NAME

       sc::IntCoorGen - IntCoorGen generates a set of simple internal coordinates for a molecule.

SYNOPSIS

       #include <coor.h>

       Inherits sc::SavableState.

   Public Member Functions
       IntCoorGen (const Ref< Molecule > &, int nextra=0, int *extra=0)
           Create an IntCoorGen given a Molecule and, optionally, extra bonds.
       IntCoorGen (const Ref< KeyVal > &)
           The KeyVal constructor.
       IntCoorGen (StateIn &)
       void save_data_state (StateOut &)
           Standard member.
       virtual void generate (const Ref< SetIntCoor > &)
           This generates a set of internal coordinates.
       virtual void print (std::ostream &out=ExEnv::out0()) const
           Print out information about this.

       Public Member Functions inherited from sc::SavableState
       SavableState & operator= (const SavableState &)
       void save_state (StateOut &)
           Save the state of the object as specified by the StateOut object.
       void save_object_state (StateOut &)
           This can be used for saving state when the exact type of the object is known for both
           the save and the restore.
       virtual void save_vbase_state (StateOut &)
           Save the virtual bases for the object.

       Public Member Functions inherited from sc::DescribedClass
       DescribedClass (const DescribedClass &)
       DescribedClass & operator= (const DescribedClass &)
       ClassDesc * class_desc () const  throw ()
           This returns the unique pointer to the ClassDesc corresponding to the given type_info
           object.
       const char * class_name () const
           Return the name of the object's exact type.
       int class_version () const
           Return the version of the class.

       Public Member Functions inherited from sc::RefCount
       int lock_ptr () const
           Lock this object.
       int unlock_ptr () const
           Unlock this object.
       void use_locks (bool inVal)
           start and stop using locks on this object
       refcount_t nreference () const
           Return the reference count.
       refcount_t reference ()
           Increment the reference count and return the new count.
       refcount_t dereference ()
           Decrement the reference count and return the new count.
       int managed () const
       void unmanage ()
           Turn off the reference counting mechanism for this object.
       int managed () const
           Return 1 if the object is managed. Otherwise return 0.

       Public Member Functions inherited from sc::Identity
       Identifier identifier ()
           Return the Identifier for this argument.

   Protected Member Functions
       void init_constants ()
       double cos_ijk (Molecule &m, int i, int j, int k)
       int hterminal (Molecule &m, BitArrayLTri &bonds, int i)
       int nearest_contact (int i, Molecule &m)
       void add_bonds (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m)
       void add_bends (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m)
       void add_tors (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m)
       void add_out (const Ref< SetIntCoor > &list, BitArrayLTri &bonds, Molecule &m)

       Protected Member Functions inherited from sc::SavableState
       SavableState (const SavableState &)
       SavableState (StateIn &)
           Each derived class StateIn CTOR handles the restore corresponding to calling
           save_object_state, save_vbase_state, and save_data_state listed above.

       Protected Member Functions inherited from sc::RefCount
       RefCount (const RefCount &)
       RefCount & operator= (const RefCount &)

   Protected Attributes
       Ref< Molecule > molecule_
       int linear_bends_
       int linear_lbends_
       int linear_tors_
       int linear_stors_
       int nextra_bonds_
       int * extra_bonds_
       double linear_bend_thres_
       double linear_tors_thres_
       double radius_scale_factor_

   Additional Inherited Members
       Static Public Member Functions inherited from sc::SavableState
       static void save_state (SavableState *s, StateOut &)
       static SavableState * restore_state (StateIn &si)
           Restores objects saved with save_state.
       static SavableState * key_restore_state (StateIn &si, const char *keyword)
           Like restore_state, but keyword is used to override values while restoring.
       static SavableState * dir_restore_state (StateIn &si, const char *objectname, const char
           *keyword=0)

Detailed Description

       IntCoorGen generates a set of simple internal coordinates for a molecule.

Constructor & Destructor Documentation

   sc::IntCoorGen::IntCoorGen (const Ref< Molecule > &, int nextra = 0, int * extra = 0)
       Create an IntCoorGen given a Molecule and, optionally, extra bonds. IntCoorGen keeps a
       reference to extra and deletes it when the destructor is called.

   sc::IntCoorGen::IntCoorGen (const Ref< KeyVal > &)
       The KeyVal constructor.

       molecule
           A Molecule object. There is no default.

       radius_scale_factor
           If the distance between two atoms is less than the radius scale factor times the sum
           of the atoms' atomic radii, then a bond is placed between the two atoms for the
           purpose of finding internal coordinates. The default is 1.1.

       linear_bend_threshold
           A bend angle in degress greater than 180 minus this keyword's floating point value is
           considered a linear bend. The default is 1.0.

       linear_tors_threshold
           The angles formed by atoms a-b-c and b-c-d are checked for near linearity. If an angle
           in degrees is greater than 180 minus this keyword's floating point value, then the
           torsion is classified as a linear torsion. The default is 1.0.

       linear_bend
           Generate BendSimpleCo objects to describe linear bends. The default is false.

       linear_lbend
           Generate pairs of LinIPSimpleCo and LinIPSimpleCo objects to describe linear bends.
           The default is true.

       linear_tors
           Generate TorsSimpleCo objects to described linear torsions. The default is false.

       linear_stors
           Generate ScaledTorsSimpleCo objects to described linear torsions. The default is true.

       extra_bonds
           This is a vector of atom numbers, where elements $2 (i-1) + 1$ and $2 i$ specify the
           atoms which are bound in extra bond $i$. The extra_bonds keyword should only be needed
           for weakly interacting fragments, otherwise all the needed bonds will be found.

Member Function Documentation

   virtual void sc::IntCoorGen::print (std::ostream & out = ExEnv::out0()) const [virtual]
       Print out information about this.

       Reimplemented from sc::DescribedClass.

   void sc::IntCoorGen::save_data_state (StateOut &) [virtual]
       Standard member.

       Reimplemented from sc::SavableState.

Author

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