| 1 |
< |
#ifndef __MOLECULESTAMP_H__ |
| 2 |
< |
#define __MOLECULESTAMP_H__ |
| 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" |
| 49 |
|
#include "types/TorsionStamp.hpp" |
| 50 |
|
#include "types/RigidBodyStamp.hpp" |
| 51 |
|
#include "types/CutoffGroupStamp.hpp" |
| 52 |
< |
#include "io/LinkedAssign.hpp" |
| 52 |
> |
#include "types/FragmentStamp.hpp" |
| 53 |
|
|
| 54 |
< |
using namespace std; |
| 55 |
< |
class MoleculeStamp{ |
| 54 |
> |
namespace oopse { |
| 55 |
> |
class MoleculeStamp : public DataHolder { |
| 56 |
> |
DeclareParameter(Name, std::string); |
| 57 |
> |
public: |
| 58 |
> |
MoleculeStamp(); |
| 59 |
> |
virtual ~MoleculeStamp(); |
| 60 |
> |
|
| 61 |
> |
bool addAtomStamp( AtomStamp* atom); |
| 62 |
> |
bool addBondStamp( BondStamp* bond); |
| 63 |
> |
bool addBendStamp( BendStamp* bend); |
| 64 |
> |
bool addTorsionStamp( TorsionStamp* torsion); |
| 65 |
> |
bool addRigidBodyStamp( RigidBodyStamp* rigidbody); |
| 66 |
> |
bool addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup); |
| 67 |
> |
bool addFragmentStamp( FragmentStamp* fragment); |
| 68 |
> |
|
| 69 |
> |
int getNAtoms() { return atomStamps_.size(); } |
| 70 |
> |
int getNBonds() { return bondStamps_.size(); } |
| 71 |
> |
int getNBends() { return bendStamps_.size(); } |
| 72 |
> |
int getNTorsions() { return torsionStamps_.size(); } |
| 73 |
> |
int getNRigidBodies() { return rigidBodyStamps_.size(); } |
| 74 |
> |
int getNCutoffGroups() { return cutoffGroupStamps_.size(); } |
| 75 |
> |
int getNIntegrable() { return nintegrable_;} |
| 76 |
> |
virtual void validate(); |
| 77 |
> |
|
| 78 |
> |
AtomStamp* getAtomStamp(int index) { return atomStamps_[index]; } |
| 79 |
> |
BondStamp* getBondStamp(int index) { return bondStamps_[index]; } |
| 80 |
> |
BendStamp* getBendStamp(int index) { return bendStamps_[index]; } |
| 81 |
> |
TorsionStamp* getTorsionStamp(int index) { return torsionStamps_[index]; } |
| 82 |
> |
RigidBodyStamp* getRigidBodyStamp(int index) { return rigidBodyStamps_[index]; } |
| 83 |
> |
CutoffGroupStamp* getCutoffGroupStamp(int index) { return cutoffGroupStamps_[index]; } |
| 84 |
> |
FragmentStamp* getFragmentStamp(int index) { return fragmentStamps_[index]; } |
| 85 |
|
|
| 86 |
< |
public: |
| 87 |
< |
MoleculeStamp(); |
| 88 |
< |
~MoleculeStamp(); |
| 89 |
< |
|
| 20 |
< |
char* assignString( char* lhs, char* rhs ); |
| 21 |
< |
char* assignDouble( char* lhs, double rhs ); |
| 22 |
< |
char* assignInt( char* lhs, int rhs ); |
| 23 |
< |
char* checkMe( void ); |
| 24 |
< |
|
| 25 |
< |
char* addAtom( AtomStamp* the_atom, int atomIndex ); |
| 26 |
< |
char* addRigidBody( RigidBodyStamp* the_rigidbody, int rigidBodyIndex ); |
| 27 |
< |
char* addCutoffGroup( CutoffGroupStamp* the_cutoffgroup, int cutoffGroupIndex ); |
| 28 |
< |
char* addBond( BondStamp* the_bond, int bondIndex ); |
| 29 |
< |
char* addBend( BendStamp* the_bend, int bendIndex ); |
| 30 |
< |
char* addTorsion( TorsionStamp* the_torsion, int torsionIndex ); |
| 31 |
< |
|
| 32 |
< |
char* getID( void ) { return name; } |
| 33 |
< |
int getNAtoms( void ) { return n_atoms; } |
| 34 |
< |
int getNBonds( void ) { return n_bonds; } |
| 35 |
< |
int getNBends( void ) { return n_bends; } |
| 36 |
< |
int getNTorsions( void ) { return n_torsions; } |
| 37 |
< |
int getNRigidBodies(void) { return n_rigidbodies; } |
| 38 |
< |
int getNCutoffGroups(void){ return n_cutoffgroups; } |
| 39 |
< |
int getNIntegrable(void) { return n_integrable; } |
| 40 |
< |
|
| 41 |
< |
AtomStamp* getAtom( int index ) { return atoms[index]; } |
| 42 |
< |
BondStamp* getBond( int index ) { return bonds[index]; } |
| 43 |
< |
BendStamp* getBend( int index ) { return bends[index]; } |
| 44 |
< |
TorsionStamp* getTorsion( int index ) { return torsions[index]; } |
| 45 |
< |
RigidBodyStamp* getRigidBody( int index ) { return rigidBodies[index]; } |
| 46 |
< |
CutoffGroupStamp* getCutoffGroup( int index ) { return cutoffGroups[index]; } |
| 47 |
< |
|
| 48 |
< |
|
| 49 |
< |
bool isBondInSameRigidBody(BondStamp*bond); |
| 50 |
< |
bool isAtomInRigidBody(int atomIndex); |
| 51 |
< |
bool isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex); |
| 52 |
< |
vector<pair<int, int> > getJointAtoms(int rb1, int rb2); |
| 86 |
> |
bool isBondInSameRigidBody(BondStamp*bond); |
| 87 |
> |
bool isAtomInRigidBody(int atomIndex); |
| 88 |
> |
bool isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex); |
| 89 |
> |
std::vector<std::pair<int, int> > getJointAtoms(int rb1, int rb2); |
| 90 |
|
|
| 91 |
< |
int haveExtras( void ) { return have_extras; } |
| 55 |
< |
LinkedAssign* getUnhandled( void ) { return unhandled; } |
| 56 |
< |
|
| 57 |
< |
static char errMsg[500]; |
| 58 |
< |
private: |
| 59 |
< |
|
| 60 |
< |
|
| 61 |
< |
char name[100]; |
| 62 |
< |
int n_atoms; |
| 63 |
< |
int n_bonds; |
| 64 |
< |
int n_bends; |
| 65 |
< |
int n_torsions; |
| 66 |
< |
int n_rigidbodies; |
| 67 |
< |
int n_cutoffgroups; |
| 68 |
< |
int n_integrable; |
| 69 |
< |
|
| 70 |
< |
int have_name, have_atoms, have_bonds, have_bends, have_torsions; |
| 71 |
< |
int have_rigidbodies, have_cutoffgroups; |
| 91 |
> |
private: |
| 92 |
|
|
| 93 |
< |
AtomStamp** atoms; |
| 94 |
< |
BondStamp** bonds; |
| 95 |
< |
BendStamp** bends; |
| 96 |
< |
TorsionStamp** torsions; |
| 97 |
< |
RigidBodyStamp** rigidBodies; |
| 98 |
< |
CutoffGroupStamp** cutoffGroups; |
| 99 |
< |
|
| 100 |
< |
LinkedAssign* unhandled; // the unhandled assignments |
| 101 |
< |
short int have_extras; |
| 93 |
> |
void fillBondInfo(); |
| 94 |
> |
void checkAtoms(); |
| 95 |
> |
void checkBonds(); |
| 96 |
> |
void checkBends(); |
| 97 |
> |
void checkTorsions(); |
| 98 |
> |
void checkRigidBodies(); |
| 99 |
> |
void checkCutoffGroups(); |
| 100 |
> |
void checkFragments(); |
| 101 |
> |
template <class Cont, class T> |
| 102 |
> |
bool addIndexSensitiveStamp(Cont& cont, T* stamp) { |
| 103 |
> |
typename Cont::iterator i; |
| 104 |
> |
int index = stamp->getIndex(); |
| 105 |
> |
bool ret = false; |
| 106 |
> |
size_t size = cont.size(); |
| 107 |
> |
|
| 108 |
> |
if (size >= index +1) { |
| 109 |
> |
if (cont[index]!= NULL) { |
| 110 |
> |
ret = false; |
| 111 |
> |
}else { |
| 112 |
> |
cont[index] = stamp; |
| 113 |
> |
ret = true; |
| 114 |
> |
} |
| 115 |
> |
} else { |
| 116 |
> |
cont.insert(cont.end(), index - cont.size() + 1, NULL); |
| 117 |
> |
cont[index] = stamp; |
| 118 |
> |
ret = true; |
| 119 |
> |
} |
| 120 |
> |
|
| 121 |
> |
return ret; |
| 122 |
> |
} |
| 123 |
> |
|
| 124 |
> |
std::vector<AtomStamp*> atomStamps_; |
| 125 |
> |
std::vector<BondStamp*> bondStamps_; |
| 126 |
> |
std::vector<BendStamp*> bendStamps_; |
| 127 |
> |
std::vector<TorsionStamp*> torsionStamps_; |
| 128 |
> |
std::vector<RigidBodyStamp*> rigidBodyStamps_; |
| 129 |
> |
std::vector<CutoffGroupStamp*> cutoffGroupStamps_; |
| 130 |
> |
std::vector<FragmentStamp*> fragmentStamps_; |
| 131 |
> |
std::vector<int> atom2Rigidbody; |
| 132 |
> |
int nintegrable_; |
| 133 |
|
}; |
| 134 |
|
|
| 135 |
+ |
} |
| 136 |
|
#endif |
