src/UseTheForce/DUFF.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * 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 Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

#include "UseTheForce/DUFF.hpp"
#include "UseTheForce/DarkSide/lj_interface.h"

namespace oopse {

//definition of createDUFF
ForceField* createDUFF() {
    return new DUFF();
}

//register createDUFF to ForceFieldCreator
ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);


ParseState DUFF::getSection(const std::string& section) {
    ParseState result;
    
    switch(section) {
        case "AtomTypes" :
            result = DUFF::AtomTypeSection;
            break;

        case "BondTypes" :
            result = DUFF::BondTypeSection;
            break;

        case "BendTypes" :
            result = DUFF::BendTypeSection;
            break;

        case "TorsionTypes" :
            result = DUFF::TorsionTypeSection;
            break;
        default:
            result = DUFF::UnknownSection;
    }

    return result;
}

void DUFF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    ffStream = openForceFiledFile(filename);
    const int bufferSize = 65535;
    std::string line;
    char buffer[bufferSize];
    int lineNo = 0;
    ParseState currentSection = DUFF::UnknownSection;
    
    while(ffStream.getline(buffer, bufferSize)){
        ++lineNo;

        line = trimSpaces(buffer);
        //a line begins with "//" is comment
        if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
            continue;
        } else {

            switch(currentSection) {
                case DUFF::AtomTypeSection :
                    parseAtomType(line, lineNo);
                    break;

                case DUFF::BondTypeSection :
                    parseBondType(line, lineNo);
                    break;

                case DUFF::BendTypeSection :
                    parseBendType(line, lineNo);
                    break;

                case DUFF::TorsionTypeSection :
                    parseTorsionType(line, lineNo);
                    break;
                    
                case DUFF::UnknownSection:
                    StringTokenizer tokenizer(line);
                    
                    std::string keyword = tokenizer.nextToken();
                    std::string section = tokenizer.nextToken();

                    ParseState newSection = getSection(section);
                    if (keyword != "begin" || keyword != "end") {
                            std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
                    } else if (keyword == "begin") {
                        if (newSection == DUFF::UnknownSection) {
                            std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
                        } else {
                            //enter a new section
                            currentSection = newSection;
                        }
                        
                    } else if (keyword == "end"){
                        if (currentSection == newSection) ) {
                            //leave a section
                            currentSection = DUFF::UnknownSection;
                        } else {                            
                            std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
                        }

                    }
                    break;
                default :
                
            }
            
        }
    }
    
    delete ffStream;
}


void DUFF::parseAtomType(const std::string& line, int lineNo){ 
    StringTokenizer tokenizer(line);
    
    if (tokenizer.countTokens() >= 4) {
        atomTypeName = tokenizer.nextToken();
        mass = tokenizer.nextTokenAsFloat();
        epsilon = tokenizer.nextTokenAsFloat();
        sigma = tokenizer.nextTokenAsFloat();

        atomType = new AtomType();
        atomType->setName(atomTypeName);
        atomType->setMass(mass);
        
        //by default, all of the properties in AtomTypeProperties is set to 0
        //In  Lennard-Jones Force Field, we only need to set Lennard-Jones to true
        atomType->setLennardJones();

        atomType->setIdent(ident);
        atomType->addProperty(new DoubleGenericData("Epsilon", epsilon));                                
        atomType->addProperty(new DoubleGenericData("Sigma", sigma));                                
        atomType->complete();
        //notify a new LJtype atom type is created
        newLJtype(&ident, &sigma, &epsilon, &status);

        //add atom type to AtomTypeContainer
        addAtomType(atomTypeName, atomType);
        ++ident;
        
    } else {
        sprintf( painCave.errMsg,
               "Not enough tokens when parsing Lennard-Jones Force Field : %s\n"
               "in line %d : %s\n",
               filename.c_str(), lineNo, line);
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();                
    }    
}

void DUFF::parseBondType(const std::string& line, int lineNo){ 

    StringTokenizer tokenizer(line);
    std::string at1;
    std::string at2;
    std::string bt;
    BondType* bondType = NULL;
    double b0;
    
    int nTokens = tokenizer.countTokens();

    if (nTokens < 4) {

        return;
    }
    
    at1 = tokenizer.nextToken();
    at2 = tokenizer.nextToken();
    bt = tokenizer.nextToken();
    b0 = tokenizer.nextTokenAsDouble();
    nTokens -= 4;

    //switch is a maintain nightmare
    switch(bt) {
        case "FixedBondType" :
            bondType = new FixedBondType();
            break;
            
        case "HarmonicBondType" :
            if (nTokens < 1) {

            } else {

                double kb = tokenizer.nextTokenAsDouble();
                bondType = new HarmonicBondType(b0, kb);
            }

            break;

        case "CubicBondType" :
            if (nTokens < 4) {

            } else {

                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bondType = new CubicBondType(b0, k3, k2, k1, k0);
            }
            break;
            
        case "QuadraticBondType" :
            if (nTokens < 5) {

            } else {

                b0 = tokenizer.nextTokenAsDouble();
                double k4 = tokenizer.nextTokenAsDouble();
                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0);
            }
            break;

        case "PolynomialBondType " :
            if (nTokens < 2 || nTokens % 2 != 0) {

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialBondType pbt = new PolynomialBondType();
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();

                    if (power < 0) {

                    } else {
                        pbt->setCoefficient(power, coefficient);
                    }
                }
            }
            
            break;

        default:
            
    }

    if (bondType != NULL) {
        addBondType(at1, at2, bondType);
    }
}

void DUFF::parseBendType(const std::string& line, int lineNo){ 
    StringTokenizer tokenizer(line);
    std::string at1;
    std::string at2;
    std::string at3;
    std::string bt;
    double theta0;
    BendType* bendType = NULL;

    int nTokens = tokenizer.countTokens();

    if (nTokens < 5) {

        return;
    }
    
    at1 = tokenizer.nextToken();
    at2 = tokenizer.nextToken();
    at3 = tokenizer.nextToken();
    bt = tokenizer.nextToken();
    theta0 = tokenizer.nextTokenAsDouble();
    nTokens -= 5;

    //switch is a maintain nightmare
    switch(bt) {
            
        case "HarmonicBendType" :
            
            if (nTokens < 1) {

            } else {

                double ktheta = tokenizer.nextTokenAsDouble();
                bendType = new HarmonicBendType(theta0, ktheta);
            }
            break;
        case "GhostBendType" :
            if (nTokens < 1) {

            } else {
                double ktheta = tokenizer.nextTokenAsDouble();
                bendType = new HarmonicBendType(theta0, ktheta);                
            }
            break;            

        case "UreyBradleyBendType" :
            if (nTokens < 3) {

            } else {
                double ktheta = tokenizer.nextTokenAsDouble();
                double s0 =  tokenizer.nextTokenAsDouble();
                double kub = tokenizer.nextTokenAsDouble();
                bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);                
            }
            break; 
            
        case "CubicBendType" :
            if (nTokens < 4) {

            } else {

                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new CubicBendType(theta0, k3, k2, k1, k0);
            }
            break;
            
        case "QuadraticBendType" :
            if (nTokens < 5) {

            } else {

                theta0 = tokenizer.nextTokenAsDouble();
                double k4 = tokenizer.nextTokenAsDouble();
                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0);
            }
            break;

        case "PolynomialBendType " :
            if (nTokens < 2 || nTokens % 2 != 0) {

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialBendType* pbt = new PolynomialBendType();
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();

                    if (power < 0) {

                    } else {
                        pbt->setCoefficient(power, coefficient);
                    }
                }
            }
            
            break;

        default:
            
    }

    if (bendType != NULL) {
        addBendType(at1, at2, at3, bendType);
    }
    
}

void DUFF::parseTorsionType(const std::string& line, int lineNo){ 
    StringTokenizer tokenizer(line);
    std::string at1;
    std::string at2;
    std::string at3;
    std::string at4;
    std::string tt;
    TorsionType* bendType = NULL;

    int nTokens = tokenizer.countTokens();

    if (nTokens < 5) {

        return;
    }
    
    at1 = tokenizer.nextToken();
    at2 = tokenizer.nextToken();
    at3 = tokenizer.nextToken();
    at4 = tokenizer.nextToken();
    tt = tokenizer.nextToken();

    nTokens -= 5;

    switch(tt) {
            
        case "CubicTorsionType" :
            if (nTokens < 4) {

            } else {

                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new CubicTorsionType(k3, k2, k1, k0);
            }
            break;
            
        case "QuadraticTorsionType" :
            if (nTokens < 5) {

            } else {

                theta0 = tokenizer.nextTokenAsDouble();
                double k4 = tokenizer.nextTokenAsDouble();
                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0);
            }
            break;

        case "PolynomialTorsionType " :
            if (nTokens < 2 || nTokens % 2 != 0) {

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialTorsionType* pbt = new PolynomialTorsionType();
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();

                    if (power < 0) {

                    } else {
                        pbt->setCoefficient(power, coefficient);
                    }
                }
            }
            
            break;
        case "CharmmTorsionType" :
            
            if (nTokens < 3 || nTokens % 3 != 0) {

            } else {
                int nSets = nTokens / 3;
  
                double kchi;
                int n;
                double delta;                
                CharmmTorsionType* ctt = new CharmmTorsionType();
                
                for (int i = 0; i < nSets; ++i) {
                    kchi = tokenizer.nextTokenAsDouble();
                    n = tokenizer.nextTokenAsInt();
                    delta = tokenizer.nextTokenAsDouble();
    
                    if (n < 0 || n > 6) {

                    } else {
                        ctt->setCharmmTorsionParameter(kchi, n, delta);
                    }
                }
            }
        default:
            
    }

    if (bendType != NULL) {
        addTorsionType(at1, at2, at3, bendType);
    }
}

} //end namespace oopse

Revision:	1757
Committed:	Fri Nov 19 00:11:33 2004 UTC (19 years, 8 months ago) by tim
File size:	15349 byte(s)
Log Message:	adding DUFF parser
#	Content
1	/*
2	* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3	*
4	* Contact: oopse@oopse.org
5	*
6	* This program is free software; you can redistribute it and/or
7	* modify it under the terms of the GNU Lesser General Public License
8	* as published by the Free Software Foundation; either version 2.1
9	* of the License, or (at your option) any later version.
10	* All we ask is that proper credit is given for our work, which includes
11	* - but is not limited to - adding the above copyright notice to the beginning
12	* of your source code files, and to any copyright notice that you may distribute
13	* with programs based on this work.
14	*
15	* This program is distributed in the hope that it will be useful,
16	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	* GNU Lesser General Public License for more details.
19	*
20	* You should have received a copy of the GNU Lesser General Public License
21	* along with this program; if not, write to the Free Software
22	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23	*
24	*/
25
26	#include "UseTheForce/DUFF.hpp"
27	#include "UseTheForce/DarkSide/lj_interface.h"
28
29	namespace oopse {
30
31	//definition of createDUFF
32	ForceField* createDUFF() {
33	return new DUFF();
34	}
35
36	//register createDUFF to ForceFieldCreator
37	ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);
38
39
40	ParseState DUFF::getSection(const std::string& section) {
41	ParseState result;
42
43	switch(section) {
44	case "AtomTypes" :
45	result = DUFF::AtomTypeSection;
46	break;
47
48	case "BondTypes" :
49	result = DUFF::BondTypeSection;
50	break;
51
52	case "BendTypes" :
53	result = DUFF::BendTypeSection;
54	break;
55
56	case "TorsionTypes" :
57	result = DUFF::TorsionTypeSection;
58	break;
59	default:
60	result = DUFF::UnknownSection;
61	}
62
63	return result;
64	}
65
66	void DUFF::parse(const std::string& filename) {
67	ifstrstream* ffStream;
68	ffStream = openForceFiledFile(filename);
69	const int bufferSize = 65535;
70	std::string line;
71	char buffer[bufferSize];
72	int lineNo = 0;
73	ParseState currentSection = DUFF::UnknownSection;
74
75	while(ffStream.getline(buffer, bufferSize)){
76	++lineNo;
77
78	line = trimSpaces(buffer);
79	//a line begins with "//" is comment
80	if ( line.empty() \|\| (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
81	continue;
82	} else {
83
84	switch(currentSection) {
85	case DUFF::AtomTypeSection :
86	parseAtomType(line, lineNo);
87	break;
88
89	case DUFF::BondTypeSection :
90	parseBondType(line, lineNo);
91	break;
92
93	case DUFF::BendTypeSection :
94	parseBendType(line, lineNo);
95	break;
96
97	case DUFF::TorsionTypeSection :
98	parseTorsionType(line, lineNo);
99	break;
100
101	case DUFF::UnknownSection:
102	StringTokenizer tokenizer(line);
103
104	std::string keyword = tokenizer.nextToken();
105	std::string section = tokenizer.nextToken();
106
107	ParseState newSection = getSection(section);
108	if (keyword != "begin" \|\| keyword != "end") {
109	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
110	} else if (keyword == "begin") {
111	if (newSection == DUFF::UnknownSection) {
112	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
113	} else {
114	//enter a new section
115	currentSection = newSection;
116	}
117
118	} else if (keyword == "end"){
119	if (currentSection == newSection) ) {
120	//leave a section
121	currentSection = DUFF::UnknownSection;
122	} else {
123	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
124	}
125
126	}
127	break;
128	default :
129
130	}
131
132	}
133	}
134
135	delete ffStream;
136	}
137
138
139	void DUFF::parseAtomType(const std::string& line, int lineNo){
140	StringTokenizer tokenizer(line);
141
142	if (tokenizer.countTokens() >= 4) {
143	atomTypeName = tokenizer.nextToken();
144	mass = tokenizer.nextTokenAsFloat();
145	epsilon = tokenizer.nextTokenAsFloat();
146	sigma = tokenizer.nextTokenAsFloat();
147
148	atomType = new AtomType();
149	atomType->setName(atomTypeName);
150	atomType->setMass(mass);
151
152	//by default, all of the properties in AtomTypeProperties is set to 0
153	//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true
154	atomType->setLennardJones();
155
156	atomType->setIdent(ident);
157	atomType->addProperty(new DoubleGenericData("Epsilon", epsilon));
158	atomType->addProperty(new DoubleGenericData("Sigma", sigma));
159	atomType->complete();
160	//notify a new LJtype atom type is created
161	newLJtype(&ident, &sigma, &epsilon, &status);
162
163	//add atom type to AtomTypeContainer
164	addAtomType(atomTypeName, atomType);
165	++ident;
166
167	} else {
168	sprintf( painCave.errMsg,
169	"Not enough tokens when parsing Lennard-Jones Force Field : %s\n"
170	"in line %d : %s\n",
171	filename.c_str(), lineNo, line);
172	painCave.severity = OOPSE_ERROR;
173	painCave.isFatal = 1;
174	simError();
175	}
176	}
177
178	void DUFF::parseBondType(const std::string& line, int lineNo){
179
180	StringTokenizer tokenizer(line);
181	std::string at1;
182	std::string at2;
183	std::string bt;
184	BondType* bondType = NULL;
185	double b0;
186
187	int nTokens = tokenizer.countTokens();
188
189	if (nTokens < 4) {
190
191	return;
192	}
193
194	at1 = tokenizer.nextToken();
195	at2 = tokenizer.nextToken();
196	bt = tokenizer.nextToken();
197	b0 = tokenizer.nextTokenAsDouble();
198	nTokens -= 4;
199
200	//switch is a maintain nightmare
201	switch(bt) {
202	case "FixedBondType" :
203	bondType = new FixedBondType();
204	break;
205
206	case "HarmonicBondType" :
207	if (nTokens < 1) {
208
209	} else {
210
211	double kb = tokenizer.nextTokenAsDouble();
212	bondType = new HarmonicBondType(b0, kb);
213	}
214
215	break;
216
217	case "CubicBondType" :
218	if (nTokens < 4) {
219
220	} else {
221
222	double k3 = tokenizer.nextTokenAsDouble();
223	double k2 = tokenizer.nextTokenAsDouble();
224	double k1 = tokenizer.nextTokenAsDouble();
225	double k0 = tokenizer.nextTokenAsDouble();
226
227	bondType = new CubicBondType(b0, k3, k2, k1, k0);
228	}
229	break;
230
231	case "QuadraticBondType" :
232	if (nTokens < 5) {
233
234	} else {
235
236	b0 = tokenizer.nextTokenAsDouble();
237	double k4 = tokenizer.nextTokenAsDouble();
238	double k3 = tokenizer.nextTokenAsDouble();
239	double k2 = tokenizer.nextTokenAsDouble();
240	double k1 = tokenizer.nextTokenAsDouble();
241	double k0 = tokenizer.nextTokenAsDouble();
242
243	bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0);
244	}
245	break;
246
247	case "PolynomialBondType " :
248	if (nTokens < 2 \|\| nTokens % 2 != 0) {
249
250	} else {
251	int nPairs = nTokens / 2;
252	int power;
253	double coefficient;
254	PolynomialBondType pbt = new PolynomialBondType();
255
256	for (int i = 0; i < nPairs; ++i) {
257	power = tokenizer.nextTokenAsInt();
258	coefficient = tokenizer.nextTokenAsDouble();
259
260	if (power < 0) {
261
262	} else {
263	pbt->setCoefficient(power, coefficient);
264	}
265	}
266	}
267
268	break;
269
270	default:
271
272	}
273
274	if (bondType != NULL) {
275	addBondType(at1, at2, bondType);
276	}
277	}
278
279	void DUFF::parseBendType(const std::string& line, int lineNo){
280	StringTokenizer tokenizer(line);
281	std::string at1;
282	std::string at2;
283	std::string at3;
284	std::string bt;
285	double theta0;
286	BendType* bendType = NULL;
287
288	int nTokens = tokenizer.countTokens();
289
290	if (nTokens < 5) {
291
292	return;
293	}
294
295	at1 = tokenizer.nextToken();
296	at2 = tokenizer.nextToken();
297	at3 = tokenizer.nextToken();
298	bt = tokenizer.nextToken();
299	theta0 = tokenizer.nextTokenAsDouble();
300	nTokens -= 5;
301
302	//switch is a maintain nightmare
303	switch(bt) {
304
305	case "HarmonicBendType" :
306
307	if (nTokens < 1) {
308
309	} else {
310
311	double ktheta = tokenizer.nextTokenAsDouble();
312	bendType = new HarmonicBendType(theta0, ktheta);
313	}
314	break;
315	case "GhostBendType" :
316	if (nTokens < 1) {
317
318	} else {
319	double ktheta = tokenizer.nextTokenAsDouble();
320	bendType = new HarmonicBendType(theta0, ktheta);
321	}
322	break;
323
324	case "UreyBradleyBendType" :
325	if (nTokens < 3) {
326
327	} else {
328	double ktheta = tokenizer.nextTokenAsDouble();
329	double s0 = tokenizer.nextTokenAsDouble();
330	double kub = tokenizer.nextTokenAsDouble();
331	bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);
332	}
333	break;
334
335	case "CubicBendType" :
336	if (nTokens < 4) {
337
338	} else {
339
340	double k3 = tokenizer.nextTokenAsDouble();
341	double k2 = tokenizer.nextTokenAsDouble();
342	double k1 = tokenizer.nextTokenAsDouble();
343	double k0 = tokenizer.nextTokenAsDouble();
344
345	bendType = new CubicBendType(theta0, k3, k2, k1, k0);
346	}
347	break;
348
349	case "QuadraticBendType" :
350	if (nTokens < 5) {
351
352	} else {
353
354	theta0 = tokenizer.nextTokenAsDouble();
355	double k4 = tokenizer.nextTokenAsDouble();
356	double k3 = tokenizer.nextTokenAsDouble();
357	double k2 = tokenizer.nextTokenAsDouble();
358	double k1 = tokenizer.nextTokenAsDouble();
359	double k0 = tokenizer.nextTokenAsDouble();
360
361	bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0);
362	}
363	break;
364
365	case "PolynomialBendType " :
366	if (nTokens < 2 \|\| nTokens % 2 != 0) {
367
368	} else {
369	int nPairs = nTokens / 2;
370	int power;
371	double coefficient;
372	PolynomialBendType* pbt = new PolynomialBendType();
373
374	for (int i = 0; i < nPairs; ++i) {
375	power = tokenizer.nextTokenAsInt();
376	coefficient = tokenizer.nextTokenAsDouble();
377
378	if (power < 0) {
379
380	} else {
381	pbt->setCoefficient(power, coefficient);
382	}
383	}
384	}
385
386	break;
387
388	default:
389
390	}
391
392	if (bendType != NULL) {
393	addBendType(at1, at2, at3, bendType);
394	}
395
396	}
397
398	void DUFF::parseTorsionType(const std::string& line, int lineNo){
399	StringTokenizer tokenizer(line);
400	std::string at1;
401	std::string at2;
402	std::string at3;
403	std::string at4;
404	std::string tt;
405	TorsionType* bendType = NULL;
406
407	int nTokens = tokenizer.countTokens();
408
409	if (nTokens < 5) {
410
411	return;
412	}
413
414	at1 = tokenizer.nextToken();
415	at2 = tokenizer.nextToken();
416	at3 = tokenizer.nextToken();
417	at4 = tokenizer.nextToken();
418	tt = tokenizer.nextToken();
419
420	nTokens -= 5;
421
422	switch(tt) {
423
424	case "CubicTorsionType" :
425	if (nTokens < 4) {
426
427	} else {
428
429	double k3 = tokenizer.nextTokenAsDouble();
430	double k2 = tokenizer.nextTokenAsDouble();
431	double k1 = tokenizer.nextTokenAsDouble();
432	double k0 = tokenizer.nextTokenAsDouble();
433
434	bendType = new CubicTorsionType(k3, k2, k1, k0);
435	}
436	break;
437
438	case "QuadraticTorsionType" :
439	if (nTokens < 5) {
440
441	} else {
442
443	theta0 = tokenizer.nextTokenAsDouble();
444	double k4 = tokenizer.nextTokenAsDouble();
445	double k3 = tokenizer.nextTokenAsDouble();
446	double k2 = tokenizer.nextTokenAsDouble();
447	double k1 = tokenizer.nextTokenAsDouble();
448	double k0 = tokenizer.nextTokenAsDouble();
449
450	bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0);
451	}
452	break;
453
454	case "PolynomialTorsionType " :
455	if (nTokens < 2 \|\| nTokens % 2 != 0) {
456
457	} else {
458	int nPairs = nTokens / 2;
459	int power;
460	double coefficient;
461	PolynomialTorsionType* pbt = new PolynomialTorsionType();
462
463	for (int i = 0; i < nPairs; ++i) {
464	power = tokenizer.nextTokenAsInt();
465	coefficient = tokenizer.nextTokenAsDouble();
466
467	if (power < 0) {
468
469	} else {
470	pbt->setCoefficient(power, coefficient);
471	}
472	}
473	}
474
475	break;
476	case "CharmmTorsionType" :
477
478	if (nTokens < 3 \|\| nTokens % 3 != 0) {
479
480	} else {
481	int nSets = nTokens / 3;
482
483	double kchi;
484	int n;
485	double delta;
486	CharmmTorsionType* ctt = new CharmmTorsionType();
487
488	for (int i = 0; i < nSets; ++i) {
489	kchi = tokenizer.nextTokenAsDouble();
490	n = tokenizer.nextTokenAsInt();
491	delta = tokenizer.nextTokenAsDouble();
492
493	if (n < 0 \|\| n > 6) {
494
495	} else {
496	ctt->setCharmmTorsionParameter(kchi, n, delta);
497	}
498	}
499	}
500	default:
501
502	}
503
504	if (bendType != NULL) {
505	addTorsionType(at1, at2, at3, bendType);
506	}
507	}
508
509	} //end namespace oopse
510