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/* |
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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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#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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#include "types/FragmentStamp.hpp" |
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namespace oopse { |
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class MoleculeStamp : public DataHolder { |
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DeclareParameter(Name, std::string); |
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public: |
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MoleculeStamp(); |
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virtual ~MoleculeStamp(); |
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bool addAtomStamp( AtomStamp* atom); |
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bool addBondStamp( BondStamp* bond); |
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bool addBendStamp( BendStamp* bend); |
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bool addTorsionStamp( TorsionStamp* torsion); |
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bool addRigidBodyStamp( RigidBodyStamp* rigidbody); |
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bool addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup); |
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bool addFragmentStamp( FragmentStamp* fragment); |
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int getNAtoms() { return atomStamps_.size(); } |
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int getNBonds() { return bondStamps_.size(); } |
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int getNBends() { return bendStamps_.size(); } |
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int getNTorsions() { return torsionStamps_.size(); } |
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int getNRigidBodies() { return rigidBodyStamps_.size(); } |
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int getNCutoffGroups() { return cutoffGroupStamps_.size(); } |
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int getNIntegrable() { return nintegrable_;} |
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virtual void validate(); |
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AtomStamp* getAtomStamp(int index) { return atomStamps_[index]; } |
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BondStamp* getBondStamp(int index) { return bondStamps_[index]; } |
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BendStamp* getBendStamp(int index) { return bendStamps_[index]; } |
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TorsionStamp* getTorsionStamp(int index) { return torsionStamps_[index]; } |
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RigidBodyStamp* getRigidBodyStamp(int index) { return rigidBodyStamps_[index]; } |
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CutoffGroupStamp* getCutoffGroupStamp(int index) { return cutoffGroupStamps_[index]; } |
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FragmentStamp* getFragmentStamp(int index) { return fragmentStamps_[index]; } |
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class MoleculeStamp{ |
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public: |
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MoleculeStamp(); |
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~MoleculeStamp(); |
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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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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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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); |
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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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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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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, have_cutoffgroups; |
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private: |
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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; |
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void fillBondInfo(); |
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void findBends(); |
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void findTorsions(); |
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template <class Cont, class T> |
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bool addIndexSensitiveStamp(Cont& cont, T* stamp) { |
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typename Cont::iterator i; |
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int index = stamp->getIndex(); |
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bool ret = false; |
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size_t size = cont.size(); |
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if (size >= index +1) { |
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if (cont[index]!= NULL) { |
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ret = false; |
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}else { |
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cont[index] = stamp; |
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ret = true; |
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} |
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} else { |
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cont.insert(cont.end(), index - cont.size() + 1, NULL); |
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cont[index] = stamp; |
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ret = true; |
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} |
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return ret; |
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} |
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std::vector<AtomStamp*> atomStamps_; |
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std::vector<BondStamp*> bondStamps_; |
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std::vector<BendStamp*> bendStamps_; |
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std::vector<TorsionStamp*> torsionStamps_; |
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std::vector<RigidBodyStamp*> rigidBodyStamps_; |
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std::vector<CutoffGroupStamp*> cutoffGroupStamps_; |
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std::vector<FragmentStamp*> fragmentStamps_; |
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std::vector<int> atom2Rigidbody; |
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int nintegrable_; |
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}; |
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} |
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#endif |