Index: include/IMP/Model.h
===================================================================
--- include/IMP/Model.h (revision 630)
+++ include/IMP/Model.h (working copy)
@@ -11,7 +11,6 @@
#include "IMP_config.h"
#include "ModelData.h"
-#include "Restraint.h"
#include "RigidBody.h"
#include "State.h"
#include "boost/noncopyable.h"
@@ -19,7 +18,8 @@
namespace IMP
{
- class Particle;
+class Particle;
+class Restraint;
//! Class for storing model, its restraints, constraints, and particles.
/** All attribute data for particles is stored through indexing in the
@@ -27,7 +27,7 @@
*/
class IMPDLLEXPORT Model: public boost::noncopyable
{
-
+ friend class Restraint;
public:
Model();
~Model();
@@ -38,39 +38,11 @@
ModelData* get_model_data() const;
IMP_CONTAINER(Particle, particle, ParticleIndex);
+ IMP_CONTAINER(State, state, StateIndex);
+ IMP_CONTAINER(Restraint, restraint, RestraintIndex);
public:
- //! Add restraint set to the model.
- /** \param[in] restraint_set Pointer to the restraint set.
- \return the index of the newly-added restraint.
- */
- RestraintIndex add_restraint(Restraint* restraint_set);
- //! Get restraint set from the model.
- /** \param[in] i The RestraintIndex returned when adding.
- \exception std::out_of_range restraint index is out of range.
- \return pointer to the restraint.
- */
- Restraint* get_restraint(RestraintIndex i) const;
-
- //! Add state to the model.
- /** \param[in] state Pointer to the state.
- \return the index of the newly-added state.
- */
- StateIndex add_state(State* state);
-
- //! Get state from the model.
- /** \param[in] i The StateIndex returned when adding.
- \exception std::out_of_range state index is out of range.
- \return pointer to the state.
- */
- State* get_state(StateIndex i) const;
-
- //! Return the total number of restraints
- unsigned int number_of_restraints() const {
- return restraints_.size();
- }
-
//! Evaluate all of the restraints in the model and return the score.
/** \param[in] calc_derivs If true, also evaluate the first derivatives.
\return The score.
@@ -109,16 +81,6 @@
//! all of the data associated with the particles
ModelData* model_data_;
- //! all base-level restraints and/or restraint sets of the model
- std::vector<Restraint*> restraints_;
-
- // all base-level restraints and/or restraint sets of the model
- std::vector<State*> states_;
-
-
- //! sets of particles that move as a single rigid body
- std::vector<RigidBody*> rigid_bodies_;
-
//! trajectory file path
std::string trajectory_path_;
bool trajectory_on_;
Index: include/IMP/Restraint.h
===================================================================
--- include/IMP/Restraint.h (revision 630)
+++ include/IMP/Restraint.h (working copy)
@@ -10,10 +10,12 @@
#include <vector>
#include <iostream>
+#include <limits>
#include "IMP_config.h"
-#include "ModelData.h"
+#include "Model.h"
#include "ScoreFunc.h"
+#include "Particle.h"
#include "DerivativeAccumulator.h"
#include "boost/noncopyable.h"
#include "utility.h"
@@ -27,8 +29,8 @@
//! Abstract class for representing restraints
class IMPDLLEXPORT Restraint : public boost::noncopyable
{
-
public:
+ //! Initialize the Restraint and its model pointer
Restraint(std::string name=std::string());
virtual ~Restraint();
@@ -37,7 +39,7 @@
derivatives.
\return Current score.
*/
- virtual Float evaluate(DerivativeAccumulator *accum) = 0;
+ virtual Float evaluate(DerivativeAccumulator *) = 0;
//! Set whether the restraint is active i.e. if it should be evaluated.
/** \param[in] is_active If true, the restraint is active.
@@ -58,7 +60,7 @@
//! Show the current restraint.
/** \param[in] out Stream to send restraint description to.
*/
- virtual void show(std::ostream& out) const;
+ virtual void show(std::ostream& out=std::cout) const;
virtual std::string version() const = 0;
@@ -77,6 +79,7 @@
Particle *get_particle(unsigned int i) const;
int add_particle(Particle *p) {
+ IMP_assert(p != NULL, "Can't add NULL particle");
particles_.push_back(p);
return particles_.size()-1;
}
@@ -88,10 +91,10 @@
model_=model;
}
-
-
//! Return the model containing this restraint
Model *get_model() const {
+ IMP_assert(model_ != NULL,
+ "get_model() called before set_model()");
return model_;
}
Index: include/IMP/State.h
===================================================================
--- include/IMP/State.h (revision 630)
+++ include/IMP/State.h (working copy)
@@ -11,7 +11,6 @@
#include <iostream>
#include "IMP_config.h"
-#include "ModelData.h"
#include "boost/noncopyable.h"
namespace IMP
@@ -50,6 +49,8 @@
//! return the stored model data
Model *get_model() const {
+ IMP_assert(model_ != NULL,
+ "Must call set_model before get_model on state");
return model_;
}
protected:
Index: include/IMP/Optimizer.h
===================================================================
--- include/IMP/Optimizer.h (revision 630)
+++ include/IMP/Optimizer.h (working copy)
@@ -34,9 +34,14 @@
virtual std::string version() const =0;
/** \return the last person to modify this restraint */
virtual std::string last_modified_by() const=0;
-
+
//! Get the model being optimized
- Model *get_model() const {return model_;}
+ Model *get_model() const {
+ IMP_assert(model_ != NULL,
+ "get_model() called before set_model() "
+ << " this can crash python");
+ return model_;
+ }
//! Set the model being optimized
/**
Index: src/Optimizer.cpp
===================================================================
--- src/Optimizer.cpp (revision 630)
+++ src/Optimizer.cpp (working copy)
@@ -14,13 +14,14 @@
//! Constructor
Optimizer::Optimizer()
{
- IMP_LOG(VERBOSE, "Created optimizer");
+ IMP_LOG(VERBOSE, "MEMORY: Optimizer created " << this << std::endl);
}
//! Destructor
Optimizer::~Optimizer()
{
+ IMP_LOG(VERBOSE, "MEMORY: Optimizer destroyed " << this << std::endl);
}
} // namespace IMP
Index: src/Model.cpp
===================================================================
--- src/Model.cpp (revision 630)
+++ src/Model.cpp (working copy)
@@ -10,6 +10,7 @@
#include "IMP/ModelData.h"
#include "IMP/Particle.h"
#include "IMP/log.h"
+#include "IMP/Restraint.h"
#include "IMP/DerivativeAccumulator.h"
#include "mystdexcept.h"
@@ -19,6 +20,7 @@
//! Constructor
Model::Model()
{
+ IMP_LOG(VERBOSE, "MEMORY: Model created " << this << std::endl);
model_data_ = new ModelData();
frame_num_ = 0;
trajectory_on_ = false;
@@ -28,19 +30,10 @@
//! Destructor
Model::~Model()
{
- IMP_LOG(VERBOSE, "Delete Model: beware of early Python calls to destructor.");
- for (ParticleIterator it=particles_begin(); it != particles_end(); ++it) {
- (*it)->set_model(NULL, ParticleIndex());
- }
+ IMP_LOG(VERBOSE, "MEMORY: Model destroyed " << this << std::endl);
IMP_CONTAINER_DELETE(Particle, particle);
- for (unsigned int i = 0; i < restraints_.size(); ++i) {
- restraints_[i]->set_model(NULL);
- delete restraints_[i];
- }
- for (unsigned int i = 0; i < states_.size(); ++i) {
- states_[i]->set_model(NULL);
- delete states_[i];
- }
+ IMP_CONTAINER_DELETE(State, state);
+ IMP_CONTAINER_DELETE(Restraint, restraint);
}
@@ -52,63 +45,17 @@
return model_data_;
}
+IMP_CONTAINER_IMPL(Model, Restraint, restraint, RestraintIndex,
+ obj->set_model(this));
-//! Add restraint set to the model.
-/** \param[in] restraint_set Pointer to the restraint set.
- \return the index of the newly-added restraint.
- */
-RestraintIndex Model::add_restraint(Restraint* restraint_set)
-{
- restraints_.push_back(restraint_set);
- RestraintIndex ri(restraints_.size() - 1);
- restraint_set->set_model(this);
- return ri;
-}
+IMP_CONTAINER_IMPL(Model, Particle, particle, ParticleIndex,
+ obj->set_model(this, index));
+IMP_CONTAINER_IMPL(Model, State, state, StateIndex,
+ obj->set_model(this));
-IMP_CONTAINER_IMPL(Model, Particle, particle, ParticleIndex,
- obj->set_model(this, index));
-//! Get state from the model.
-/** \param[in] i The StateIndex returned when adding.
- \exception std::out_of_range state index is out of range.
- \return pointer to the state.
- */
-State* Model::get_state(StateIndex i) const
-{
- IMP_check(i.get_index() < states_.size(),
- "Out of range State requested",
- std::out_of_range("Invalid State requested"));
- return states_[i.get_index()];
-}
-
-
-//! Add state to the model.
-/** \param[in] state Pointer to the state.
- \return the index of the newly-added state.
-*/
-StateIndex Model::add_state(State* state)
-{
- state->set_model(this);
- states_.push_back(state);
- return states_.size() - 1;
-}
-
-
-//! Get restraint set from the model.
-/** \param[in] i The RestraintIndex returned when adding.
- \exception std::out_of_range restraint index is out of range.
- \return pointer to the restraint.
- */
-Restraint* Model::get_restraint(RestraintIndex i) const
-{
- IMP_check(i.get_index() < restraints_.size(),
- "Out of range restraint requested",
- std::out_of_range("Invalid restraint requested"));
- return restraints_[i.get_index()];
-}
-
//! Evaluate all of the restraints in the model and return the score.
/** \param[in] calc_derivs If true, also evaluate the first derivatives.
\return The score.
@@ -118,38 +65,54 @@
// One or more particles may have been activated or deactivated.
// Check each restraint to see if it changes its active status.
IMP_LOG(VERBOSE,
- "Model evaluate (" << restraints_.size() << " restraint sets):");
+ "Model evaluate (" << number_of_restraints() << " restraints):"
+ << std::endl);
+
if (model_data_->check_particles_active()) {
- for (size_t i = 0; i < restraints_.size(); i++) {
- restraints_[i]->check_particles_active();
+ IMP_LOG(VERBOSE,
+ "Checking for active particles " << std::flush);
+
+ for (RestraintIterator it = restraints_begin();
+ it != restraints_end(); ++it) {
+ (*it)->check_particles_active();
+ IMP_LOG(VERBOSE, "." << std::flush);
}
model_data_->set_check_particles_active(false);
+ IMP_LOG(VERBOSE, "done." << std::endl);
}
// If calcualting derivatives, first set all derivatives to zero
if (calc_derivs)
model_data_->zero_derivatives();
- for (size_t i = 0; i < states_.size(); i++) {
- IMP_LOG(VERBOSE, "Updating state " << states_[i]->get_name() << ":");
- states_[i]->update();
+ IMP_LOG(VERBOSE,
+ "Updating States " << std::flush);
+ for (StateIterator it = states_begin(); it != states_end(); ++it) {
+ (*it)->update();
+ IMP_LOG(VERBOSE, "." << std::flush);
}
+ IMP_LOG(VERBOSE, "done." << std::endl);
// evaluate all of the active restraints to get score (and derivatives)
// for current state of the model
Float score = 0.0;
DerivativeAccumulator accum;
DerivativeAccumulator *accpt = (calc_derivs ? &accum : NULL);
- for (size_t i = 0; i < restraints_.size(); i++) {
- IMP_LOG(VERBOSE,
- "Evaluating restraint " << restraints_[i]->get_name() << ":");
- if (restraints_[i]->get_is_active()) {
- score += restraints_[i]->evaluate(accpt);
- }
- IMP_LOG(VERBOSE, "Cumulative score: " << score);
+ IMP_LOG(VERBOSE,
+ "Evaluating restraints " << calc_derivs << std::endl);
+ for (RestraintIterator it = restraints_begin();
+ it != restraints_end(); ++it) {
+ IMP_LOG(VERBOSE, (*it)->get_name() << ": " << std::flush);
+ Float tscore=0;
+ if ((*it)->get_is_active()) {
+ tscore = (*it)->evaluate(accpt);
+ }
+ IMP_LOG(VERBOSE, tscore << std::endl);
+ score+= tscore;
}
+ IMP_LOG(VERBOSE, "done." << std::endl);
// if trajectory is on and we are calculating derivatives, save state in
// trajectory file
@@ -158,7 +121,7 @@
if (calc_derivs)
save_state();
- IMP_LOG(VERBOSE, "Final score: " << score);
+ IMP_LOG(VERBOSE, "Final score: " << score << std::endl);
return score;
}
@@ -239,17 +202,12 @@
out << "version: " << version() << " ";
out << "last_modified_by: " << last_modified_by() << std::endl;
out << number_of_particles() << " particles" << std::endl;
- for (ParticleConstIterator it=particles_begin();
- it != particles_end(); ++it) {
- (*it)->show(out);
+ out << "Restraints:" << std::endl;
+ for (RestraintConstIterator it = restraints_begin();
+ it != restraints_end(); ++it) {
+ out << (*it)->get_name() << std::endl;
}
- for (size_t i = 0; i < restraints_.size(); i++) {
- out << std::endl << "* Restraint *" << std::endl;
-
- restraints_[i]->show(out);
- }
-
internal::show_attributes(out);
}
Index: src/Restraint.cpp
===================================================================
--- src/Restraint.cpp (revision 630)
+++ src/Restraint.cpp (working copy)
@@ -19,7 +19,7 @@
Restraint::Restraint(std::string name): name_(name)
{
model_ = NULL;
- IMP_LOG(VERBOSE, "Restraint constructed");
+ IMP_LOG(VERBOSE, "MEMORY: Restraint constructed " << this << std::endl);
is_active_ = true; // active by default
are_particles_active_ = true; // active by default
}
@@ -28,11 +28,7 @@
//! Destructor
Restraint::~Restraint()
{
- IMP_LOG(VERBOSE, "Restraint deleted");
- IMP_assert(get_model() == NULL,
- "Attemping to delete restraint while it is still in a model.\n"
- << " This probably reflects premature destruction"
- << " of python references.\n");
+ IMP_LOG(VERBOSE, "MEMORY: Restraint deleted " << this << std::endl);
}
@@ -76,9 +72,11 @@
*/
void Restraint::check_particles_active()
{
+ IMP_assert(get_model() != NULL,
+ "Add Restraint to Model before calling check_particles_active");
are_particles_active_ = true;
for (size_t i = 0; i < particles_.size(); i++) {
- if (!particles_[i]->get_is_active()) {
+ if (!get_particle(i)->get_is_active()) {
are_particles_active_ = false;
return;
}
Index: src/Particle.cpp
===================================================================
--- src/Particle.cpp (revision 630)
+++ src/Particle.cpp (working copy)
@@ -17,18 +17,14 @@
//! Constructor
Particle::Particle(): model_(NULL)
{
- IMP_LOG(VERBOSE, "create particle" << std::endl);
is_active_ = true;
+ IMP_LOG(VERBOSE, "MEMORY: Particle created " << pi_ << std::endl);
}
//! Constructor
Particle::~Particle()
{
- IMP_LOG(VERBOSE, "destroy particle " << *this << std::endl);
- IMP_assert(get_model() == NULL,
- "Attemping to delete particle while it is still in a model.\n"
- << " This probably reflects premature destruction"
- << " of python references.\n");
+ IMP_LOG(VERBOSE, "MEMORY: Particle deleted " << pi_ << std::endl);
}