sc_ConnollyShape - Man Page

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, SCVector3 &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 already 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 function 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 *objectname, 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 already 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 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)
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 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.

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 already 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, SCVector3 & 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

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Info

Thu Jan 19 2023 Version 2.3.1 MPQC