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#ifndef __MOLECULESTAMP_H__ |
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#define __MOLECULESTAMP_H__ |
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#include <vector> |
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#include <utility> |
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#include "AtomStamp.hpp" |
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#include "BondStamp.hpp" |
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#include "BendStamp.hpp" |
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#include "TorsionStamp.hpp" |
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#include "RigidBodyStamp.hpp" |
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#include "CutoffGroupStamp.hpp" |
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#include "LinkedAssign.hpp" |
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using namespace std; |
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class MoleculeStamp{ |
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public: |
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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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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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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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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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bool isBondInSameRigidBody(BondStamp*bond); |
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bool isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex); |
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vector<pair<int, int> > getJointAtoms(int rb1, int rb2); |
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int haveExtras( void ) { return have_extras; } |
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LinkedAssign* getUnhandled( void ) { return unhandled; } |
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static char errMsg[500]; |
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private: |
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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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int have_name, have_atoms, have_bonds, have_bends, have_torsions; |
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int have_rigidbodies; |
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int have_rigidbodies, have_cutoffgroups; |
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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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LinkedAssign* unhandled; // the unhandled assignments |
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short int have_extras; |
