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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_MOLECULESTAMP_HPP |
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#define TYPES_MOLECULESTAMP_HPP |
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#include <vector> |
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#include <utility> |
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#include "types/AtomStamp.hpp" |
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#include "types/BondStamp.hpp" |
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#include "types/BendStamp.hpp" |
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#include "types/TorsionStamp.hpp" |
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#include "types/RigidBodyStamp.hpp" |
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#include "types/CutoffGroupStamp.hpp" |
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#include "io/LinkedAssign.hpp" |
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|
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|
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class MoleculeStamp{ |
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|
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public: |
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MoleculeStamp(); |
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~MoleculeStamp(); |
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|
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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* addAtom( AtomStamp* the_atom, int atomIndex ); |
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char* addRigidBody( RigidBodyStamp* the_rigidbody, int rigidBodyIndex ); |
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char* addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, int cutoffGroupIndex ); |
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char* addBond( BondStamp* the_bond, int bondIndex ); |
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char* addBend( BendStamp* the_bend, int bendIndex ); |
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char* addTorsion( TorsionStamp* the_torsion, int torsionIndex ); |
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|
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char* getID( void ) { return name; } |
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int getNAtoms( void ) { return n_atoms; } |
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int getNBonds( void ) { return n_bonds; } |
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int getNBends( void ) { return n_bends; } |
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int getNTorsions( void ) { return n_torsions; } |
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int getNRigidBodies(void) { return n_rigidbodies; } |
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int getNCutoffGroups(void){ return n_cutoffgroups; } |
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int getNIntegrable(void) { return n_integrable; } |
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|
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AtomStamp* getAtom( int index ) { return atoms[index]; } |
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BondStamp* getBond( int index ) { return bonds[index]; } |
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BendStamp* getBend( int index ) { return bends[index]; } |
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TorsionStamp* getTorsion( int index ) { return torsions[index]; } |
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RigidBodyStamp* getRigidBody( int index ) { return rigidBodies[index]; } |
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CutoffGroupStamp* getCutoffGroup( int index ) { return cutoffGroups[index]; } |
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|
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|
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bool isBondInSameRigidBody(BondStamp*bond); |
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bool isAtomInRigidBody(int atomIndex); |
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bool isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex); |
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std::vector<std::pair<int, int> > getJointAtoms(int rb1, int rb2); |
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|
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int haveExtras( void ) { return have_extras; } |
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LinkedAssign* getUnhandled( void ) { return unhandled; } |
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|
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static char errMsg[500]; |
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private: |
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|
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|
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char name[100]; |
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int n_atoms; |
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int n_bonds; |
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int n_bends; |
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int n_torsions; |
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int n_rigidbodies; |
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int n_cutoffgroups; |
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int n_integrable; |
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|
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int have_name, have_atoms, have_bonds, have_bends, have_torsions; |
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int have_rigidbodies, have_cutoffgroups; |
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|
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AtomStamp** atoms; |
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BondStamp** bonds; |
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BendStamp** bends; |
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TorsionStamp** torsions; |
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RigidBodyStamp** rigidBodies; |
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CutoffGroupStamp** cutoffGroups; |
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|
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LinkedAssign* unhandled; // the unhandled assignments |
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short int have_extras; |
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}; |
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|
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#endif |