 0;
324			simError();
325			}
326
327			char charBuffer[BUFF_SIZE];
328			if ((*ifsP)) {
329			while(ifsP->getline(charBuffer,BUFF_SIZE))
330			ParseLine(charBuffer);
331	chuckv	3453
332	chuckv	3450	if (ifs1)
333			ifs1.close();
334			if (ifs2)
335			ifs2.close();
336			if (ifs3)
337			ifs3.close();
338			if (ifs4)
339			ifs4.close();
340
341			if (GetSize() == 0) {
342			sprintf( painCave.errMsg,
343			"ElementsTable error.\n"
344			"\tCannot initialize database %s \n", filename_.c_str());
345			painCave.isFatal = 0;
346			simError();
347			}
348	gezelter	3319
349			}
350
351			}
352			}