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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include "io/TorsionTypesSectionParser.hpp" |
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#include "types/TorsionType.hpp" |
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#include "types/CubicTorsionType.hpp" |
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#include "types/QuarticTorsionType.hpp" |
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#include "types/PolynomialTorsionType.hpp" |
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#include "types/CharmmTorsionType.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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namespace oopse { |
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chuckv |
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TorsionTypesSectionParser::TorsionTypesSectionParser(ForceFieldOptions& options) : options_(options){ |
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setSectionName("TorsionTypes"); |
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stringToEnumMap_["GhostTorsion"] == ttGhostTorsion; |
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stringToEnumMap_["Cubic"] = ttCubic; |
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stringToEnumMap_["Quartic"] = ttQuartic; |
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stringToEnumMap_["Polynomial"] = ttPolynomial; |
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stringToEnumMap_["Charmm"] = ttCharmm; |
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} |
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|
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void TorsionTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){ |
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StringTokenizer tokenizer(line); |
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TorsionType* torsionType = NULL; |
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int nTokens = tokenizer.countTokens(); |
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if (nTokens < 5) { |
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return; |
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} |
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std::string at1 = tokenizer.nextToken(); |
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std::string at2 = tokenizer.nextToken(); |
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std::string at3 = tokenizer.nextToken(); |
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std::string at4 = tokenizer.nextToken(); |
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TorsionTypeEnum tt = getTorsionTypeEnum(tokenizer.nextToken()); |
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nTokens -= 5; |
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switch(tt) { |
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|
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case TorsionTypesSectionParser::ttGhostTorsion: |
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if (nTokens < 4) { |
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|
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} else { |
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|
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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tim |
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torsionType = new CubicTorsionType(k3, k2, k1, k0); |
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} |
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break; |
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|
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case TorsionTypesSectionParser::ttCubic : |
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if (nTokens < 4) { |
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|
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} else { |
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|
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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torsionType = new CubicTorsionType(k3, k2, k1, k0); |
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} |
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break; |
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case TorsionTypesSectionParser::ttQuartic: |
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if (nTokens < 5) { |
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} else { |
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|
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double k4 = tokenizer.nextTokenAsDouble(); |
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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torsionType = new QuarticTorsionType( k4, k3, k2, k1, k0); |
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} |
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break; |
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case TorsionTypesSectionParser::ttPolynomial: |
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if (nTokens < 2 || nTokens % 2 != 0) { |
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} else { |
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int nPairs = nTokens / 2; |
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int power; |
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double coefficient; |
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PolynomialTorsionType* ptt = new PolynomialTorsionType(); |
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for (int i = 0; i < nPairs; ++i) { |
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power = tokenizer.nextTokenAsInt(); |
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coefficient = tokenizer.nextTokenAsDouble(); |
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ptt->setCoefficient(power, coefficient); |
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} |
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} |
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break; |
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case TorsionTypesSectionParser::ttCharmm: |
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if (nTokens < 3 || nTokens % 3 != 0) { |
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} else { |
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int nSets = nTokens / 3; |
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std::vector<CharmmTorsionParameter> parameters; |
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for (int i = 0; i < nSets; ++i) { |
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CharmmTorsionParameter currParam; |
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currParam.kchi = tokenizer.nextTokenAsDouble(); |
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currParam.n = tokenizer.nextTokenAsInt(); |
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currParam.delta = tokenizer.nextTokenAsDouble(); |
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parameters.push_back(currParam); |
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} |
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CharmmTorsionType* ctt = new CharmmTorsionType(parameters); |
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} |
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break; |
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case TorsionTypesSectionParser::ttUnknown : |
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default: |
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break; |
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} |
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if (torsionType != NULL) { |
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ff.addTorsionType(at1, at2, at3, at4, torsionType); |
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} |
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} |
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TorsionTypesSectionParser::TorsionTypeEnum TorsionTypesSectionParser::getTorsionTypeEnum(const std::string& str) { |
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std::map<std::string, TorsionTypeEnum>::iterator i; |
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i = stringToEnumMap_.find(str); |
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return i == stringToEnumMap_.end() ? TorsionTypesSectionParser::ttUnknown : i->second; |
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} |
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} //end namespace oopse |
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