home | help 
sc::ConnollyShape(3)		      MPQC		    sc::ConnollyShape(3)

NAME
     sc::ConnollyShape	- DiscreteConnollyShape and ConnollyShape should produce
     the same result.

SYNOPSIS
     #include <molshape.h>

     Inherits sc::Shape.

   Public Member Functions
     ConnollyShape (const Ref< KeyVal > &)
     void initialize (const Ref< Molecule > &, double probe_radius)
     void clear ()
     double distance_to_surface (const SCVector3 &r, SCVector3 *grad=0) const
     void boundingbox (double valuemin, double valuemax, SCVector3  &p1,  SCVec-
	 tor3 &p2)

     Public Member Functions inherited from sc::Shape
     Shape (const Ref< KeyVal > &keyval)
     virtual  double distance_to_surface (const SCVector3 &r, SCVector3 *grad=0)
	 const =0
     virtual int is_outside (const SCVector3 &r) const
     void compute ()
	 Recompute at least the results that have compute true and are	not  al-
	 ready computed.
     void  interpolate	(const	SCVector3  &p1, const SCVector3 &p2, double val,
	 SCVector3 &result)
     int value_implemented () const
	 Information about the availability of values, gradients, and hessians.

     Public Member Functions inherited from sc::Volume
     Volume (const Ref< KeyVal > &)
     void set_gradient (const SCVector3 &g)
     void set_gradient (RefSCVector &g)
     void get_gradient (SCVector3 &g)
     void set_x (const SCVector3 &x)
     void set_x (const RefSCVector &x)
	 Set and retrieve the coordinate values.
     void get_x (SCVector3 &x)
     virtual void boundingbox (double valuemin, double valuemax, SCVector3  &p1,
	 SCVector3 &p2)=0
     virtual  void interpolate (const SCVector3 &p1, const SCVector3 &p2, double
	 value, SCVector3 &result)
     virtual void solve (const	SCVector3  &p,	const  SCVector3  &grad,  double
	 value, SCVector3 &result)

     Public Member Functions inherited from sc::Function
     virtual RefSCVector gradient ()
     int gradient_needed () const
     int do_gradient (int)
     virtual void set_desired_gradient_accuracy (double)
     virtual double actual_gradient_accuracy () const
     virtual double desired_gradient_accuracy () const
     AccResultRefSCVector & gradient_result ()
     virtual RefSymmSCMatrix hessian ()
     int hessian_needed () const
     int do_hessian (int)
     virtual void set_desired_hessian_accuracy (double)
     virtual double actual_hessian_accuracy () const
     virtual double desired_hessian_accuracy () const
     AccResultRefSymmSCMatrix & hessian_result ()
     virtual void guess_hessian (RefSymmSCMatrix &)
	 Compute a quick, approximate hessian.
     virtual RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
     virtual int gradient_implemented () const
     virtual int hessian_implemented () const
     RefSCVector get_x () const
     const RefSCVector & get_x_no_copy () const
     virtual Ref< NonlinearTransform > change_coordinates ()
	 An optimizer can call change coordinates periodically to give the func-
	 tion an opportunity to change its coordinate system.
     virtual void print (std::ostream &=ExEnv::out0()) const
	 Print information about the object.
     Function ()
     Function (StateIn &)
     Function (const Function &)
     Function  (const  Ref<  KeyVal  >	&,  double  funcacc=DBL_EPSILON,  double
	 gradacc=DBL_EPSILON, double hessacc=DBL_EPSILON)
	 The keyval constructor reads the following keywords:
     virtual ~Function ()
     Function & operator= (const Function &)
     Ref< SCMatrixKit > matrixkit () const
	 Return the SCMatrixKit used to construct vectors and matrices.
     RefSCDimension dimension () const
	 Return the SCDimension of the problem.
     virtual void save_data_state (StateOut &)
	 Save the base classes (with save_data_state) and  the	members  in  the
	 same order that the StateIn CTOR initializes them.
     virtual double value ()
	 Return the value of the function.
     int value_needed () const
	 Returns nonzero if the current value is not up-to-date.
     int do_value (int)
	 If  passed  a nonzero number, compute the value the next time compute()
	 is called.
     AccResultdouble & value_result ()
     virtual void set_desired_value_accuracy (double)
	 Set the accuracy to which the value is to be computed.
     virtual double actual_value_accuracy () const
	 Return the accuracy with which the value has been computed.
     virtual double desired_value_accuracy () const
	 Return the accuracy with which the value is to be computed.

     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.
     virtual void save_data_state (StateOut &)
	 Save  the  base  classes  (with save_data_state) and the members in the
	 same order that the StateIn CTOR initializes them.

     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.
     virtual void print (std::ostream &=ExEnv::out0()) const
	 Print the object.

     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.

     Public Member Functions inherited from sc::Compute
     virtual void obsolete ()
	 Marks all results as being out of date.

   Static Public Member Functions
     static void print_counts (std::ostream &=ExEnv::out0())

     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	*object-
	 name, const char *keyword=0)

   Additional Inherited Members
     Protected Member Functions inherited from sc::Volume
     double & interpolation_accuracy ()
     virtual void compute ()=0
	 Recompute  at	least the results that have compute true and are not al-
	 ready computed.
     virtual void failure (const char *)

     Protected Member Functions inherited from sc::Function
     virtual void set_value (double)
     virtual void set_hessian (RefSymmSCMatrix &)
     virtual void set_matrixkit (const Ref< SCMatrixKit > &)
	 Set the SCMatrixKit that should be used to construct the requisite vec-
	 tors and matrices.
     virtual void set_dimension (const RefSCDimension &)
     virtual void set_actual_value_accuracy (double)
     virtual void set_actual_gradient_accuracy (double)
     virtual void set_actual_hessian_accuracy (double)
     RefSCVector & get_x_reference ()
	 Get read/write access to the coordinates for modification.
     void do_change_coordinates (const Ref< NonlinearTransform > &)
	 Change the coordinate system and apply the given transform to	interme-
	 diates matrices and vectors.

     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 &)
     virtual void compute ()=0
	 Recompute at least the results that have compute true and are	not  al-
	 ready computed.

     Protected Attributes inherited from sc::Function
     Ref< SCMatrixKit > matrixkit_
	 Used to construct new matrices.
     RefSCVector x_
	 The variables.
     RefSCDimension dim_
	 The dimension of x_.
     AccResultdouble value_
	 The value of the function at x_.
     AccResultRefSCVector gradient_
	 The gradient at x_.
     AccResultRefSymmSCMatrix hessian_
	 The hessian at x_.

Detailed Description
     DiscreteConnollyShape and ConnollyShape should produce the same result.

     The  discrete version is a shape union of discrete subshapes and is slower.
     These classes describe the solvent accessible surface of a molecule.

Member Function Documentation
   void sc::ConnollyShape::boundingbox (double valuemin, double valuemax, SCVec-
     tor3 & p1, SCVector3 & p2) [virtual]
     Implements sc::Volume.

   double sc::ConnollyShape::distance_to_surface (const SCVector3 & r, SCVector3
     * grad = 0) const [virtual]
     Implements sc::Shape.

Author
     Generated automatically by Doxygen for MPQC from the source code.

Version 2.3.1			 Thu Sep 3 2026 	    sc::ConnollyShape(3)
home | help