Index: kernel/include/IMP.h
===================================================================
--- kernel/include/IMP.h (revision 338)
+++ kernel/include/IMP.h (working copy)
@@ -50,8 +50,11 @@
#include "IMP/restraints/PairConnectivityRestraint.h"
#include "IMP/restraints/ExclusionVolumeRestraint.h"
#include "IMP/restraints/NonbondedRestraint.h"
+#include "IMP/restraints/BondDecoratorRestraint.h"
#include "IMP/score_states/NonbondedListScoreState.h"
+#include "IMP/score_states/BipartiteNonbondedListScoreState.h"
#include "IMP/score_states/BondedListScoreState.h"
+#include "IMP/score_states/bonded_lists/BondDecoratorListScoreState.h"
/**
\namespace IMP The IMP namespace.
Index: kernel/include/IMP/decorators/bond_decorators.h
===================================================================
--- kernel/include/IMP/decorators/bond_decorators.h (revision 338)
+++ kernel/include/IMP/decorators/bond_decorators.h (working copy)
@@ -30,6 +30,8 @@
extern IMPDLLEXPORT bool bond_keys_initialized_;
extern IMPDLLEXPORT IntKey bond_type_key_;
extern IMPDLLEXPORT IntKey bond_order_key_;
+extern IMPDLLEXPORT FloatKey bond_length_key_;
+extern IMPDLLEXPORT FloatKey bond_stiffness_key_;
} // namespace internal
@@ -48,7 +50,8 @@
public:
//! The types a bond can have right now
enum Type {UNKNOWN=-1,
- COVALENT, HYDROGEN, DISULPHIDE, SALT, PEPTIDE
+ COVALENT, HYDROGEN, DISULPHIDE, SALT, PEPTIDE,
+ CUSTOM
};
//! Get the atom i of the bond
@@ -61,6 +64,11 @@
UNKNOWN);
IMP_DECORATOR_GET_SET_OPT(order, internal::bond_order_key_, Int, Int, 1);
+
+ 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_OUTPUT_OPERATOR(BondDecorator);
@@ -81,7 +89,7 @@
}
- //! Get a BondDecorator of the ith child
+ //! Get a BondDecorator of the ith bond
/** \return decorator of the ith child, or throw and exception if there
is no such bond
*/
@@ -90,12 +98,30 @@
internal::bond_graph_data_);
return BondDecorator::cast(p);
}
+
+ //! Get a BondedDecorator of the ith bonded particle
+ /** \return decorator of the ith child, or throw and exception if there
+ is no such bond
+
+ \note I don't entirely like having this here as it duplicates
+ functionality available otherwise, however it is such a fundamental
+ operation and kind of a pain to write. It also means that we
+ could later pull the edge endpoints into the vertex if
+ desired.
+ */
+ BondedDecorator get_bonded(unsigned int i) const {
+ Particle *p= graph_get_edge(get_particle(), i,
+ internal::bond_graph_data_);
+ BondDecorator bd= BondDecorator::cast(p);
+ if (bd.get_bonded(0) == *this) return bd.get_bonded(1);
+ else return bd.get_bonded(0);
+ }
};
IMP_OUTPUT_OPERATOR(BondedDecorator);
-BondedDecorator BondDecorator::get_bonded(unsigned int i) const
+inline BondedDecorator BondDecorator::get_bonded(unsigned int i) const
{
Particle *p= graph_get_node(get_particle(), i,
internal::bond_graph_data_);
@@ -111,6 +137,25 @@
IMPDLLEXPORT
BondDecorator bond(BondedDecorator a, BondedDecorator b, Int t);
+
+//! Connect the two wrapped particles by a custom bond.
+/** \param[in] a The first Particle as a BondedDecorator
+ \param[in] b The second Particle as a BondedDecorator
+ \param[in] length The length of the bond.
+ \param[in] stiffness The stiffness of the bond.
+ \return BondDecorator of the bond Particle.
+ */
+IMPDLLEXPORT
+inline BondDecorator custom_bond(BondedDecorator a, BondedDecorator b,
+ Float length, Float stiffness=-1) {
+ IMP_assert(length>=0, "Length must be positive");
+ BondDecorator bd=bond(a,b, BondDecorator::CUSTOM);
+ bd.set_length(length);
+ if (stiffness >=0) bd.set_stiffness(stiffness);
+ return bd;
+}
+
+
//! Destroy the bond connecting to particles.
/** \param[in] b The bond.
*/
Index: kernel/include/IMP/restraints/SConscript
===================================================================
--- kernel/include/IMP/restraints/SConscript (revision 338)
+++ kernel/include/IMP/restraints/SConscript (working copy)
@@ -5,7 +5,7 @@
'SphericalRestraint.h', 'DistanceRestraint.h', 'AngleRestraint.h',
'DihedralRestraint.h', 'RestraintSet.h', 'ExclusionVolumeRestraint.h',
'TorusRestraint.h', 'PairConnectivityRestraint.h',
- 'NonbondedRestraint.h']
+ 'NonbondedRestraint.h', 'BondDecoratorRestraint.h']
# Install the include files:
includedir = os.path.join(env['includedir'], 'IMP', 'restraints')
Index: kernel/include/IMP/score_states/SConscript
===================================================================
--- kernel/include/IMP/score_states/SConscript (revision 338)
+++ kernel/include/IMP/score_states/SConscript (working copy)
@@ -1,9 +1,12 @@
import os.path
Import('env')
-files = ['BondedListScoreState.h', 'NonbondedListScoreState.h']
+files = ['BondedListScoreState.h', 'NonbondedListScoreState.h',
+ 'BipartiteNonbondedListScoreState.h']
# Install the include files:
includedir = os.path.join(env['includedir'], 'IMP', 'score_states')
inst = env.Install(includedir, files)
env.Alias('install', inst)
+
+SConscript('bonded_lists/SConscript')
Index: kernel/include/IMP/score_states/bonded_lists/BondDecoratorListScoreState.h
===================================================================
--- kernel/include/IMP/score_states/bonded_lists/BondDecoratorListScoreState.h (revision 0)
+++ kernel/include/IMP/score_states/bonded_lists/BondDecoratorListScoreState.h (revision 0)
@@ -0,0 +1,57 @@
+/**
+ * \file BondedListScoreState.h
+ * \brief Allow iteration through pairs of a set of atoms.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+
+#ifndef __IMP_BONDEDDECORLISTSCORESTATE_H
+#define __IMP_BONDEDDECORLISTSCORESTATE_H
+
+#include "../BondedListScoreState.h"
+#include "../../decorators/bond_decorators.h"
+#include <vector>
+
+namespace IMP
+{
+ class BondDecoratorListScoreState;
+ typedef Index<BondDecoratorListScoreState> BondDecoratorListIndex;
+
+ //! Keep track of particles that are connected by BondDecorator bonds.
+ /**
+ We also may want to add lazy rescanning of bonds rather than doing
+ it every update call and a faster lookup of bonds.
+ */
+ class IMPDLLEXPORT BondDecoratorListScoreState: public BondedListScoreState {
+ std::vector<BondDecorator> bonds_;
+ Particles ps_;
+ public:
+ //! Find bonds amongst the following points.
+ /**
+ \param [in] ps The set of particles to use.
+ */
+ BondDecoratorListScoreState(const Particles &ps);
+ virtual ~BondDecoratorListScoreState(){}
+ //IMP_SCORE_STATE("0.5", "Daniel Russel");
+
+ virtual void set_particles(const Particles &ps);
+
+ virtual bool are_bonded(Particle *a, Particle *b) const;
+
+ virtual void update();
+
+ //! This iterates through the pairs of bonded particles
+ /**
+ \precondition update() must be called first for this to be valid.
+ */
+ typedef std::vector<BondDecorator>::const_iterator BondIterator;
+ BondIterator bonds_begin() const {
+ return bonds_.begin();
+ }
+ BondIterator bonds_end() const {
+ return bonds_.end();
+ }
+ };
+
+}
+#endif
Index: kernel/include/IMP/score_states/bonded_lists/SConscript
===================================================================
--- kernel/include/IMP/score_states/bonded_lists/SConscript (revision 0)
+++ kernel/include/IMP/score_states/bonded_lists/SConscript (revision 0)
@@ -0,0 +1,9 @@
+import os.path
+Import('env')
+
+files = ['BondDecoratorListScoreState.h']
+
+# Install the include files:
+includedir = os.path.join(env['includedir'], 'IMP', 'score_states', 'bonded_lists')
+inst = env.Install(includedir, files)
+env.Alias('install', inst)
Index: kernel/pyext/IMP.i
===================================================================
--- kernel/pyext/IMP.i (revision 338)
+++ kernel/pyext/IMP.i (working copy)
@@ -28,6 +28,9 @@
%pythonprepend RestraintSet::add_restraint %{
args[1].thisown=0
%}
+ %pythonprepend NonbondedListScoreState::add_bonded_list %{
+ args[1].thisown=0
+ %}
%pythonprepend DistanceRestraint::DistanceRestraint %{
args[2].thisown=0
%}
@@ -46,6 +49,9 @@
%pythonprepend NonbondedRestraint::NonbondedRestraint %{
args[1].thisown=0
%}
+ %pythonprepend BondDecoratorRestraint::BondDecoratorRestraint %{
+ args[1].thisown=0
+ %}
%pythonprepend DistancePairScore::DistancePairScore %{
args[1].thisown=0
%}
@@ -108,10 +114,14 @@
%include "IMP/restraints/PairConnectivityRestraint.h"
%include "IMP/restraints/ExclusionVolumeRestraint.h"
%include "IMP/restraints/NonbondedRestraint.h"
+%include "IMP/restraints/BondDecoratorRestraint.h"
%include "IMP/score_states/BondedListScoreState.h"
%include "IMP/score_states/NonbondedListScoreState.h"
+%include "IMP/score_states/BipartiteNonbondedListScoreState.h"
+%include "IMP/score_states/bonded_lists/BondDecoratorListScoreState.h"
%include "IMP/RigidBody.h"
+
namespace IMP {
%template(IntIndex) Index<Int>;
%template(FloatIndex) Index<Float>;
@@ -120,6 +130,7 @@
%template(RestraintIndex) Index<RestraintTag>;
%template(ScoreStateIndex) Index<ScoreStateTag>;
%template(OptimizerStateIndex) Index<OptimizerStateTag>;
+ %template(BondeListIndex) Index<BondedListScoreState>;
%template(FloatKey) Key<Float>;
%template(IntKey) Key<Int>;
%template(StringKey) Key<String>;
Index: kernel/src/SConscript
===================================================================
--- kernel/src/SConscript (revision 338)
+++ kernel/src/SConscript (working copy)
@@ -9,6 +9,7 @@
optimizers_files = SConscript('optimizers/SConscript')
decorators_files = SConscript('decorators/SConscript')
unary_functions_files = SConscript('unary_functions/SConscript')
+score_states_files = SConscript('score_states/SConscript')
pair_scores_files = SConscript('pair_scores/SConscript')
score_states_files = SConscript('score_states/SConscript')
Index: kernel/src/decorators/bond_decorators.cpp
===================================================================
--- kernel/src/decorators/bond_decorators.cpp (revision 338)
+++ kernel/src/decorators/bond_decorators.cpp (working copy)
@@ -19,6 +19,7 @@
FloatKey bond_length_key_;
IntKey bond_type_key_;
IntKey bond_order_key_;
+FloatKey bond_stiffness_key_;
} // namespace internal
@@ -54,6 +55,8 @@
internal::bond_graph_data_= internal::GraphData("bond");
internal::bond_type_key_= IntKey("bond type");
internal::bond_order_key_=IntKey("bond order");
+ internal::bond_length_key_=FloatKey("bond length");
+ internal::bond_stiffness_key_=FloatKey("bond stiffness");
internal::bond_keys_initialized_=true;
}
}
Index: kernel/src/restraints/SConscript
===================================================================
--- kernel/src/restraints/SConscript (revision 338)
+++ kernel/src/restraints/SConscript (working copy)
@@ -5,7 +5,7 @@
'SphericalRestraint.cpp', 'RestraintSet.cpp',
'DistanceRestraint.cpp', 'AngleRestraint.cpp', 'DihedralRestraint.cpp',
'TorusRestraint.cpp', 'ExclusionVolumeRestraint.cpp',
- 'NonbondedRestraint.cpp']
+ 'NonbondedRestraint.cpp', 'BondDecoratorRestraint.cpp']
files = [File(x) for x in files]
Return('files')
Index: kernel/src/score_states/SConscript
===================================================================
--- kernel/src/score_states/SConscript (revision 338)
+++ kernel/src/score_states/SConscript (working copy)
@@ -1,6 +1,9 @@
Import('env')
-files = ['NonbondedListScoreState.cpp']
+bd_files= SConscript('bonded_lists/SConscript')
+files = ['NonbondedListScoreState.cpp',
+ 'BipartiteNonbondedListScoreState.cpp'] +bd_files
+
files = [File(x) for x in files]
Return('files')
Index: kernel/test/states/test_nonbonded_list.py
===================================================================
--- kernel/test/states/test_nonbonded_list.py (revision 338)
+++ kernel/test/states/test_nonbonded_list.py (working copy)
@@ -13,10 +13,17 @@
def show(self, t):
print "One Pair"
+class OneScore(IMP.UnaryFunction):
+ def __init__(self):
+ IMP.UnaryFunction.__init__(self)
+ def __call__(self, *args):
+ return 100
+ def show(self, *args):
+ print "One score"
class TestNBL(IMP.test.TestCase):
def setUp(self):
- IMP.set_log_level(IMP.TERSE)
+ IMP.set_log_level(IMP.VERBOSE)
def test_it(self):
"""Test the nonbonded list and restraint which uses it"""
@@ -28,14 +35,66 @@
d.set_x(0)
d.set_y(1)
d.set_z(1)
- s= IMP.NonbondedListScoreState(m.get_particles(), 100)
+ s= IMP.NonbondedListScoreState(m.get_particles())
m.add_score_state(s)
o= OnePair()
r= IMP.NonbondedRestraint(s, o)
m.add_restraint(r)
score= m.evaluate(False)
self.assertEqual(score, 45, "Wrong score")
+ def test_bl(self):
+ """Test the bonded list"""
+ m= IMP.Model()
+ bds=[]
+ for i in range(0,10):
+ p= IMP.Particle()
+ m.add_particle(p)
+ d=IMP.XYZDecorator.create(p)
+ d.set_x(0)
+ d.set_y(1)
+ d.set_z(1)
+ bds.append(IMP.BondedDecorator.create(p))
+ pts=IMP.Particles()
+ for p in m.get_particles():
+ pts.append(p)
+ for i in range(1,10):
+ IMP.custom_bond(bds[i-1], bds[i], 1, .1)
+ s= IMP.NonbondedListScoreState(pts)
+ b= IMP.BondDecoratorListScoreState(pts)
+ s.add_bonded_list(b)
+ m.add_score_state(s)
+ o= OnePair()
+ r= IMP.NonbondedRestraint(s, o)
+ os=OneScore()
+ print os(6)
+ br= IMP.BondDecoratorRestraint(b, os)
+ m.add_restraint(r)
+ m.add_restraint(br)
+ score= m.evaluate( False )
+ self.assertEqual(score, 900+45-9, "Wrong score")
+ def test_bnbl(self):
+ """Test the bipartite nonbonded list and restraint which uses it"""
+ m= IMP.Model()
+ ps0=IMP.Particles()
+ ps1=IMP.Particles()
+ for i in range(0,10):
+ p= IMP.Particle()
+ m.add_particle(p)
+ d=IMP.XYZDecorator.create(p)
+ d.set_x(0)
+ d.set_y(1)
+ d.set_z(1)
+ if (i < 5):
+ ps0.append(p)
+ else:
+ ps1.append(p)
+ s= IMP.BipartiteNonbondedListScoreState(ps0, ps1)
+ m.add_score_state(s)
+ o= OnePair()
+ r= IMP.NonbondedRestraint(s, o)
+ m.add_restraint(r)
+ score= m.evaluate(False)
+ self.assertEqual(score, 25, "Wrong score")
-
if __name__ == '__main__':
unittest.main()
Index: kernel/include/IMP/restraints/BondDecoratorRestraint.h
===================================================================
--- kernel/include/IMP/restraints/BondDecoratorRestraint.h (revision 0)
+++ kernel/include/IMP/restraints/BondDecoratorRestraint.h (revision 0)
@@ -0,0 +1,52 @@
+/**
+ * \file BondDecoratorRestraint.h
+ * \brief Apply a UnaryFunction to all bonded pairs.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_BOND_DECORATOR_RESTRAINT_H
+#define __IMP_BOND_DECORATOR_RESTRAINT_H
+
+#include "../IMP_config.h"
+#include "../Restraint.h"
+
+#include <iostream>
+
+namespace IMP
+{
+
+class BondDecoratorListScoreState;
+class UnaryFunction;
+
+//! Restrain all pairs of non-bonded particles
+/**
+ This restraint currently only works for bonds which have their
+ length set explicitly. Eventually we should add a table for standard
+ molecular bonds.
+
+ The bond stiffness is assumed to be 1 if it is not specified in
+ the bond. This can become a parameter eventually.
+ */
+class IMPDLLEXPORT BondDecoratorRestraint : public Restraint
+{
+public:
+ //! Create the bond restraint.
+ /** \param[in] bl The BondDecoratorListScoreState to use to get the list
+ of bonds.
+ \param[in] f The UnaryFunction to apply to the particles.
+ */
+ BondDecoratorRestraint(BondDecoratorListScoreState *nbl, UnaryFunction *f);
+ virtual ~BondDecoratorRestraint(){}
+
+ IMP_RESTRAINT("0.5", "Daniel Russel");
+
+protected:
+ BondDecoratorListScoreState *bl_;
+ std::auto_ptr<UnaryFunction> f_;
+};
+
+} // namespace IMP
+
+#endif /* __IMP_BOND_DECORATOR_RESTRAINT_H */
Index: kernel/src/score_states/bonded_lists/BondDecoratorListScoreState.cpp
===================================================================
--- kernel/src/score_states/bonded_lists/BondDecoratorListScoreState.cpp (revision 0)
+++ kernel/src/score_states/bonded_lists/BondDecoratorListScoreState.cpp (revision 0)
@@ -0,0 +1,47 @@
+/**
+ * \file BondDecoratorListScoreState.h
+ * \brief Allow iteration through pairs of a set of atoms.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+#include "IMP/score_states/bonded_lists/BondDecoratorListScoreState.h"
+
+namespace IMP
+{
+BondDecoratorListScoreState
+::BondDecoratorListScoreState(const Particles &ps): ps_(ps) {
+}
+
+void BondDecoratorListScoreState::update() {
+ bonds_.clear();
+ for (unsigned int i=0; i< ps_.size(); ++i) {
+ BondedDecorator di= BondedDecorator::cast(ps_[i]);
+ ParticleIndex pi= ps_[i]->get_index();
+ for (unsigned int j=0; j< di.get_number_of_bonds(); ++j) {
+ BondedDecorator dj= di.get_bonded(j);
+ if (di < dj) {
+ bonds_.push_back(di.get_bond(j));
+ }
+ }
+ }
+ IMP_LOG(VERBOSE, "Found " << bonds_.size() << " bonds"<< std::endl);
+}
+
+void BondDecoratorListScoreState::set_particles(const Particles &ps) {
+ ps_=ps;
+ bonds_.clear();
+}
+
+
+bool BondDecoratorListScoreState::are_bonded(Particle *a, Particle *b) const {
+ try {
+ BondedDecorator da= BondedDecorator::cast(a);
+ BondedDecorator db= BondedDecorator::cast(b);
+ return get_bond(da, db) != BondDecorator();
+ } catch (...) {
+ IMP_LOG(VERBOSE, "Exception thrown in are_bonded"<< std::endl);
+ }
+ return false;
+}
+
+}
Index: kernel/src/score_states/bonded_lists/SConscript
===================================================================
--- kernel/src/score_states/bonded_lists/SConscript (revision 0)
+++ kernel/src/score_states/bonded_lists/SConscript (revision 0)
@@ -0,0 +1,6 @@
+Import('env')
+
+files = ['BondDecoratorListScoreState.cpp']
+
+files = [File(x) for x in files]
+Return('files')
Index: kernel/src/decorators/bond_decorators.cpp
===================================================================
--- kernel/src/decorators/bond_decorators.cpp (revision 338)
+++ kernel/src/decorators/bond_decorators.cpp (working copy)
@@ -19,6 +19,7 @@
FloatKey bond_length_key_;
IntKey bond_type_key_;
IntKey bond_order_key_;
+FloatKey bond_stiffness_key_;
} // namespace internal
@@ -54,6 +55,8 @@
internal::bond_graph_data_= internal::GraphData("bond");
internal::bond_type_key_= IntKey("bond type");
internal::bond_order_key_=IntKey("bond order");
+ internal::bond_length_key_=FloatKey("bond length");
+ internal::bond_stiffness_key_=FloatKey("bond stiffness");
internal::bond_keys_initialized_=true;
}
}