MPQC  3.0.0-alpha
sc::DiscreteConnollyShape Class Reference

DiscreteConnollyShape and ConnollyShape should produce the same result. More...

#include <chemistry/molecule/molshape.h>

Inheritance diagram for sc::DiscreteConnollyShape:
sc::UnionShape sc::Shape sc::Volume sc::Function sc::SavableState sc::Compute sc::DescribedClass sc::RefCount

Public Member Functions

 DiscreteConnollyShape (const Ref< KeyVal > &)
 
void initialize (const Ref< Molecule > &, double probe_radius)
 
- Public Member Functions inherited from sc::UnionShape
void add_shape (Ref< Shape >)
 
double distance_to_surface (const SCVector3 &r, SCVector3 *grad=0) const
 
int is_outside (const SCVector3 &r) const
 
void boundingbox (double valuemin, double valuemax, SCVector3 &p1, SCVector3 &p2)
 
int gradient_implemented () const
 
- Public Member Functions inherited from sc::Shape
 Shape (const Ref< KeyVal > &keyval)
 
void compute ()
 Recompute at least the results that have compute true and are not already computed. More...
 
void interpolate (const SCVector3 &p1, const SCVector3 &p2, double val, SCVector3 &result)
 
int value_implemented () const
 
- 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 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
 
AccResultRefSCVectorgradient_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
 
AccResultRefSymmSCMatrixhessian_result ()
 
virtual bool desired_value_accuracy_set_to_default () const
 
virtual bool desired_gradient_accuracy_set_to_default () const
 
virtual bool desired_hessian_accuracy_set_to_default () const
 
virtual void guess_hessian (RefSymmSCMatrix &)
 Compute a quick, approximate hessian.
 
virtual RefSymmSCMatrix inverse_hessian (RefSymmSCMatrix &)
 
virtual int hessian_implemented () const
 
RefSCVector get_x () const
 
const RefSCVectorget_x_no_copy () const
 
virtual Ref< NonlinearTransformchange_coordinates ()
 An optimizer can call change coordinates periodically to give the function an opportunity to change its coordinate system. More...
 
virtual void print (std::ostream &=ExEnv::out0()) const
 Print information about the object.
 
void print_desired_accuracy (std::ostream &=ExEnv::out0()) const
 similar to print(), but only prins desired accuracies
 
virtual bool throw_if_tolerance_exceeded () const
 Overridden Compute member.
 
 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: More...
 
virtual ~Function ()
 
Functionoperator= (const Function &)
 
Ref< SCMatrixKitmatrixkit () 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. More...
 
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. More...
 
AccResultdoublevalue_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
SavableStateoperator= (const SavableState &)
 
void save_state (StateOut &)
 Save the state of the object as specified by the StateOut object. More...
 
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. More...
 
virtual void save_vbase_state (StateOut &)
 Save the virtual bases for the object. More...
 
- Public Member Functions inherited from sc::DescribedClass
 DescribedClass (const DescribedClass &)
 
DescribedClassoperator= (const DescribedClass &)
 
ClassDescclass_desc () const MPQC__NOEXCEPT
 This returns the unique pointer to the ClassDesc corresponding to the given type_info object. More...
 
const char * class_name () const
 Return the name of the object's exact type.
 
int class_version () const
 Return the version of the class.
 
Ref< DescribedClassref ()
 Return this object wrapped up in a Ref smart pointer. More...
 
- Public Member Functions inherited from sc::RefCount
size_t identifier () const
 Return the unique identifier for this object that can be compared for different objects of different types. More...
 
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. More...
 
- Public Member Functions inherited from sc::Compute
virtual void obsolete ()
 Marks all results as being out of date. More...
 

Additional Inherited Members

- Static Public Member Functions inherited from sc::SavableState
static void save_state (SavableState *s, StateOut &)
 
static SavableStaterestore_state (StateIn &si)
 Restores objects saved with save_state. More...
 
static SavableStatekey_restore_state (StateIn &si, const char *keyword)
 Like restore_state, but keyword is used to override values while restoring.
 
static SavableStatedir_restore_state (StateIn &si, const char *objectname, const char *keyword=0)
 
- Protected Member Functions inherited from sc::Volume
double & interpolation_accuracy ()
 
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 vectors 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)
 
RefSCVectorget_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 intermediates 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. More...
 
- Protected Member Functions inherited from sc::RefCount
 RefCount (const RefCount &)
 
RefCountoperator= (const RefCount &)
 
- Protected Attributes inherited from sc::UnionShape
std::set< Ref< Shape > > _shapes
 
- Protected Attributes inherited from sc::Function
Ref< SCMatrixKitmatrixkit_
 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_.
 
bool desired_value_accuracy_set_to_default_
 
bool desired_gradient_accuracy_set_to_default_
 
bool desired_hessian_accuracy_set_to_default_
 
bool throw_if_tolerance_exceeded_
 

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.


The documentation for this class was generated from the following file:

Generated at Sun Jan 26 2020 23:24:04 for MPQC 3.0.0-alpha using the documentation package Doxygen 1.8.16.