Index: include/IMP/ModelData.h
===================================================================
--- include/IMP/ModelData.h (revision 650)
+++ include/IMP/ModelData.h (working copy)
@@ -79,6 +79,8 @@
\return value of particle float attribute.
*/
Float get_value(const FloatIndex idx) const {
+ IMP_assert(idx.get_index() < float_data_.size(),
+ "Out of range index requested");
return float_data_[idx.get_index()].value_;
}
@@ -122,6 +124,8 @@
\return value of particle float attribute.
*/
Int get_value(const IntIndex idx) const {
+ IMP_assert(idx.get_index() < int_data_.size(),
+ "Out of range int requested");
return int_data_[idx.get_index()];
}
@@ -144,6 +148,8 @@
\return value of particle string attribute.
*/
String get_value(const StringIndex idx) const {
+ IMP_assert(idx.get_index() < string_data_.size(),
+ "Out of range string requested");
return string_data_[idx.get_index()];
}
Index: include/IMP/boost/noncopyable.h
===================================================================
--- include/IMP/boost/noncopyable.h (revision 650)
+++ include/IMP/boost/noncopyable.h (working copy)
@@ -1,36 +0,0 @@
-// Boost noncopyable.hpp header file --------------------------------------//
-
-// (C) Copyright Beman Dawes 1999-2003. Distributed under the Boost
-// Software License, Version 1.0. (See accompanying file
-// LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
-
-// See http://www.boost.org/libs/utility for documentation.
-
-#ifndef BOOST_NONCOPYABLE_HPP_INCLUDED
-#define BOOST_NONCOPYABLE_HPP_INCLUDED
-namespace IMP {
-namespace boost {
-
-// Private copy constructor and copy assignment ensure classes derived from
-// class noncopyable cannot be copied.
-
-// Contributed by Dave Abrahams
-
-namespace noncopyable_ // protection from unintended ADL
-{
- class noncopyable
- {
- protected:
- noncopyable() {}
- ~noncopyable() {}
- private: // emphasize the following members are private
- noncopyable( const noncopyable& );
- const noncopyable& operator=( const noncopyable& );
- };
-}
-
-typedef noncopyable_::noncopyable noncopyable;
-
-} // namespace boost
-} // namespace IMP
-#endif // BOOST_NONCOPYABLE_HPP_INCLUDED
Index: include/IMP/boost/SConscript
===================================================================
--- include/IMP/boost/SConscript (revision 650)
+++ include/IMP/boost/SConscript (working copy)
@@ -1,10 +0,0 @@
-import os.path
-Import('env')
-
-files = ['noncopyable.h']
-
-
-# Install the include files:
-includedir = os.path.join(env['includedir'], 'IMP', 'boost')
-inst = env.Install(includedir, files)
-env.Alias('install', inst)
Index: include/IMP/Model.h
===================================================================
--- include/IMP/Model.h (revision 650)
+++ include/IMP/Model.h (working copy)
@@ -13,7 +13,7 @@
#include "ModelData.h"
#include "RigidBody.h"
#include "State.h"
-#include "boost/noncopyable.h"
+#include "Object.h"
namespace IMP
{
@@ -25,7 +25,7 @@
/** All attribute data for particles is stored through indexing in the
model_data_ structure.
*/
-class IMPDLLEXPORT Model: public boost::noncopyable
+class IMPDLLEXPORT Model: public Object
{
friend class Restraint;
public:
Index: include/IMP/SConscript
===================================================================
--- include/IMP/SConscript (revision 650)
+++ include/IMP/SConscript (working copy)
@@ -4,7 +4,8 @@
files = ['base_types.h', 'Index.h', 'ScoreFunc.h', 'Model.h',
'Particle.h', 'State.h', 'IMP_config.h', 'ModelData.h', 'RigidBody.h',
'log.h', 'DerivativeAccumulator.h', 'Key.h', 'AttributeTable.h',
- 'utility.h', 'Restraint.h', 'Optimizer.h', 'DecoratorBase.h']
+ 'utility.h', 'Restraint.h', 'Optimizer.h', 'DecoratorBase.h',
+ 'Object.h']
# Install the include files:
includedir = os.path.join(env['includedir'], 'IMP')
@@ -15,4 +16,3 @@
SConscript('restraints/SConscript')
SConscript('optimizers/SConscript')
SConscript('decorators/SConscript')
-SConscript('boost/SConscript')
Index: include/IMP/Particle.h
===================================================================
--- include/IMP/Particle.h (revision 650)
+++ include/IMP/Particle.h (working copy)
@@ -14,7 +14,7 @@
#include "base_types.h"
#include "Model.h"
#include "Restraint.h"
-#include "boost/noncopyable.h"
+#include "Object.h"
#include "utility.h"
#include "Key.h"
#include "AttributeTable.h"
@@ -32,7 +32,7 @@
optimization. Removing particles and their attributes would cause
problems in the way attribute values are indexed and should not be done.
*/
-class IMPDLLEXPORT Particle : public boost::noncopyable
+class IMPDLLEXPORT Particle : public Object
{
friend class Model;
public:
Index: include/IMP/utility.h
===================================================================
--- include/IMP/utility.h (revision 650)
+++ include/IMP/utility.h (working copy)
@@ -169,13 +169,16 @@
IndexType index(lcname##_vector_.size()); \
lcname##_vector_.push_back(obj); \
init; \
+ IMP_CHECK_OBJECT(obj); \
return index; \
} \
Ucname *Class::get_##lcname(IndexType i) const { \
IMP_check(i.get_index() < lcname##_vector_.size(), \
"Index " << i << " out of range", \
IndexException(#Ucname)); \
- return lcname##_vector_[i.get_index()]; \
+ Ucname *r= lcname##_vector_[i.get_index()]; \
+ IMP_CHECK_OBJECT(r); \
+ return r; \
} \
@@ -193,6 +196,8 @@
} \
lcname##_vector_.clear();
+//! Call the assert_is_valid method in the object base
+#define IMP_CHECK_OBJECT(obj) (obj)->assert_is_valid()
namespace IMP {
//! Compute the square of a number
Index: include/IMP/Object.h
===================================================================
--- include/IMP/Object.h (revision 0)
+++ include/IMP/Object.h (revision 0)
@@ -0,0 +1,39 @@
+/**
+ * \file Object.h
+ * \brief A shared base class to help in debugging and things.
+ *
+ * Copyright 2007 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_OBJECT_H
+#define __IMP_OBJECT_H
+#include <IMP/log.h>
+
+namespace IMP {
+/**
+ Currently this just makes the object noncopyable and adds heuristic checks
+ to make sure the memory has not been freed.
+
+ \note Do not use NDEBUG to remove check_value_ as that changes the memory
+ layout and causes bad things to happen. It should get wrapped in some
+ sort of marco later.
+ */
+class IMPDLLEXPORT Object {
+protected:
+ Object();
+ ~Object();
+
+public:
+ //! Throw an assertion if the object has been freed
+ void assert_is_valid() const;
+
+private:
+ Object(const Object &o){}
+ const Object& operator=(const Object &o) {return *this;}
+
+ double check_value_;
+};
+
+}
+#endif
Index: include/IMP/Restraint.h
===================================================================
--- include/IMP/Restraint.h (revision 650)
+++ include/IMP/Restraint.h (working copy)
@@ -17,7 +17,7 @@
#include "ScoreFunc.h"
#include "Particle.h"
#include "DerivativeAccumulator.h"
-#include "boost/noncopyable.h"
+#include "Object.h"
#include "utility.h"
#include "log.h"
@@ -27,7 +27,7 @@
class Model;
//! Abstract class for representing restraints
-class IMPDLLEXPORT Restraint : public boost::noncopyable
+class IMPDLLEXPORT Restraint : public Object
{
public:
//! Initialize the Restraint and its model pointer
@@ -76,14 +76,6 @@
name_=name;
}
- 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;
- }
-
//! The model the restraint is part of.
/** \param[in] model The model.
*/
@@ -98,11 +90,30 @@
return model_;
}
+ protected:
+ 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;
+ }
+
//! Return the number of particles this restraint knows about
unsigned int number_of_particles() const {
return particles_.size();
}
+ //! Clear the internal list of particles
+ void clear_particles() {
+ return particles_.clear();
+ }
+
+ //! Replace the set of particles used by the restraint
+ void set_particles(const Particles &ps) {
+ particles_= ps;
+ }
+
private:
//! all of the particle data
Model* model_;
Index: include/IMP/decorators/graph_base.h
===================================================================
--- include/IMP/decorators/graph_base.h (revision 650)
+++ include/IMP/decorators/graph_base.h (working copy)
@@ -36,13 +36,16 @@
IMPDLLEXPORT Particle* graph_connect(Particle* a, Particle* b,
- const GraphData &d);
+ const GraphData &d);
+IMPDLLEXPORT void graph_disconnect(Particle* bond,
+ const GraphData &d);
+
IMPDLLEXPORT Particle* graph_get_edge(Particle* a, int i,
- const GraphData &d);
+ const GraphData &d);
IMPDLLEXPORT Particle* graph_get_neighbor(Particle* a, int i,
- const GraphData &d);
+ const GraphData &d);
IMPDLLEXPORT unsigned int graph_get_number_of_edges(Particle *a,
const GraphData &d);
Index: include/IMP/decorators/bond_decorators.h
===================================================================
--- include/IMP/decorators/bond_decorators.h (revision 650)
+++ include/IMP/decorators/bond_decorators.h (working copy)
@@ -30,6 +30,7 @@
extern IMPDLLEXPORT FloatKey bond_length_key_;
extern IMPDLLEXPORT IntKey bond_type_key_;
extern IMPDLLEXPORT IntKey bond_order_key_;
+extern IMPDLLEXPORT FloatKey bond_stiffness_key_;
} // namespace internal
@@ -48,7 +49,7 @@
public:
//! The types a bond can have right now
enum Type {UNKNOWN=-1,
- COVALENT, HYDROGEN, DISULPHINE, SALT, PEPTIDE
+ COVALENT, HYDROGEN, DISULPHINE, SALT, PEPTIDE, HIGHORDER
};
//! Get the atom i of the bond
@@ -61,6 +62,10 @@
IMP_DECORATOR_GET_SET_OPT(length, internal::bond_length_key_, Float,
Float, -1);
+ IMP_DECORATOR_GET_SET_OPT(stiffness, internal::bond_stiffness_key_, Float,
+ Float, -1);
+
+
IMP_DECORATOR_GET_SET_OPT(type, internal::bond_type_key_, Int, Int,
UNKNOWN);
@@ -81,7 +86,7 @@
public:
- int get_number_of_bonds() const {
+ unsigned int number_of_bonds() const {
return graph_get_number_of_edges(get_particle(),
internal::bond_graph_data_);
}
@@ -101,10 +106,10 @@
IMP_OUTPUT_OPERATOR(BondedDecorator);
-BondedDecorator BondDecorator::get_atom(unsigned int i) const
+inline BondedDecorator BondDecorator::get_atom(unsigned int i) const
{
Particle *p= graph_get_node(get_particle(), i,
- internal::bond_graph_data_);
+ internal::bond_graph_data_);
return BondedDecorator::cast(p);
}
@@ -112,16 +117,33 @@
/** \param[in] a The first Particle as a BondedDecorator
\param[in] b The second Particle as a BondedDecorator
\param[in] t The type to use for the bond
+ \param[in] l The length of the bond. Negative values are ignored.
+ \param[in] s The stiffness of the bond. Negative values are ignored.
\return BondDecorator of the bond Particle.
*/
IMPDLLEXPORT
-BondDecorator bond(BondedDecorator a, BondedDecorator b, Int t);
+BondDecorator bond(BondedDecorator a, BondedDecorator b, Int t,
+ Float l=-1, Float s = -1);
+//! Destroy the bond connecting to particles.
+/** \param[in] b The bond.
+ */
+IMPDLLEXPORT
+void unbond(BondDecorator b);
+
+
//! Get all the particles connected to the current one via a path of bonds.
IMPDLLEXPORT
Particles get_bonded(BondedDecorator a);
+//! Get the bond between two particles.
+/**
+ BondDecorator() is returned if the particles are not bonded.
+ */
+IMPDLLEXPORT
+BondDecorator get_bond(BondedDecorator a, BondedDecorator b);
+
} // namespace IMP
#endif /* __IMP_BOND_DECORATORS_H */
Index: include/IMP/State.h
===================================================================
--- include/IMP/State.h (revision 650)
+++ include/IMP/State.h (working copy)
@@ -11,14 +11,14 @@
#include <iostream>
#include "IMP_config.h"
-#include "boost/noncopyable.h"
+#include "Object.h"
namespace IMP
{
class Model;
//! Shared state.
-class IMPDLLEXPORT State : public boost::noncopyable
+class IMPDLLEXPORT State : public Object
{
friend class Model;
void set_model(Model* model);
Index: include/IMP/Optimizer.h
===================================================================
--- include/IMP/Optimizer.h (revision 650)
+++ include/IMP/Optimizer.h (working copy)
@@ -12,14 +12,16 @@
#include "IMP_config.h"
#include "base_types.h"
-#include "Model.h"
+#include "Object.h"
#include "utility.h"
namespace IMP
{
+class Model;
+
//! Base class for all optimizers
-class IMPDLLEXPORT Optimizer
+class IMPDLLEXPORT Optimizer: public Object
{
public:
Optimizer();
Index: include/IMP/ScoreFunc.h
===================================================================
--- include/IMP/ScoreFunc.h (revision 650)
+++ include/IMP/ScoreFunc.h (working copy)
@@ -11,6 +11,7 @@
#include "IMP_config.h"
#include "base_types.h"
+#include "Object.h"
namespace IMP
{
@@ -20,7 +21,7 @@
could be maintained for both the score calls and the score and partial
derivative calls.
*/
-class IMPDLLEXPORT ScoreFunc
+ class IMPDLLEXPORT ScoreFunc: public Object
{
public:
ScoreFunc() {}
@@ -71,11 +72,11 @@
*/
Float harmonic(Float feature, Float& deriv);
-
void show(std::ostream &out=std::cout) const
{
out << "Harmonic: " << mean_ << " and " << sd_ << std::endl;
}
+
protected:
Float mean_;
Float sd_;
Index: src/Model.cpp
===================================================================
--- src/Model.cpp (revision 650)
+++ src/Model.cpp (working copy)
@@ -20,7 +20,6 @@
//! Constructor
Model::Model()
{
- IMP_LOG(VERBOSE, "MEMORY: Model created " << this << std::endl);
model_data_ = new ModelData();
frame_num_ = 0;
trajectory_on_ = false;
@@ -30,7 +29,6 @@
//! Destructor
Model::~Model()
{
- IMP_LOG(VERBOSE, "MEMORY: Model destroyed " << this << std::endl);
IMP_CONTAINER_DELETE(Particle, particle);
IMP_CONTAINER_DELETE(State, state);
IMP_CONTAINER_DELETE(Restraint, restraint);
@@ -89,6 +87,7 @@
IMP_LOG(VERBOSE,
"Updating States " << std::flush);
for (StateIterator it = states_begin(); it != states_end(); ++it) {
+ IMP_CHECK_OBJECT(*it);
(*it)->update();
IMP_LOG(VERBOSE, "." << std::flush);
}
@@ -104,6 +103,7 @@
"Evaluating restraints " << calc_derivs << std::endl);
for (RestraintIterator it = restraints_begin();
it != restraints_end(); ++it) {
+ IMP_CHECK_OBJECT(*it);
IMP_LOG(VERBOSE, (*it)->get_name() << ": " << std::flush);
Float tscore=0;
if ((*it)->get_is_active()) {
@@ -205,6 +205,7 @@
out << "Restraints:" << std::endl;
for (RestraintConstIterator it = restraints_begin();
it != restraints_end(); ++it) {
+ IMP_CHECK_OBJECT(*it);
out << (*it)->get_name() << std::endl;
}
Index: src/Particle.cpp
===================================================================
--- src/Particle.cpp (revision 650)
+++ src/Particle.cpp (working copy)
@@ -18,13 +18,11 @@
Particle::Particle(): model_(NULL)
{
is_active_ = true;
- IMP_LOG(VERBOSE, "MEMORY: Particle created " << pi_ << std::endl);
}
//! Constructor
Particle::~Particle()
{
- IMP_LOG(VERBOSE, "MEMORY: Particle deleted " << pi_ << std::endl);
}
@@ -61,7 +59,6 @@
void Particle::add_attribute(FloatKey name, const Float value,
bool is_optimized)
{
- IMP_LOG(VERBOSE, "add_float: " << name);
IMP_assert(model_ != NULL,
"Particle must be added to Model before an attributes are added");
float_indexes_.insert(name, model_->get_model_data()->add_float(value));
@@ -77,7 +74,6 @@
*/
void Particle::add_attribute(IntKey name, const Int value)
{
- IMP_LOG(VERBOSE, "add_int: " << name);
IMP_assert(model_ != NULL,
"Particle must be added to Model before an attributes are added");
int_indexes_.insert(name, model_->get_model_data()->add_int(value));
Index: src/Object.cpp
===================================================================
--- src/Object.cpp (revision 0)
+++ src/Object.cpp (revision 0)
@@ -0,0 +1,16 @@
+#include "IMP/Object.h"
+
+namespace IMP {
+Object::Object(){
+ check_value_=111111111;
+}
+Object::~Object() {
+ assert_is_valid();
+ check_value_=666666666;
+}
+
+void Object::assert_is_valid() const {
+ IMP_assert(check_value_==111111111,
+ "Previously freed object is not valid: " << this);
+}
+}
Index: src/SConscript
===================================================================
--- src/SConscript (revision 650)
+++ src/SConscript (working copy)
@@ -12,7 +12,7 @@
# Source files
files = ['base_types.cpp', 'ScoreFunc.cpp', 'Model.cpp', 'ModelData.cpp',
'Particle.cpp', 'RigidBody.cpp', 'State.cpp', 'Log.cpp',
- 'Restraint.cpp', 'Optimizer.cpp'
+ 'Restraint.cpp', 'Optimizer.cpp', 'Object.cpp'
] + decorators_files + restraints_files + optimizers_files
# Build the shared library:
Index: src/Restraint.cpp
===================================================================
--- src/Restraint.cpp (revision 650)
+++ src/Restraint.cpp (working copy)
@@ -19,7 +19,6 @@
Restraint::Restraint(std::string name): name_(name)
{
model_ = NULL;
- IMP_LOG(VERBOSE, "MEMORY: Restraint constructed " << this << std::endl);
is_active_ = true; // active by default
are_particles_active_ = true; // active by default
}
@@ -28,7 +27,6 @@
//! Destructor
Restraint::~Restraint()
{
- IMP_LOG(VERBOSE, "MEMORY: Restraint deleted " << this << std::endl);
}
Index: src/restraints/DistanceRestraint.cpp
===================================================================
--- src/restraints/DistanceRestraint.cpp (revision 650)
+++ src/restraints/DistanceRestraint.cpp (working copy)
@@ -63,6 +63,9 @@
*/
Float DistanceRestraint::evaluate(DerivativeAccumulator *accum)
{
+
+ IMP_CHECK_OBJECT(score_func_);
+
Float d2=0, delta[3];
Float score;
Index: src/restraints/SphericalRestraint.cpp
===================================================================
--- src/restraints/SphericalRestraint.cpp (revision 650)
+++ src/restraints/SphericalRestraint.cpp (working copy)
@@ -42,6 +42,7 @@
Float SphericalRestraint::evaluate(DerivativeAccumulator *accum)
{
+ IMP_CHECK_OBJECT(score_func_);
Float d2=0;
Float diff[3];
Index: src/State.cpp
===================================================================
--- src/State.cpp (revision 650)
+++ src/State.cpp (working copy)
@@ -18,14 +18,14 @@
State::State(std::string name) : name_(name)
{
model_ = NULL;
- IMP_LOG(VERBOSE, "State constructed");
+ IMP_LOG(VERBOSE, "State constructed " << name << std::endl);
}
//! Destructor
State::~State()
{
- IMP_LOG(VERBOSE, "State deleted");
+ IMP_LOG(VERBOSE, "State deleted " << get_name() << std::endl);
}
Index: src/decorators/bond_decorators.cpp
===================================================================
--- src/decorators/bond_decorators.cpp (revision 650)
+++ src/decorators/bond_decorators.cpp (working copy)
@@ -15,6 +15,7 @@
GraphData bond_graph_data_;
bool bond_keys_initialized_=false;
FloatKey bond_length_key_;
+FloatKey bond_stiffness_key_;
IntKey bond_type_key_;
IntKey bond_order_key_;
}
@@ -36,6 +37,7 @@
} else {
internal::bond_graph_data_= internal::GraphData("bond");
internal::bond_length_key_=FloatKey("bond length");
+ internal::bond_stiffness_key_=FloatKey("bond stiffness");
internal::bond_type_key_= IntKey("bond type");
internal::bond_order_key_=IntKey("bond order");
internal::bond_keys_initialized_=true;
@@ -53,15 +55,21 @@
BondDecorator bond(BondedDecorator a, BondedDecorator b,
- Int t)
+ Int t, Float l, Float s)
{
Particle *p= internal::graph_connect(a.get_particle(), b.get_particle(),
internal::bond_graph_data_);
BondDecorator bd= BondDecorator::cast(p);
bd.set_type(t);
+ if (l >= 0) bd.set_length(l);
+ if (s >= 0) bd.set_stiffness(s);
return bd;
}
+void unbond(BondDecorator b) {
+ graph_disconnect(b.get_particle(), internal::bond_graph_data_);
+}
+
Particles get_bonded(BondedDecorator a) {
Particles out;
internal::graph_connected_component(a.get_particle(),
@@ -70,4 +78,14 @@
return out;
}
+BondDecorator get_bond(BondedDecorator a, BondedDecorator b) {
+ for (unsigned int i=0; i < a.number_of_bonds(); ++i) {
+ BondDecorator bd= a.get_bond(i);
+ if (bd.get_atom(0) == b || bd.get_atom(1) == b) {
+ return bd;
+ }
+ }
+ return BondDecorator();
}
+
+}
Index: src/decorators/graph_base.cpp
===================================================================
--- src/decorators/graph_base.cpp (revision 650)
+++ src/decorators/graph_base.cpp (working copy)
@@ -34,30 +34,52 @@
ParticleIndex pi=m->add_particle(p);
p->add_attribute(d.node_keys_[0], a->get_index().get_index());
p->add_attribute(d.node_keys_[1], b->get_index().get_index());
- {
- int nc= graph_get_number_of_edges(a, d);
+ for (int i=0; i< 2; ++i) {
+ Particle *cp=((i==0)?a:b);
+ int nc= graph_get_number_of_edges(cp, d);
IntKey nm=graph_get_edge_key(nc, d);
- a->add_attribute(nm, p->get_index().get_index());
- if (a->has_attribute(d.num_edges_key_)) {
- a->set_value(d.num_edges_key_, nc+1);
+ if (!cp->has_attribute(nm)) {
+ cp->add_attribute(nm, p->get_index().get_index());
} else {
- a->add_attribute(d.num_edges_key_, nc+1);
+ cp->set_value(nm, p->get_index().get_index());
}
- }
- {
- int nc= graph_get_number_of_edges(b, d);
- IntKey nm=graph_get_edge_key(nc, d);
- b->add_attribute(nm, p->get_index().get_index());
- if (b->has_attribute(d.num_edges_key_)) {
- b->set_value(d.num_edges_key_, nc+1);
+ if (cp->has_attribute(d.num_edges_key_)) {
+ cp->set_value(d.num_edges_key_, nc+1);
} else {
- b->add_attribute(d.num_edges_key_, nc+1);
+ cp->add_attribute(d.num_edges_key_, nc+1);
}
}
return a->get_model()->get_particle(pi);
}
+void graph_disconnect(Particle* e, const GraphData &d)
+{
+ ParticleIndex pi=e->get_index();
+ Particle *p[2];
+ p[0]= graph_get_node(e, 0, d);
+ p[1]= graph_get_node(e, 1, d);
+ for (int i=0; i< 2; ++i) {
+ int shift=0;
+ Int nc= p[i]->get_value(d.num_edges_key_);
+ for (int j=0; j< nc; ++j) {
+ if (graph_get_edge(p[i], j, d) == e) {
+ IMP_assert(shift==0, "duplicate edges found in graph_base");
+ shift=-1;
+ } else {
+ Int v = p[i]->get_value(graph_get_edge_key(j, d));
+ p[i]->set_value(graph_get_edge_key(j+shift, d), v);
+ }
+ }
+ p[i]->set_value(graph_get_edge_key(nc-1, d), -1);
+ IMP_assert(shift==-1, "no edge found");
+ IMP_assert(nc > 0, "Too few edges");
+ p[i]->set_value(d.num_edges_key_, nc-1);
+ }
+ e->set_is_active(false);
+}
+
+
Particle* graph_get_edge(Particle* a, int i, const GraphData &d)
{
IntKey nm= graph_get_edge_key(i, d);
Index: src/optimizers/ConjugateGradients.cpp
===================================================================
--- src/optimizers/ConjugateGradients.cpp (revision 650)
+++ src/optimizers/ConjugateGradients.cpp (working copy)
@@ -9,6 +9,7 @@
#include "IMP/log.h"
#include "IMP/optimizers/ConjugateGradients.h"
+#include "IMP/Model.h"
namespace IMP
{
Index: src/optimizers/SteepestDescent.cpp
===================================================================
--- src/optimizers/SteepestDescent.cpp (revision 650)
+++ src/optimizers/SteepestDescent.cpp (working copy)
@@ -7,6 +7,7 @@
#include "IMP/log.h"
#include "IMP/optimizers/SteepestDescent.h"
+#include "IMP/Model.h"
namespace IMP
{
Index: src/ScoreFunc.cpp
===================================================================
--- src/ScoreFunc.cpp (revision 650)
+++ src/ScoreFunc.cpp (working copy)
@@ -15,8 +15,6 @@
//! Destructor
Harmonic::~Harmonic()
{
- IMP_LOG(VERBOSE,
- "Delete Harmonic: beware of early Python calls to destructor.");
}
//! Calculate harmonic score with respect to the given feature.
@@ -72,8 +70,6 @@
//! Destructor
HarmonicLowerBound::~HarmonicLowerBound()
{
- IMP_LOG(VERBOSE, "Delete HarmonicLowerBound: beware of early Python "
- << "calls to destructor.");
}
//! Calculate lower-bound harmonic score with respect to the given feature.
@@ -109,8 +105,6 @@
//! Destructor
HarmonicUpperBound::~HarmonicUpperBound()
{
- IMP_LOG(VERBOSE, "Delete HarmonicUpperBound: beware of early Python "
- << "calls to destructor.");
}
Index: src/ModelData.cpp
===================================================================
--- src/ModelData.cpp (revision 650)
+++ src/ModelData.cpp (working copy)
@@ -32,15 +32,13 @@
*/
FloatIndex ModelData::add_float(const Float value)
{
- FloatIndex f_index;
int size = float_data_.size();
float_data_.resize(size + 1);
- f_index = FloatIndex(size);//.set_index(size);
- float_data_[f_index.get_index()].value_ = value;
+ float_data_[size].value_ = value;
- return f_index;
+ return FloatIndex(size);
}
@@ -50,6 +48,8 @@
*/
void ModelData::set_value(const FloatIndex idx, const Float value)
{
+ IMP_assert(idx.get_index() < float_data_.size(),
+ "Out of range float requested");
float_data_[idx.get_index()].value_ = value;
}
@@ -61,6 +61,8 @@
*/
void ModelData::add_to_deriv(const FloatIndex idx, Float value)
{
+ IMP_assert(idx.get_index() < float_data_.size(),
+ "Out of range float requested");
float_data_[idx.get_index()].deriv_ += value;
}
@@ -70,6 +72,8 @@
*/
Float ModelData::get_deriv(const FloatIndex idx) const
{
+ IMP_assert(idx.get_index() < float_data_.size(),
+ "Out of range float requested");
return float_data_[idx.get_index()].deriv_;
}
@@ -79,6 +83,8 @@
*/
bool ModelData::get_is_optimized(const FloatIndex idx) const
{
+ IMP_assert(idx.get_index() < float_data_.size(),
+ "Out of range float requested");
return float_data_[idx.get_index()].is_optimized_;
}
@@ -88,6 +94,8 @@
*/
void ModelData::set_is_optimized(const FloatIndex idx, bool is_optimized)
{
+ IMP_assert(idx.get_index() < float_data_.size(),
+ "Out of range float requested");
float_data_[idx.get_index()].is_optimized_ = is_optimized;
}
@@ -110,15 +118,12 @@
*/
IntIndex ModelData::add_int(const Int value)
{
- IntIndex i_index;
int size = int_data_.size();
int_data_.resize(size + 1);
+ int_data_[size] = value;
- i_index = IntIndex(size);
- int_data_[i_index.get_index()] = value;
-
- return i_index;
+ return IntIndex(size);
}
//! Set particle attribute value.
@@ -127,6 +132,8 @@
*/
void ModelData::set_value(const IntIndex idx, const Int value)
{
+ IMP_assert(idx.get_index() < int_data_.size(),
+ "Out of range int requested");
int_data_[idx.get_index()] = value;
}
@@ -139,15 +146,13 @@
*/
StringIndex ModelData::add_string(const String value)
{
- StringIndex s_index;
int size = string_data_.size();
string_data_.resize(size + 1);
- s_index = StringIndex(size);
- string_data_[s_index.get_index()] = value;
+ string_data_[size] = value;
- return s_index;
+ return StringIndex(size);
}
//! Set particle attribute value.
@@ -156,6 +161,8 @@
*/
void ModelData::set_value(const StringIndex idx, const String value)
{
+ IMP_assert(idx.get_index() < string_data_.size(),
+ "Out of range string requested");
string_data_[idx.get_index()] = value;
}
Index: pyext/IMP_macros.i
===================================================================
--- pyext/IMP_macros.i (revision 650)
+++ pyext/IMP_macros.i (working copy)
@@ -23,8 +23,8 @@
public:\
typedef Name This;\
public: Name(); \
- static Name create(Particle *p);\
- static Name cast(Particle *p);\
+ static Name create(::IMP::Particle *p);\
+ static Name cast(::IMP::Particle *p);\
void show(std::ostream &out=std::cout, std::string pre="")
#define IMP_DECORATOR_ARRAY_DECL(a, b)
#define IMP_CONTAINER(Ucname, lcname, IndexType) \
Index: pyext/SConscript
===================================================================
--- pyext/SConscript (revision 650)
+++ pyext/SConscript (working copy)
@@ -5,11 +5,11 @@
# Get a modified build environment suitable for building Python extensions:
e = get_pyext_environment(env, cplusplus=True)
e.Append(CPPPATH='#/include')
-e.Append(LIBPATH='../src', LIBS='imp')
+e.Append(LIBPATH='../src', LIBS=['imp', 'gmalloc'])
# Build the Python extension from SWIG interface file:
pyext = e.LoadableModule('_IMP', 'IMP.i',
- SWIGFLAGS='-python -c++ -naturalvar -Iinclude')
+ SWIGFLAGS='-D_GLIBCXX_DEBUG -python -c++ -naturalvar -Iinclude')
# IMP.py file should also be generated; copy to IMP subdirectory:
pymod_gen = File('IMP.py')
e.Depends(pymod_gen, pyext)
Index: pyext/IMP.i
===================================================================
--- pyext/IMP.i (revision 650)
+++ pyext/IMP.i (working copy)
@@ -34,10 +34,10 @@
%feature("director");
+%include "IMP/Object.h"
%include "IMP/Index.h"
%include "IMP/base_types.h"
%include "IMP.h"
-%include "IMP/boost/noncopyable.h"
%include "IMP/Key.h"
%include "IMP/ScoreFunc.h"
%include "IMP/ModelData.h"