Index: kernel/include/IMP/score_states/MaxChangeScoreState.h
===================================================================
--- kernel/include/IMP/score_states/MaxChangeScoreState.h (revision 385)
+++ kernel/include/IMP/score_states/MaxChangeScoreState.h (working copy)
@@ -25,8 +25,6 @@
Particles ps_;
float max_change_;
public:
- IMP_LIST(Particle, particle, Particle*);
-
MaxChangeScoreState(const FloatKeys &keys):keys_(keys){}
virtual ~MaxChangeScoreState(){}
@@ -38,6 +36,7 @@
return max_change_;
}
+ IMP_LIST(public, Particle, particle, Particle*);
};
} // namespace IMP
Index: kernel/include/IMP/Restraint.h
===================================================================
--- kernel/include/IMP/Restraint.h (revision 385)
+++ kernel/include/IMP/Restraint.h (working copy)
@@ -29,12 +29,6 @@
and then various functions which are applied to the tuples.
*/
-/** \defgroup restraint General purpose restraints
- Classes to define and help in defining restraints. The restraints
- typically involve a Restraint which defines the set of tuples of Particles
- and then various functions which are applied to the tuples.
- */
-
//! Abstract class for representing restraints
class IMPDLLEXPORT Restraint : public Object
{
@@ -81,8 +75,7 @@
return model_;
}
-protected:
- IMP_LIST(Particle, particle, Particle*)
+ IMP_LIST(protected, Particle, particle, Particle*)
private:
Model* model_;
Index: kernel/include/IMP/optimizers/MonteCarlo.h
===================================================================
--- kernel/include/IMP/optimizers/MonteCarlo.h (revision 385)
+++ kernel/include/IMP/optimizers/MonteCarlo.h (working copy)
@@ -23,6 +23,8 @@
accepted or rejected based on the Metropolis criteria. Optionally, a
number of local optimization steps are taken before the step is
accepted or rejected.
+
+ \ingroup optimizer
*/
class IMPDLLEXPORT MonteCarlo: public Optimizer
{
Index: kernel/include/IMP/optimizers/movers/NormalMover.h
===================================================================
--- kernel/include/IMP/optimizers/movers/NormalMover.h (revision 385)
+++ kernel/include/IMP/optimizers/movers/NormalMover.h (working copy)
@@ -17,7 +17,8 @@
//! Modify a set of continuous variables.
/** The variables are perturbed within a ball of the
- given radius.
+ given radius.
+ \ingroup mover
*/
class IMPDLLEXPORT NormalMover :public MoverBase
{
Index: kernel/include/IMP/optimizers/movers/BallMover.h
===================================================================
--- kernel/include/IMP/optimizers/movers/BallMover.h (revision 385)
+++ kernel/include/IMP/optimizers/movers/BallMover.h (working copy)
@@ -17,7 +17,8 @@
//! Modify a set of continuous variables.
/** The variables are perturbed within a ball of the
- given radius.
+ given radius.
+ \ingroup mover
*/
class IMPDLLEXPORT BallMover :public MoverBase
{
Index: kernel/include/IMP/optimizers/Mover.h
===================================================================
--- kernel/include/IMP/optimizers/Mover.h (revision 385)
+++ kernel/include/IMP/optimizers/Mover.h (working copy)
@@ -21,8 +21,14 @@
class Mover;
typedef Index<Mover> MoverIndex;
+/** \ingroup optimizer
+ \addtogroup mover Monte Carlo movers
+ Classes which move particles around. Currently used
+ for MonteCarlo optimization.
+ */
+
//! A class to make a monte carlo move.
-/** You probably want to use MoverBase if you are implementing a Mover. .
+/** You probably want to use MoverBase if you are implementing a Mover.
*/
class IMPDLLEXPORT Mover: public Object
{
Index: kernel/include/IMP/Optimizer.h
===================================================================
--- kernel/include/IMP/Optimizer.h (revision 385)
+++ kernel/include/IMP/Optimizer.h (working copy)
@@ -63,8 +63,8 @@
IMP_CONTAINER(OptimizerState, optimizer_state, OptimizerStateIndex);
protected:
- //! Update optimizer state, at each successful step
- void update_state();
+ //! Update optimizer state, should be called at each successful step
+ void update_states();
private:
Model *model_;
Index: kernel/include/IMP/macros.h
===================================================================
--- kernel/include/IMP/macros.h (revision 385)
+++ kernel/include/IMP/macros.h (working copy)
@@ -213,7 +213,9 @@
/** \internal
*/
-#define IMP_CONTAINER_CORE(Ucname, lcname, Data, IndexType, Container) \
+#define IMP_CONTAINER_CORE(protection, Ucname, lcname, Data, IndexType,\
+ Container) \
+ protection: \
/** \short Add an object.
\param[in] obj Pointer to the object
\return index of object within the object
@@ -248,7 +250,10 @@
return lcname##_vector_.begin();} \
Ucname##ConstIterator lcname##s_end() const { \
return lcname##_vector_.end();} \
- Container lcname##_vector_;
+ private: \
+ /** \internal */ \
+ Container lcname##_vector_; \
+ protection:
/** \internal
*/
@@ -278,22 +283,23 @@
/**
Such a container adds public methods add_foo, get_foo, number_of_foo
and a private type foo_iterator, with methods foo_begin, foo_end.
+ \param[in] protection The level of protection for the container.
\param[in] Ucname The name of the type in uppercase
\param[in] lcname The name of the type in lower case
\param[in] Data The type of the data to store.
\param[in] Onchanged Code to get executed every time the container
changes
- Eventually we can add removal and correctness checks.
- Note that the type Ucnames must be declared and be a vector of
+ \note the type Ucnames must be declared and be a vector of
Data.
*/
-#define IMP_LIST(Ucname, lcname, Data) \
+#define IMP_LIST(protection, Ucname, lcname, Data) \
+ protection: \
/** \short Clear the contents of the container */ \
void clear_##lcname##s(); \
/** \short Remove any occurences of d from the container */ \
void erase_##lcname(Data d); \
- IMP_CONTAINER_CORE(Ucname, lcname, Data, unsigned int, \
+ IMP_CONTAINER_CORE(protection, Ucname, lcname, Data, unsigned int, \
IMP::internal::Vector<Data>)
@@ -335,12 +341,17 @@
\param[in] IndexType The type to use for the index. This should be
an instantiation of Index<T> or something similar.
- Eventually we can add removal and correctness checks.
+ \note The type Ucnames must be declared and be a vector of
+ Data.
+ \note these containers are always public
*/
#define IMP_CONTAINER(Ucname, lcname, IndexType) \
+ private: \
+ /** \internal
+ This is an implementation detail.*/ \
typedef IMP::internal::ObjectContainer<Ucname, IndexType> \
Ucname##Container; \
- IMP_CONTAINER_CORE(Ucname, lcname, Ucname*, IndexType, \
+ IMP_CONTAINER_CORE(public, Ucname, lcname, Ucname*, IndexType,\
Ucname##Container)
Index: kernel/src/Optimizer.cpp
===================================================================
--- kernel/src/Optimizer.cpp (revision 385)
+++ kernel/src/Optimizer.cpp (working copy)
@@ -25,7 +25,7 @@
}
//! Update optimizer state, at each successful step
-void Optimizer::update_state()
+void Optimizer::update_states()
{
IMP_LOG(VERBOSE,
"Updating OptimizerStates " << std::flush);
Index: kernel/src/optimizers/ConjugateGradients.cpp
===================================================================
--- kernel/src/optimizers/ConjugateGradients.cpp (revision 385)
+++ kernel/src/optimizers/ConjugateGradients.cpp (working copy)
@@ -276,7 +276,7 @@
/* Begin the major iteration loop. */
g40:
- update_state();
+ update_states();
/* Begin linear search. alpha is the steplength. */
if (gradient_direction) {
@@ -429,7 +429,7 @@
for (i = 0; i < n; i++) {
model_data->set_value(float_indices[i], x[i]);
}
- update_state();
+ update_states();
return f;
}
Index: kernel/src/optimizers/SteepestDescent.cpp
===================================================================
--- kernel/src/optimizers/SteepestDescent.cpp (revision 385)
+++ kernel/src/optimizers/SteepestDescent.cpp (working copy)
@@ -90,7 +90,7 @@
temp_vals[i] - temp_derivs[i]
* current_step_size);
}
- update_state();
+ update_states();
// check the new model
new_score = get_model()->evaluate(false);
Index: kernel/src/optimizers/MonteCarlo.cpp
===================================================================
--- kernel/src/optimizers/MonteCarlo.cpp (revision 385)
+++ kernel/src/optimizers/MonteCarlo.cpp (working copy)
@@ -37,10 +37,7 @@
Float MonteCarlo::optimize(unsigned int max_steps)
{
IMP_CHECK_OBJECT(this);
- for (OptimizerStateIterator it= optimizer_states_begin();
- it != optimizer_states_end(); ++it) {
- (*it)->update();
- }
+ update_states();
prior_energy_ =get_model()->evaluate(0);
IMP_LOG(VERBOSE, "MC Initial energy is " << prior_energy_ << std::endl);
::boost::uniform_real<> rand(0,1);
@@ -90,10 +87,7 @@
if (accept) {
++stat_forward_steps_taken_;
prior_energy_= next_energy;
- for (OptimizerStateIterator it= optimizer_states_begin();
- it != optimizer_states_end(); ++it) {
- (*it)->update();
- }
+ update_states();
} else {
++stat_num_failures_;
}
Index: kernel/src/optimizers/MolecularDynamics.cpp
===================================================================
--- kernel/src/optimizers/MolecularDynamics.cpp (revision 385)
+++ kernel/src/optimizers/MolecularDynamics.cpp (working copy)
@@ -133,7 +133,7 @@
Float score = model->evaluate(true);
for (unsigned int i = 0; i < max_steps; ++i) {
- update_state();
+ update_states();
step();
score = model->evaluate(true);
}