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#ifndef __SIMSETUP_H__ |
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#define __SIMSETUP_H__ |
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#include "MakeStamps.hpp" |
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#include "Globals.hpp" |
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#include "ForceFields.hpp" |
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#include "SimInfo.hpp" |
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#include "ReadWrite.hpp" |
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|
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// this routine is defined in BASS_interface.cpp |
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void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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class SimSetup{ |
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public: |
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SimSetup(); |
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~SimSetup(); |
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void setSimInfo( SimInfo* the_simnfo ) { simnfo = the_simnfo; } |
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void parseFile( char* fileName ); |
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void createSim( void ); |
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|
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private: |
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void makeAtoms( void ); |
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void makeMolecules( void ); |
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void makeBonds( void ); |
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void makeBends( void ); |
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void makeTorsions( void ); |
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|
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void initFromBass( void ); |
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void makeElement( double x, double y, double z ); |
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|
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MakeStamps* stamps; |
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Globals* globals; |
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char* inFileName; |
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SimInfo* simnfo; |
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int n_components; |
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char force_field[100]; |
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char ensemble[100]; |
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Component** the_components; |
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int* components_nmol; |
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MoleculeStamp** comp_stamps; //the stamps matching the components |
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int tot_nmol; |
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int tot_atoms; |
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int tot_bonds; |
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int tot_bends; |
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int tot_torsions; |
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int tot_SRI; |
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|
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Atom** the_atoms; |
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SRI** the_sris; |
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LRI* longRange; |
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ex_pair *the_excludes; |
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Molecule* the_molecules; |
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ForceFields* the_ff; |
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// needed by makeElement |
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int current_mol; |
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int current_comp_mol; |
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int current_comp; |
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int current_atom_ndx; |
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}; |
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#endif |
