| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* 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 |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
* publication of scientific results based in part on use of the |
| 11 |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
* the article in which the program was described (Matthew |
| 13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
* |
| 18 |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
#ifndef TYPES_MOLECULESTAMP_HPP |
| 43 |
#define TYPES_MOLECULESTAMP_HPP |
| 44 |
#include <vector> |
| 45 |
#include <utility> |
| 46 |
#include "types/AtomStamp.hpp" |
| 47 |
#include "types/BondStamp.hpp" |
| 48 |
#include "types/BendStamp.hpp" |
| 49 |
#include "types/TorsionStamp.hpp" |
| 50 |
#include "types/RigidBodyStamp.hpp" |
| 51 |
#include "types/CutoffGroupStamp.hpp" |
| 52 |
#include "io/LinkedAssign.hpp" |
| 53 |
|
| 54 |
|
| 55 |
class MoleculeStamp{ |
| 56 |
|
| 57 |
public: |
| 58 |
MoleculeStamp(); |
| 59 |
~MoleculeStamp(); |
| 60 |
|
| 61 |
char* assignString( char* lhs, char* rhs ); |
| 62 |
char* assignDouble( char* lhs, double rhs ); |
| 63 |
char* assignInt( char* lhs, int rhs ); |
| 64 |
char* checkMe( void ); |
| 65 |
|
| 66 |
char* addAtom( AtomStamp* the_atom, int atomIndex ); |
| 67 |
char* addRigidBody( RigidBodyStamp* the_rigidbody, int rigidBodyIndex ); |
| 68 |
char* addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, int cutoffGroupIndex ); |
| 69 |
char* addBond( BondStamp* the_bond, int bondIndex ); |
| 70 |
char* addBend( BendStamp* the_bend, int bendIndex ); |
| 71 |
char* addTorsion( TorsionStamp* the_torsion, int torsionIndex ); |
| 72 |
|
| 73 |
char* getID( void ) { return name; } |
| 74 |
int getNAtoms( void ) { return n_atoms; } |
| 75 |
int getNBonds( void ) { return n_bonds; } |
| 76 |
int getNBends( void ) { return n_bends; } |
| 77 |
int getNTorsions( void ) { return n_torsions; } |
| 78 |
int getNRigidBodies(void) { return n_rigidbodies; } |
| 79 |
int getNCutoffGroups(void){ return n_cutoffgroups; } |
| 80 |
int getNIntegrable(void) { return n_integrable; } |
| 81 |
|
| 82 |
AtomStamp* getAtom( int index ) { return atoms[index]; } |
| 83 |
BondStamp* getBond( int index ) { return bonds[index]; } |
| 84 |
BendStamp* getBend( int index ) { return bends[index]; } |
| 85 |
TorsionStamp* getTorsion( int index ) { return torsions[index]; } |
| 86 |
RigidBodyStamp* getRigidBody( int index ) { return rigidBodies[index]; } |
| 87 |
CutoffGroupStamp* getCutoffGroup( int index ) { return cutoffGroups[index]; } |
| 88 |
|
| 89 |
|
| 90 |
bool isBondInSameRigidBody(BondStamp*bond); |
| 91 |
bool isAtomInRigidBody(int atomIndex); |
| 92 |
bool isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex); |
| 93 |
std::vector<std::pair<int, int> > getJointAtoms(int rb1, int rb2); |
| 94 |
|
| 95 |
int haveExtras( void ) { return have_extras; } |
| 96 |
LinkedAssign* getUnhandled( void ) { return unhandled; } |
| 97 |
|
| 98 |
static char errMsg[500]; |
| 99 |
private: |
| 100 |
|
| 101 |
|
| 102 |
char name[100]; |
| 103 |
int n_atoms; |
| 104 |
int n_bonds; |
| 105 |
int n_bends; |
| 106 |
int n_torsions; |
| 107 |
int n_rigidbodies; |
| 108 |
int n_cutoffgroups; |
| 109 |
int n_integrable; |
| 110 |
|
| 111 |
int have_name, have_atoms, have_bonds, have_bends, have_torsions; |
| 112 |
int have_rigidbodies, have_cutoffgroups; |
| 113 |
|
| 114 |
AtomStamp** atoms; |
| 115 |
BondStamp** bonds; |
| 116 |
BendStamp** bends; |
| 117 |
TorsionStamp** torsions; |
| 118 |
RigidBodyStamp** rigidBodies; |
| 119 |
CutoffGroupStamp** cutoffGroups; |
| 120 |
|
| 121 |
LinkedAssign* unhandled; // the unhandled assignments |
| 122 |
short int have_extras; |
| 123 |
}; |
| 124 |
|
| 125 |
#endif |
