MPQC
3.0.0-alpha
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DiscreteConnollyShape and ConnollyShape should produce the same result. More...
#include <chemistry/molecule/molshape.h>
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 |
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 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 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. 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 () |
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. 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... | |
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. 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 &) | |
DescribedClass & | operator= (const DescribedClass &) |
ClassDesc * | class_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< DescribedClass > | ref () |
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 SavableState * | restore_state (StateIn &si) |
Restores objects saved with save_state. More... | |
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) |
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) |
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. More... | |
Protected Member Functions inherited from sc::RefCount | |
RefCount (const RefCount &) | |
RefCount & | operator= (const RefCount &) |
Protected Attributes inherited from sc::UnionShape | |
std::set< Ref< Shape > > | _shapes |
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_. | |
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_ |
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.