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tim |
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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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#ifndef TYPES_ATOMSTAMP_HPP
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#define TYPES_ATOMSTAMP_HPP
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#include <set>
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#include <vector>
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#include "types/DataHolder.hpp"
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namespace oopse {
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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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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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gezelter |
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int getFirstBondedAtom(AtomIter& ai) {
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tim |
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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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gezelter |
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int getNextBondedAtom(AtomIter& ai) {
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tim |
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++ai;
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return ai != bondedAtoms_.end() ? *ai : -1;
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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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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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#endif
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