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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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|
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#ifndef TYPES_ATOMSTAMP_HPP |
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#define TYPES_ATOMSTAMP_HPP |
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|
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#include "io/LinkedAssign.hpp" |
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|
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class AtomStamp{ |
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|
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public: |
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AtomStamp(); |
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~AtomStamp(); |
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|
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void setPosition( double x, double y, double z ); |
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void setOrientation( double phi, double theta, double psi ); |
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char* assignString( char* lhs, char* rhs ); |
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char* assignDouble( char* lhs, double rhs ); |
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char* assignInt( char* lhs, int rhs ); |
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char* checkMe( void ); |
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|
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char* getType( void ) { return type; } |
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short int havePosition( void ) { return have_position; } |
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short int haveOrientation( void ) { return have_orientation; } |
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double getPosX( void ) { return pos[0]; } |
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double getPosY( void ) { return pos[1]; } |
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double getPosZ( void ) { return pos[2]; } |
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double getEulerPhi( void ) { return ornt[0]; } |
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double getEulerTheta( void ) { return ornt[1]; } |
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double getEulerPsi( void ) { return ornt[2]; } |
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|
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|
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private: |
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|
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double pos[3]; //the position vector |
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short int have_position; // boolean for positions |
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double ornt[3]; // the Euler angles |
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short int have_orientation; |
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char type[100]; // the type name of the atom |
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short int have_type; |
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|
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LinkedAssign* unhandled; // the list of unhandled assignments |
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short int have_extras; |
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}; |
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|
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#endif |
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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 |
5 |
> |
* non-exclusive, royalty free, license to use, modify and |
6 |
> |
* 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 |
12 |
> |
* 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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|
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#ifndef TYPES_ATOMSTAMP_HPP |
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#define TYPES_ATOMSTAMP_HPP |
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|
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#include <set> |
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#include <vector> |
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|
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#include "types/DataHolder.hpp" |
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namespace oopse { |
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|
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class AtomStamp : public DataHolder { |
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DeclareParameter(Type, std::string); |
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public: |
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AtomStamp(int index); |
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public: |
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|
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bool setPosition(const std::vector<double>& pos); |
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bool setOrientation(const std::vector<double>& ort); |
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bool havePosition() { return havePos_; } |
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bool haveOrientation() { return haveOrt_; } |
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double getPosX() { return position_[0]; } |
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double getPosY() { return position_[1]; } |
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double getPosZ() { return position_[2]; } |
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double getEulerPhi() { return orientation_[0]; } |
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double getEulerTheta() { return orientation_[1]; } |
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double getEulerPsi() { return orientation_[2]; } |
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int getIndex() { return index_;} |
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virtual void validate(); |
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typedef std::set<int>::iterator AtomIter; |
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typedef std::vector<int>::iterator BondIter; |
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int getFirstBonedAtom(AtomIter& ai) { |
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ai = bondedAtoms_.begin(); |
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return ai != bondedAtoms_.end() ? *ai : -1; |
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} |
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|
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int getNextBonedAtom(AtomIter& ai) { |
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++ai; |
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return ai != bondedAtoms_.end() ? *ai : -1; |
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} |
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|
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int getFirstBond(BondIter& bi) { |
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bi = bonds_.begin(); |
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return bi != bonds_.end()? *bi: -1; |
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} |
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int getNextBond(BondIter& bi) { |
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++bi; |
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return bi != bonds_.end()? *bi: -1; |
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} |
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|
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void addBond(int bondIndex) {bonds_.push_back(bondIndex);} |
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void addBondedAtom(int atomIndex) {bondedAtoms_.insert(atomIndex);} |
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private: |
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Vector3d position_; |
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Vector3d orientation_; |
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bool havePos_; |
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bool haveOrt_; |
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int index_; |
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std::vector<int> bonds_; |
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std::set<int> bondedAtoms_; |
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}; |
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|
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} |
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#endif |