Index: kernel/include/IMP/restraints/ConnectivityRestraint.h
===================================================================
--- kernel/include/IMP/restraints/ConnectivityRestraint.h (revision 441)
+++ kernel/include/IMP/restraints/ConnectivityRestraint.h (working copy)
@@ -15,7 +15,6 @@
#include "../IMP_config.h"
#include "../Restraint.h"
-#include "../ScoreFuncParams.h"
#include "../internal/kernel_version_info.h"
#include "DistanceRestraint.h"
Index: kernel/include/IMP.h
===================================================================
--- kernel/include/IMP.h (revision 441)
+++ kernel/include/IMP.h (working copy)
@@ -1,82 +1,89 @@
/**
- * \file IMP.h \brief IMP, an Integrative Modeling Platform.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
+* \\file IMP.h \\brief IMP, an Integrative Modeling Platform.
+*
+* Copyright 2007-8 Sali Lab. All rights reserved.
+*
+*/
#ifndef __IMP_H
#define __IMP_H
-
-#include "IMP/IMP_config.h"
-#include "IMP/log.h"
-#include "IMP/random.h"
-#include "IMP/base_types.h"
-#include "IMP/Particle.h"
-#include "IMP/Optimizer.h"
-#include "IMP/Restraint.h"
-#include "IMP/exception.h"
-#include "IMP/UnaryFunction.h"
-#include "IMP/unary_functions/Harmonic.h"
-#include "IMP/unary_functions/HarmonicLowerBound.h"
-#include "IMP/unary_functions/HarmonicUpperBound.h"
-#include "IMP/unary_functions/OpenCubicSpline.h"
-#include "IMP/unary_functions/ClosedCubicSpline.h"
-#include "IMP/unary_functions/Cosine.h"
-#include "IMP/unary_functions/Linear.h"
-#include "IMP/ScoreFuncParams.h"
-#include "IMP/Model.h"
-#include "IMP/PairScore.h"
-#include "IMP/SingletonScore.h"
-#include "IMP/TripletScore.h"
-#include "IMP/Vector3D.h"
-#include "IMP/VersionInfo.h"
-#include "IMP/decorators/HierarchyDecorator.h"
-#include "IMP/decorators/MolecularHierarchyDecorator.h"
-#include "IMP/decorators/NameDecorator.h"
-#include "IMP/decorators/AtomDecorator.h"
-#include "IMP/decorators/ResidueDecorator.h"
-#include "IMP/decorators/XYZDecorator.h"
-#include "IMP/decorators/bond_decorators.h"
-#include "IMP/optimizers/SteepestDescent.h"
-#include "IMP/optimizers/ConjugateGradients.h"
-#include "IMP/optimizers/MolecularDynamics.h"
-#include "IMP/optimizers/MonteCarlo.h"
-#include "IMP/optimizers/Mover.h"
-#include "IMP/optimizers/MoverBase.h"
-#include "IMP/optimizers/movers/BallMover.h"
-#include "IMP/optimizers/movers/NormalMover.h"
-#include "IMP/optimizers/states/VRMLLogOptimizerState.h"
-#include "IMP/optimizers/states/CMMLogOptimizerState.h"
-#include "IMP/optimizers/states/VelocityScalingOptimizerState.h"
-#include "IMP/pair_scores/DistancePairScore.h"
-#include "IMP/pair_scores/SphereDistancePairScore.h"
-#include "IMP/singleton_scores/DistanceToSingletonScore.h"
-#include "IMP/triplet_scores/AngleTripletScore.h"
-#include "IMP/restraints/RestraintSet.h"
-#include "IMP/restraints/DistanceRestraint.h"
-#include "IMP/restraints/AngleRestraint.h"
-#include "IMP/restraints/DihedralRestraint.h"
-#include "IMP/restraints/TorusRestraint.h"
-#include "IMP/restraints/ProximityRestraint.h"
-#include "IMP/restraints/ConnectivityRestraint.h"
-#include "IMP/restraints/PairConnectivityRestraint.h"
-#include "IMP/restraints/ExclusionVolumeRestraint.h"
-#include "IMP/restraints/NonbondedRestraint.h"
-#include "IMP/restraints/BondDecoratorRestraint.h"
-#include "IMP/restraints/SingletonListRestraint.h"
-#include "IMP/restraints/PairListRestraint.h"
-#include "IMP/restraints/TripletChainRestraint.h"
-#include "IMP/score_states/BipartiteNonbondedListScoreState.h"
-#include "IMP/score_states/MaxChangeScoreState.h"
-#include "IMP/score_states/NonbondedListScoreState.h"
-#include "IMP/score_states/BondedListScoreState.h"
-#include "IMP/score_states/BondDecoratorListScoreState.h"
-#include "IMP/score_states/AllNonbondedListScoreState.h"
-#include "IMP/score_states/AllSphereNonbondedListScoreState.h"
-
-/**
- \namespace IMP The IMP namespace.
- */
-
+#include <IMP/DecoratorBase.h>
+#include <IMP/DerivativeAccumulator.h>
+#include <IMP/IMP_config.h>
+#include <IMP/Index.h>
+#include <IMP/Key.h>
+#include <IMP/Model.h>
+#include <IMP/Optimizer.h>
+#include <IMP/OptimizerState.h>
+#include <IMP/PairScore.h>
+#include <IMP/Particle.h>
+#include <IMP/Restraint.h>
+#include <IMP/ScoreState.h>
+#include <IMP/SingletonScore.h>
+#include <IMP/TripletScore.h>
+#include <IMP/UnaryFunction.h>
+#include <IMP/Vector3D.h>
+#include <IMP/VersionInfo.h>
+#include <IMP/base_types.h>
+#include <IMP/exception.h>
+#include <IMP/log.h>
+#include <IMP/macros.h>
+#include <IMP/random.h>
+#include <IMP/utility.h>
+#include <IMP/decorators/AtomDecorator.h>
+#include <IMP/decorators/HierarchyDecorator.h>
+#include <IMP/decorators/MolecularHierarchyDecorator.h>
+#include <IMP/decorators/NameDecorator.h>
+#include <IMP/decorators/ResidueDecorator.h>
+#include <IMP/decorators/XYZDecorator.h>
+#include <IMP/decorators/bond_decorators.h>
+#include <IMP/decorators/macros.h>
+#include <IMP/decorators/utility.h>
+#include <IMP/internal/AttributeTable.h>
+#include <IMP/internal/Grid3D.h>
+#include <IMP/internal/Object.h>
+#include <IMP/internal/ObjectContainer.h>
+#include <IMP/internal/ObjectPointer.h>
+#include <IMP/internal/ParticleGrid.h>
+#include <IMP/internal/Vector.h>
+#include <IMP/internal/graph_base.h>
+#include <IMP/internal/kernel_version_info.h>
+#include <IMP/optimizers/ConjugateGradients.h>
+#include <IMP/optimizers/MolecularDynamics.h>
+#include <IMP/optimizers/MonteCarlo.h>
+#include <IMP/optimizers/Mover.h>
+#include <IMP/optimizers/MoverBase.h>
+#include <IMP/optimizers/SteepestDescent.h>
+#include <IMP/pair_scores/DistancePairScore.h>
+#include <IMP/pair_scores/SphereDistancePairScore.h>
+#include <IMP/restraints/AngleRestraint.h>
+#include <IMP/restraints/BondDecoratorRestraint.h>
+#include <IMP/restraints/ConnectivityRestraint.h>
+#include <IMP/restraints/DihedralRestraint.h>
+#include <IMP/restraints/DistanceRestraint.h>
+#include <IMP/restraints/NonbondedRestraint.h>
+#include <IMP/restraints/PairListRestraint.h>
+#include <IMP/restraints/RestraintSet.h>
+#include <IMP/restraints/SingletonListRestraint.h>
+#include <IMP/restraints/TripletChainRestraint.h>
+#include <IMP/score_states/AllNonbondedListScoreState.h>
+#include <IMP/score_states/AllSphereNonbondedListScoreState.h>
+#include <IMP/score_states/BipartiteNonbondedListScoreState.h>
+#include <IMP/score_states/BondDecoratorListScoreState.h>
+#include <IMP/score_states/BondedListScoreState.h>
+#include <IMP/score_states/MaxChangeScoreState.h>
+#include <IMP/score_states/NonbondedListScoreState.h>
+#include <IMP/singleton_scores/DistanceToSingletonScore.h>
+#include <IMP/triplet_scores/AngleTripletScore.h>
+#include <IMP/unary_functions/ClosedCubicSpline.h>
+#include <IMP/unary_functions/Cosine.h>
+#include <IMP/unary_functions/Harmonic.h>
+#include <IMP/unary_functions/HarmonicLowerBound.h>
+#include <IMP/unary_functions/HarmonicUpperBound.h>
+#include <IMP/unary_functions/Linear.h>
+#include <IMP/unary_functions/OpenCubicSpline.h>
+#include <IMP/optimizers/movers/BallMover.h>
+#include <IMP/optimizers/movers/NormalMover.h>
+#include <IMP/optimizers/states/CMMLogOptimizerState.h>
+#include <IMP/optimizers/states/VRMLLogOptimizerState.h>
+#include <IMP/optimizers/states/VelocityScalingOptimizerState.h>
#endif /* __IMP_H */
Index: kernel/pyext/IMP.i
===================================================================
--- kernel/pyext/IMP.i (revision 441)
+++ kernel/pyext/IMP.i (working copy)
@@ -100,7 +100,6 @@
%include "IMP/unary_functions/ClosedCubicSpline.h"
%include "IMP/unary_functions/Cosine.h"
%include "IMP/unary_functions/Linear.h"
-%include "IMP/ScoreFuncParams.h"
%include "IMP/DerivativeAccumulator.h"
%include "IMP/Restraint.h"
%include "IMP/ScoreState.h"
@@ -140,11 +139,7 @@
%include "IMP/restraints/AngleRestraint.h"
%include "IMP/restraints/TripletChainRestraint.h"
%include "IMP/restraints/DihedralRestraint.h"
-%include "IMP/restraints/TorusRestraint.h"
-%include "IMP/restraints/ProximityRestraint.h"
%include "IMP/restraints/ConnectivityRestraint.h"
-%include "IMP/restraints/PairConnectivityRestraint.h"
-%include "IMP/restraints/ExclusionVolumeRestraint.h"
%include "IMP/restraints/NonbondedRestraint.h"
%include "IMP/restraints/BondDecoratorRestraint.h"
%include "IMP/restraints/SingletonListRestraint.h"
Index: kernel/test/pair_connectivity/test_pair_connectivity.py
===================================================================
--- kernel/test/pair_connectivity/test_pair_connectivity.py (revision 441)
+++ kernel/test/pair_connectivity/test_pair_connectivity.py (working copy)
@@ -1,181 +0,0 @@
-import unittest
-import os
-import IMP
-import IMP.test
-import IMP.utils
-
-class PairConnectivityRestraintTests(IMP.test.TestCase):
- """Test pair connectivity restraints."""
-
- def setUp(self):
- """Build test model and optimizer"""
- self.imp_model = IMP.Model()
- self.particles = []
- self.restraint_sets = []
- self.rsrs = []
-
- for p in range(12):
- self.particles.append(IMP.utils.XYZParticle(self.imp_model,
- 0., 0., 0.))
- p1 = self.particles[0]
- radkey= IMP.FloatKey("radius")
- pkey=IMP.IntKey("protein")
- idkey=IMP.IntKey("id")
-
- p1.add_attribute(radkey, 1.0, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 1)
-
- p1 = self.particles[1]
- p1.add_attribute(radkey, 1.0, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 2)
-
- p1 = self.particles[2]
- p1.add_attribute(radkey, 1.0, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 3)
-
- p1 = self.particles[3]
- p1.add_attribute(radkey, 1.5, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 4)
-
- p1 = self.particles[4]
- p1.add_attribute(radkey, 1.5, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 5)
-
- p1 = self.particles[5]
- p1.add_attribute(radkey, 1.5, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 6)
-
- p1 = self.particles[6]
- p1.add_attribute(radkey, 1.5, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 7)
-
- p1 = self.particles[7]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 8)
-
- p1 = self.particles[8]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 9)
-
- p1 = self.particles[9]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 10)
-
- p1 = self.particles[10]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 11)
-
- p1 = self.particles[11]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 12)
-
- self.opt = IMP.ConjugateGradients()
- self.opt.set_model(self.imp_model)
- self.opt.set_threshold(1e-4)
-
- def _run_test_pair_connectivity(self, use_python):
- """Test pair connectivity restraint.
- All particles in a single protein should be connected, and all
- proteins should be connected, either directly or indirectly
- through other proteins """
- rs = IMP.RestraintSet("connect")
- self.restraint_sets.append(rs)
- self.imp_model.add_restraint(rs)
-
- # add connectivity restraints
-
- particle_indexes1 = IMP.Ints()
- particle_indexes2 = IMP.Ints()
- rsrs = []
- # connect 2 proteins together by two beads
- particle_indexes1.clear()
- for i in range(0, 5):
- particle_indexes1.push_back(i)
- particle_indexes2.clear()
- for i in range(5, 12):
- particle_indexes2.push_back(i)
- num_connects = 3
-
- if use_python:
- # set up exclusion volumes using a Python loop:
- IMP.utils.set_up_exclusion_volumes(self.imp_model, self.particles,
- IMP.FloatKey("radius"), rsrs)
- else:
- # use the C++ exclusion volume restraint:
- score_func_params = IMP.BasicScoreFuncParams("harmonic_lower_bound",
- 0.0, 0.1)
- rsrs.append(IMP.ExclusionVolumeRestraint(self.imp_model,
- particle_indexes1,
- particle_indexes2,
- IMP.FloatKey("radius"),
- score_func_params))
-
- # it should work whether this is True or False
- # However, if it is False, the close pairs should all be between
- # distinct particles
- particle_reuse = False
- score_func_params = IMP.BasicScoreFuncParams("harmonic_upper_bound",
- 0.0, 0.1)
- rsrs.append(IMP.PairConnectivityRestraint(self.imp_model,
- particle_indexes1,
- particle_indexes2,
- IMP.FloatKey("radius"),
- score_func_params,
- num_connects, particle_reuse))
-
- # add restraints
- for i in range(len(rsrs)):
- rs.add_restraint(rsrs[i])
-
- self.randomize_particles(self.particles, 50.0)
- self.opt.optimize(55)
-
- # min distances
- min_dist = []
- for i in range(num_connects):
- min_dist.append(10000000)
-
- for (i, pi) in enumerate(self.particles[0:5]):
- icoord = (pi.x(), pi.y(), pi.z())
- irad = pi.get_value(IMP.FloatKey("radius"))
- for (j, pj) in enumerate(self.particles[5:12]):
- jcoord = (pj.x(), pj.y(), pj.z())
- jrad = pj.get_value(IMP.FloatKey("radius"))
- d = self.get_distance(icoord, jcoord) - irad - jrad
- found = False
- for k in range(num_connects):
- if not found:
- if d < min_dist[k]:
- found = True
-
- if found:
- d1 = min_dist[k]
- min_dist[k] = d
- d = d1
-
- for i in range(num_connects):
- self.assert_(min_dist[i] < 0.05,
- "min distance for any pair condition")
-
- def test_pair_connectivity_python(self):
- """Test pair connectivity restraint using Python exclusion volumes"""
- self._run_test_pair_connectivity(True)
-
- def test_pair_connectivity_c(self):
- """Test pair connectivity restraint using C++ exclusion volumes"""
- self._run_test_pair_connectivity(False)
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/test/pair_connectivity/test_pair_connectivity.py
===================================================================
--- kernel/test/pair_connectivity/test_pair_connectivity.py (revision 441)
+++ kernel/test/pair_connectivity/test_pair_connectivity.py (working copy)
@@ -1,181 +0,0 @@
-import unittest
-import os
-import IMP
-import IMP.test
-import IMP.utils
-
-class PairConnectivityRestraintTests(IMP.test.TestCase):
- """Test pair connectivity restraints."""
-
- def setUp(self):
- """Build test model and optimizer"""
- self.imp_model = IMP.Model()
- self.particles = []
- self.restraint_sets = []
- self.rsrs = []
-
- for p in range(12):
- self.particles.append(IMP.utils.XYZParticle(self.imp_model,
- 0., 0., 0.))
- p1 = self.particles[0]
- radkey= IMP.FloatKey("radius")
- pkey=IMP.IntKey("protein")
- idkey=IMP.IntKey("id")
-
- p1.add_attribute(radkey, 1.0, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 1)
-
- p1 = self.particles[1]
- p1.add_attribute(radkey, 1.0, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 2)
-
- p1 = self.particles[2]
- p1.add_attribute(radkey, 1.0, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 3)
-
- p1 = self.particles[3]
- p1.add_attribute(radkey, 1.5, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 4)
-
- p1 = self.particles[4]
- p1.add_attribute(radkey, 1.5, False)
- p1.add_attribute(pkey, 1)
- p1.add_attribute(idkey, 5)
-
- p1 = self.particles[5]
- p1.add_attribute(radkey, 1.5, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 6)
-
- p1 = self.particles[6]
- p1.add_attribute(radkey, 1.5, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 7)
-
- p1 = self.particles[7]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 8)
-
- p1 = self.particles[8]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 9)
-
- p1 = self.particles[9]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 10)
-
- p1 = self.particles[10]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 11)
-
- p1 = self.particles[11]
- p1.add_attribute(radkey, 2.0, False)
- p1.add_attribute(pkey, 2)
- p1.add_attribute(idkey, 12)
-
- self.opt = IMP.ConjugateGradients()
- self.opt.set_model(self.imp_model)
- self.opt.set_threshold(1e-4)
-
- def _run_test_pair_connectivity(self, use_python):
- """Test pair connectivity restraint.
- All particles in a single protein should be connected, and all
- proteins should be connected, either directly or indirectly
- through other proteins """
- rs = IMP.RestraintSet("connect")
- self.restraint_sets.append(rs)
- self.imp_model.add_restraint(rs)
-
- # add connectivity restraints
-
- particle_indexes1 = IMP.Ints()
- particle_indexes2 = IMP.Ints()
- rsrs = []
- # connect 2 proteins together by two beads
- particle_indexes1.clear()
- for i in range(0, 5):
- particle_indexes1.push_back(i)
- particle_indexes2.clear()
- for i in range(5, 12):
- particle_indexes2.push_back(i)
- num_connects = 3
-
- if use_python:
- # set up exclusion volumes using a Python loop:
- IMP.utils.set_up_exclusion_volumes(self.imp_model, self.particles,
- IMP.FloatKey("radius"), rsrs)
- else:
- # use the C++ exclusion volume restraint:
- score_func_params = IMP.BasicScoreFuncParams("harmonic_lower_bound",
- 0.0, 0.1)
- rsrs.append(IMP.ExclusionVolumeRestraint(self.imp_model,
- particle_indexes1,
- particle_indexes2,
- IMP.FloatKey("radius"),
- score_func_params))
-
- # it should work whether this is True or False
- # However, if it is False, the close pairs should all be between
- # distinct particles
- particle_reuse = False
- score_func_params = IMP.BasicScoreFuncParams("harmonic_upper_bound",
- 0.0, 0.1)
- rsrs.append(IMP.PairConnectivityRestraint(self.imp_model,
- particle_indexes1,
- particle_indexes2,
- IMP.FloatKey("radius"),
- score_func_params,
- num_connects, particle_reuse))
-
- # add restraints
- for i in range(len(rsrs)):
- rs.add_restraint(rsrs[i])
-
- self.randomize_particles(self.particles, 50.0)
- self.opt.optimize(55)
-
- # min distances
- min_dist = []
- for i in range(num_connects):
- min_dist.append(10000000)
-
- for (i, pi) in enumerate(self.particles[0:5]):
- icoord = (pi.x(), pi.y(), pi.z())
- irad = pi.get_value(IMP.FloatKey("radius"))
- for (j, pj) in enumerate(self.particles[5:12]):
- jcoord = (pj.x(), pj.y(), pj.z())
- jrad = pj.get_value(IMP.FloatKey("radius"))
- d = self.get_distance(icoord, jcoord) - irad - jrad
- found = False
- for k in range(num_connects):
- if not found:
- if d < min_dist[k]:
- found = True
-
- if found:
- d1 = min_dist[k]
- min_dist[k] = d
- d = d1
-
- for i in range(num_connects):
- self.assert_(min_dist[i] < 0.05,
- "min distance for any pair condition")
-
- def test_pair_connectivity_python(self):
- """Test pair connectivity restraint using Python exclusion volumes"""
- self._run_test_pair_connectivity(True)
-
- def test_pair_connectivity_c(self):
- """Test pair connectivity restraint using C++ exclusion volumes"""
- self._run_test_pair_connectivity(False)
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/test/xml/model.xml
===================================================================
--- kernel/test/xml/model.xml (revision 441)
+++ kernel/test/xml/model.xml (working copy)
@@ -1,200 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<imp xmlns='http://www.salilab.org/xml/imp' xmlns:imp='http://www.salilab.org/xml/imp'>
- <particles>
- <particle id="0">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>2.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>1</value>
- </int>
- </particle>
-
- <particle id="1">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>2.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>1</value>
- </int>
- </particle>
-
- <particle id="2">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>2.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>1</value>
- </int>
- </particle>
-
- <particle id="3">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.5</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>2</value>
- </int>
- </particle>
-
- <particle id="4">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.5</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>2</value>
- </int>
- </particle>
-
- <particle id="5">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.5</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>2</value>
- </int>
- </particle>
-
- <particle id="6">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.5</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>2</value>
- </int>
- </particle>
-
- <particle id="7">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
-
- <particle id="8">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
-
- <particle id="9">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
-
- <particle id="10">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
-
- <particle id="11">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
- </particles>
-
- <restraint_set name='exclusion_volumes'>
- <distance_restraint>
- <particle_pairs>
- <all_pairs>0 1 2 3 4 5 6 7 8 9 10 11</all_pairs>
- </particle_pairs>
- <score_func>harmonic_lower_bound</score_func>
- <distance_attribute>radius</distance_attribute>
- <sd>0.1</sd>
- </distance_restraint>
- </restraint_set>
-
- <restraint_set name='torus'>
- <torus_restraint>
- <particle_list>0 1 2 3 4 5 6 7 8 9 10 11</particle_list>
- <score_func>harmonic_upper_bound</score_func>
- <main_radius>50</main_radius>
- <tube_radius>8</tube_radius>
- <sd>0.1</sd>
- </torus_restraint>
- </restraint_set>
-
- <restraint_set name='connections'>
- <distance_restraint>
- <particle_pairs>
- <pair>0 1</pair>
- <pair>1 2</pair>
- <pair>3 4</pair>
- <pair>4 5</pair>
- <pair>5 6</pair>
- <pair>7 8</pair>
- <pair>8 9</pair>
- <pair>9 10</pair>
- <pair>10 11</pair>
- </particle_pairs>
- <score_func>harmonic_upper_bound</score_func>
- <distance_attribute>radius</distance_attribute>
- <sd>0.1</sd>
- </distance_restraint>
- </restraint_set>
-</imp>
Index: kernel/test/xml/invalid.xml
===================================================================
--- kernel/test/xml/invalid.xml (revision 441)
+++ kernel/test/xml/invalid.xml (working copy)
@@ -1,19 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<imp xmlns='http://www.salilab.org/xml/imp' xmlns:imp='http://www.salilab.org/xml/imp'>
- <particles>
- <particle id="0">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- </particle>
- </particles>
-
- <restraint_set name='torus'>
- <torus_restraint>
- <particle_list>0</particle_list>
- <main_radius>50</main_radius>
- <tube_radius>8</tube_radius>
- <sd>0.1</sd>
- </torus_restraint>
- </restraint_set>
-</imp>
Index: kernel/test/xml/test_xml.py
===================================================================
--- kernel/test/xml/test_xml.py (revision 441)
+++ kernel/test/xml/test_xml.py (working copy)
@@ -1,53 +0,0 @@
-import unittest
-import os
-import IMP.test, IMP
-import IMP.xml_loader
-
-class XMLTests(IMP.test.TestCase):
- """Test XML file loading"""
-
- def setUp(self):
- """Set up IMP model"""
- self.imp_model = IMP.Model()
-
- def test_invalid_xml(self):
- """Check reading of invalid XML files"""
- self.assertRaises(IMP.xml_loader.MalformedError,
- IMP.xml_loader.load_imp_model, self.imp_model,
- "xml/invalid.xml")
-
- def test_xml(self):
- """Check reading of XML files"""
- self.doc = IMP.xml_loader.load_imp_model(self.imp_model,
- "xml/model.xml")
-
- # test particles
- num_particles = 0
- for p in self.imp_model.get_particles():
- radius = p.get_value(IMP.FloatKey("radius"))
- protein = p.get_value(IMP.IntKey("protein"))
- num_particles = num_particles + 1
- if protein == 1:
- self.assert_(radius == 2.0, "protein1 beads should have radius 2.0")
- elif protein == 2:
- self.assert_(radius == 1.5, "protein2 beads should have radius 1.5")
- elif protein == 3:
- self.assert_(radius == 1.0, "protein3 beads should have radius 1.0")
-
- self.assert_(num_particles == 12, "number of particles is incorrect")
-
- # test restraint sets
- #restraint_sets = self.imp_model.get_restraints
- self.assertEqual(self.imp_model.number_of_restraints(), 3,
- "xml file contains three restraint sets")
-
- # test restraints
- score = self.imp_model.get_restraint(IMP.RestraintIndex(0)).evaluate(None)
- self.assert_((score > 16000) and (score < 17000), "expecting a score of 16198.2236328 not : " + str(score))
- score = self.imp_model.get_restraint(IMP.RestraintIndex(1)).evaluate(None)
- self.assert_((score > 624000) and (score < 625000), "expecting a score of 624531.0625 not : " + str(score))
- score = self.imp_model.get_restraint(IMP.RestraintIndex(2)).evaluate(None)
- self.assert_((score > -100) and (score < 100), "expecting a score of 0.0 not : " + str(score))
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/test/xml/run_xml.py
===================================================================
--- kernel/test/xml/run_xml.py (revision 441)
+++ kernel/test/xml/run_xml.py (working copy)
@@ -1,39 +0,0 @@
-import modeller
-import modeller.optimizers
-import IMP
-import IMP.modeller_intf
-import IMP.utils
-import IMP.xml_loader
-
-model = IMP.Model()
-
-# load document from an XML file
-doc = IMP.xml_loader.load_imp_model(model, "test.xml")
-
-# intialize Modeller
-modeller.log.level(0,0,0,0,0)
-env = modeller.environ()
-env.io.atom_files_directory = '../data/'
-env.edat.dynamic_sphere = False
-env.libs.topology.read(file='$(LIB)/top_heav.lib')
-env.libs.parameters.read(file='$(LIB)/par.lib')
-
-
-# add IMP model and restraints as an energy term to Modeller model
-t = env.edat.energy_terms
-t.append(IMP.modeller_intf.IMPRestraints(model, model.particles))
-
-# get particles for Modeller
-mdl = IMP.modeller_intf.create_particles_from_imp(env, model)
-
-atmsel = modeller.selection(mdl)
-atoms = mdl.atoms
-atmsel.randomize_xyz(deviation=100.0)
-
-model.set_up_trajectory("trajectory.txt")
-opt = modeller.optimizers.conjugate_gradients()
-new_mdl = opt.optimize (atmsel, max_iterations=55, actions=None)
-print atmsel.energy()
-
-IMP.utils.show_distances(model.particles)
-mdl.write(file='out_test_xml.pdb', model_format='PDB')
Index: kernel/test/xml/model.xml
===================================================================
--- kernel/test/xml/model.xml (revision 441)
+++ kernel/test/xml/model.xml (working copy)
@@ -1,200 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<imp xmlns='http://www.salilab.org/xml/imp' xmlns:imp='http://www.salilab.org/xml/imp'>
- <particles>
- <particle id="0">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>2.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>1</value>
- </int>
- </particle>
-
- <particle id="1">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>2.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>1</value>
- </int>
- </particle>
-
- <particle id="2">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>2.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>1</value>
- </int>
- </particle>
-
- <particle id="3">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.5</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>2</value>
- </int>
- </particle>
-
- <particle id="4">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.5</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>2</value>
- </int>
- </particle>
-
- <particle id="5">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.5</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>2</value>
- </int>
- </particle>
-
- <particle id="6">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.5</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>2</value>
- </int>
- </particle>
-
- <particle id="7">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
-
- <particle id="8">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
-
- <particle id="9">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
-
- <particle id="10">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
-
- <particle id="11">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- <float name="radius">
- <value>1.0</value>
- <optimize>F</optimize>
- </float>
- <int name="protein">
- <value>3</value>
- </int>
- </particle>
- </particles>
-
- <restraint_set name='exclusion_volumes'>
- <distance_restraint>
- <particle_pairs>
- <all_pairs>0 1 2 3 4 5 6 7 8 9 10 11</all_pairs>
- </particle_pairs>
- <score_func>harmonic_lower_bound</score_func>
- <distance_attribute>radius</distance_attribute>
- <sd>0.1</sd>
- </distance_restraint>
- </restraint_set>
-
- <restraint_set name='torus'>
- <torus_restraint>
- <particle_list>0 1 2 3 4 5 6 7 8 9 10 11</particle_list>
- <score_func>harmonic_upper_bound</score_func>
- <main_radius>50</main_radius>
- <tube_radius>8</tube_radius>
- <sd>0.1</sd>
- </torus_restraint>
- </restraint_set>
-
- <restraint_set name='connections'>
- <distance_restraint>
- <particle_pairs>
- <pair>0 1</pair>
- <pair>1 2</pair>
- <pair>3 4</pair>
- <pair>4 5</pair>
- <pair>5 6</pair>
- <pair>7 8</pair>
- <pair>8 9</pair>
- <pair>9 10</pair>
- <pair>10 11</pair>
- </particle_pairs>
- <score_func>harmonic_upper_bound</score_func>
- <distance_attribute>radius</distance_attribute>
- <sd>0.1</sd>
- </distance_restraint>
- </restraint_set>
-</imp>
Index: kernel/test/xml/invalid.xml
===================================================================
--- kernel/test/xml/invalid.xml (revision 441)
+++ kernel/test/xml/invalid.xml (working copy)
@@ -1,19 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<imp xmlns='http://www.salilab.org/xml/imp' xmlns:imp='http://www.salilab.org/xml/imp'>
- <particles>
- <particle id="0">
- <float name="x"/>
- <float name="y"/>
- <float name="z"/>
- </particle>
- </particles>
-
- <restraint_set name='torus'>
- <torus_restraint>
- <particle_list>0</particle_list>
- <main_radius>50</main_radius>
- <tube_radius>8</tube_radius>
- <sd>0.1</sd>
- </torus_restraint>
- </restraint_set>
-</imp>
Index: kernel/test/xml/test_xml.py
===================================================================
--- kernel/test/xml/test_xml.py (revision 441)
+++ kernel/test/xml/test_xml.py (working copy)
@@ -1,53 +0,0 @@
-import unittest
-import os
-import IMP.test, IMP
-import IMP.xml_loader
-
-class XMLTests(IMP.test.TestCase):
- """Test XML file loading"""
-
- def setUp(self):
- """Set up IMP model"""
- self.imp_model = IMP.Model()
-
- def test_invalid_xml(self):
- """Check reading of invalid XML files"""
- self.assertRaises(IMP.xml_loader.MalformedError,
- IMP.xml_loader.load_imp_model, self.imp_model,
- "xml/invalid.xml")
-
- def test_xml(self):
- """Check reading of XML files"""
- self.doc = IMP.xml_loader.load_imp_model(self.imp_model,
- "xml/model.xml")
-
- # test particles
- num_particles = 0
- for p in self.imp_model.get_particles():
- radius = p.get_value(IMP.FloatKey("radius"))
- protein = p.get_value(IMP.IntKey("protein"))
- num_particles = num_particles + 1
- if protein == 1:
- self.assert_(radius == 2.0, "protein1 beads should have radius 2.0")
- elif protein == 2:
- self.assert_(radius == 1.5, "protein2 beads should have radius 1.5")
- elif protein == 3:
- self.assert_(radius == 1.0, "protein3 beads should have radius 1.0")
-
- self.assert_(num_particles == 12, "number of particles is incorrect")
-
- # test restraint sets
- #restraint_sets = self.imp_model.get_restraints
- self.assertEqual(self.imp_model.number_of_restraints(), 3,
- "xml file contains three restraint sets")
-
- # test restraints
- score = self.imp_model.get_restraint(IMP.RestraintIndex(0)).evaluate(None)
- self.assert_((score > 16000) and (score < 17000), "expecting a score of 16198.2236328 not : " + str(score))
- score = self.imp_model.get_restraint(IMP.RestraintIndex(1)).evaluate(None)
- self.assert_((score > 624000) and (score < 625000), "expecting a score of 624531.0625 not : " + str(score))
- score = self.imp_model.get_restraint(IMP.RestraintIndex(2)).evaluate(None)
- self.assert_((score > -100) and (score < 100), "expecting a score of 0.0 not : " + str(score))
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/test/xml/run_xml.py
===================================================================
--- kernel/test/xml/run_xml.py (revision 441)
+++ kernel/test/xml/run_xml.py (working copy)
@@ -1,39 +0,0 @@
-import modeller
-import modeller.optimizers
-import IMP
-import IMP.modeller_intf
-import IMP.utils
-import IMP.xml_loader
-
-model = IMP.Model()
-
-# load document from an XML file
-doc = IMP.xml_loader.load_imp_model(model, "test.xml")
-
-# intialize Modeller
-modeller.log.level(0,0,0,0,0)
-env = modeller.environ()
-env.io.atom_files_directory = '../data/'
-env.edat.dynamic_sphere = False
-env.libs.topology.read(file='$(LIB)/top_heav.lib')
-env.libs.parameters.read(file='$(LIB)/par.lib')
-
-
-# add IMP model and restraints as an energy term to Modeller model
-t = env.edat.energy_terms
-t.append(IMP.modeller_intf.IMPRestraints(model, model.particles))
-
-# get particles for Modeller
-mdl = IMP.modeller_intf.create_particles_from_imp(env, model)
-
-atmsel = modeller.selection(mdl)
-atoms = mdl.atoms
-atmsel.randomize_xyz(deviation=100.0)
-
-model.set_up_trajectory("trajectory.txt")
-opt = modeller.optimizers.conjugate_gradients()
-new_mdl = opt.optimize (atmsel, max_iterations=55, actions=None)
-print atmsel.energy()
-
-IMP.utils.show_distances(model.particles)
-mdl.write(file='out_test_xml.pdb', model_format='PDB')
Index: kernel/test/modeller/test_exclusion_volumes.py
===================================================================
--- kernel/test/modeller/test_exclusion_volumes.py (revision 441)
+++ kernel/test/modeller/test_exclusion_volumes.py (working copy)
@@ -1,239 +0,0 @@
-import modeller, unittest
-import modeller
-import modeller.optimizers
-import os
-import IMP
-import IMP.modeller_intf
-import IMP.test
-
-radius = IMP.FloatKey("radius")
-
-class ExclusionVolumeRestraintTests(IMP.test.TestCase):
- """Test exclusion volume restraints"""
-
- def setUp(self):
- """set up Modeller with exclusion volumes restraints """
- modeller.log.level(0,0,0,0,0)
-
- self.env = modeller.environ()
- self.env.io.atom_files_directory = '../data/'
- self.env.edat.dynamic_sphere = False
- self.env.libs.topology.read(file='$(LIB)/top_heav.lib')
- self.env.libs.parameters.read(file='$(LIB)/par.lib')
-
- self.imp_model = IMP.Model()
- self.particles = []
- self.restraint_sets = []
- self.rsrs = []
-
- self.t = self.env.edat.energy_terms
- self.t.append(IMP.modeller_intf.IMPRestraints(self.imp_model,
- self.particles))
-
- self.modeller_model = IMP.modeller_intf.create_particles(12, self.env,
- self.imp_model,
- self.particles)
- p1 = self.particles[0]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 1)
-
- p1 = self.particles[1]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 2)
-
- p1 = self.particles[2]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 3)
-
- p1 = self.particles[3]
- p1.add_attribute(radius, 1.5, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 4)
-
- p1 = self.particles[4]
- p1.add_attribute(radius, 1.5, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 5)
-
- p1 = self.particles[5]
- p1.add_attribute(radius, 1.5, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 6)
-
- p1 = self.particles[6]
- p1.add_attribute(radius, 1.5, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 7)
-
- p1 = self.particles[7]
- p1.add_attribute(radius, 2.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 8)
-
- p1 = self.particles[8]
- p1.add_attribute(radius, 2.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 9)
-
- p1 = self.particles[9]
- p1.add_attribute(radius, 2.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 10)
-
- p1 = self.particles[10]
- p1.add_attribute(radius, 2.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 11)
-
- p1 = self.particles[11]
- p1.add_attribute(radius, 2.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 12)
-
- self.atmsel = modeller.selection(self.modeller_model)
-
- self.opt = modeller.optimizers.conjugate_gradients()
-
-
- def test_exclusion_volumes_one_list(self):
- """Test exclusion volumes (intra-protein).
- All particles in a single protein should be connected but should
- not be closer than allowed by their VDW radii."""
- rs = IMP.RestraintSet("one_list")
- self.restraint_sets.append(rs)
- self.imp_model.add_restraint(rs)
-
- # add connectivity restraints
-
- particle_indexes1 = IMP.Ints()
- particle_indexes2 = IMP.Ints()
- rsrs = []
-
- # connect 2 proteins together by two beads
- particle_indexes1.clear()
- for i in range(0, 5):
- particle_indexes1.push_back(i)
- particle_indexes2.clear()
- for i in range(5, 12):
- particle_indexes2.push_back(i)
-
- # connect the beads within the two proteins together
- for i in range(0, 4):
- p1 = self.particles[i]
- p2 = self.particles[i+1]
- mean = p1.get_value(radius) + p2.get_value(radius)
- sf = IMP.HarmonicUpperBound(mean, 0.1)
- rsrs.append(IMP.DistanceRestraint(p1, p2, sf))
-
- for i in range(5, 11):
- p1 = self.particles[i]
- p2 = self.particles[i+1]
- mean = p1.get_value(radius) + p2.get_value(radius)
- sf = IMP.HarmonicUpperBound(mean, 0.1)
- rsrs.append(IMP.DistanceRestraint(p1, p2, sf))
-
- # create the exclusion volume for each protein
- score_func_params_lb = IMP.BasicScoreFuncParams("harmonic_lower_bound", 0.0, 0.1)
- rsrs.append(IMP.ExclusionVolumeRestraint(self.imp_model, particle_indexes1, radius, score_func_params_lb))
- rsrs.append(IMP.ExclusionVolumeRestraint(self.imp_model, particle_indexes2, radius, score_func_params_lb))
-
- # add restraints
- for i in range(len(rsrs)):
- rs.add_restraint(rsrs[i])
-
- self.atmsel.randomize_xyz(deviation=100.0)
- new_mdl = self.opt.optimize (self.atmsel, max_iterations=100, actions=None)
- self.modeller_model.write (file='out_exclusion_volume_one_list.pdb', model_format='PDB')
-
- coords = self.load_coordinates('out_exclusion_volume_one_list.pdb')
- os.unlink('out_exclusion_volume_one_list.pdb')
-
- # check min distances for intra-protein pairs
- for i in range(0, 4):
- for j in range(i+1, 5):
- d = self.get_distance(coords[i], coords[j]) - self.particles[i].get_value(radius) - self.particles[j].get_value(radius)
- self.assert_(d > -0.05, "particles "+str(i)+" and "+str(j)+" are too close together.")
-
- for i in range(5, 11):
- for j in range(i+1, 12):
- d = self.get_distance(coords[i], coords[j]) - self.particles[i].get_value(radius) - self.particles[j].get_value(radius)
- self.assert_(d > -0.05, "particles "+str(i)+" and "+str(j)+" are too close together.")
-
-
- def test_exclusion_volumes_two_lists(self):
- """Test exclusion volumes (intra- and inter-protein).
- All particles in a single protein should be connected and the two
- proteins should be connected in four locations but beads should
- not be closer than allowed by their VDW radii."""
- rs = IMP.RestraintSet("two_lists")
- self.restraint_sets.append(rs)
- self.imp_model.add_restraint(rs)
-
- # add connectivity restraints
-
- particle_indexes1 = IMP.Ints()
- particle_indexes2 = IMP.Ints()
- rsrs = []
-
- # connect 2 proteins together by two beads
- particle_indexes1.clear()
- for i in range(0, 5):
- particle_indexes1.push_back(i)
- particle_indexes2.clear()
- for i in range(5, 12):
- particle_indexes2.push_back(i)
-
- # connect the beads within the two proteins together
- for i in range(0, 4):
- p1 = self.particles[i]
- p2 = self.particles[i+1]
- mean = p1.get_value(radius) + p2.get_value(radius)
- sf = IMP.HarmonicUpperBound(mean, 0.1)
- rsrs.append(IMP.DistanceRestraint(p1, p2, sf))
-
- for i in range(5, 11):
- p1 = self.particles[i]
- p2 = self.particles[i+1]
- mean = p1.get_value(radius) + p2.get_value(radius)
- sf = IMP.HarmonicUpperBound(mean, 0.1)
- rsrs.append(IMP.DistanceRestraint(p1, p2, sf))
-
- # create the exclusion volume for each protein
- score_func_params_lb = IMP.BasicScoreFuncParams("harmonic_lower_bound", 0.0, 0.1)
- rsrs.append(IMP.ExclusionVolumeRestraint(self.imp_model, particle_indexes1, radius, score_func_params_lb))
- rsrs.append(IMP.ExclusionVolumeRestraint(self.imp_model, particle_indexes2, radius, score_func_params_lb))
-
- # connect the beads within the two proteins together
- # get 4 distinct pairs
- num_connects = 4
- particle_reuse = False
- score_func_params_ub = IMP.BasicScoreFuncParams("harmonic_upper_bound",
- 0.0, 0.1)
- rsrs.append(IMP.PairConnectivityRestraint(self.imp_model, particle_indexes1, particle_indexes2, radius, score_func_params_ub, num_connects, particle_reuse))
-
- # create the exclusion volume for each protein
- score_func_params_lb = IMP.BasicScoreFuncParams("harmonic_lower_bound", 0.0, 0.1)
- rsrs.append(IMP.ExclusionVolumeRestraint(self.imp_model, particle_indexes1, particle_indexes2, radius, score_func_params_lb))
-
- # add restraints
- for i in range(len(rsrs)):
- rs.add_restraint(rsrs[i])
-
- self.atmsel.randomize_xyz(deviation=100.0)
- new_mdl = self.opt.optimize (self.atmsel, max_iterations=200, actions=None)
- self.modeller_model.write (file='out_exclusion_volume_two_lists.pdb', model_format='PDB')
-
- coords = self.load_coordinates('out_exclusion_volume_two_lists.pdb')
- os.unlink('out_exclusion_volume_two_lists.pdb')
-
- # check min distances for intra-protein and inter-protein pairs
- for i in range(0, 11):
- for j in range(i+1, 12):
- d = self.get_distance(coords[i], coords[j]) - self.particles[i].get_value(radius) - self.particles[j].get_value(radius)
- self.assert_(d > -0.05, "particles "+str(i)+" and "+str(j)+" are too close together.")
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/test/modeller/test_proximity.py
===================================================================
--- kernel/test/modeller/test_proximity.py (revision 441)
+++ kernel/test/modeller/test_proximity.py (working copy)
@@ -1,127 +0,0 @@
-import modeller, unittest
-import modeller
-import modeller.optimizers
-import os
-import IMP
-import IMP.modeller_intf
-import IMP.utils
-import IMP.test
-
-radius = IMP.FloatKey("radius")
-
-class ProximityRestraintTests(IMP.test.TestCase):
- """Test proximity restraints"""
-
- def setUp(self):
- """set up Modeller with proximity restraints """
- modeller.log.level(0,0,0,0,0)
-
- self.env = modeller.environ()
- self.env.io.atom_files_directory = '../data/'
- self.env.edat.dynamic_sphere = False
- self.env.libs.topology.read(file='$(LIB)/top_heav.lib')
- self.env.libs.parameters.read(file='$(LIB)/par.lib')
-
- self.imp_model = IMP.Model()
- self.particles = []
- self.restraint_sets = []
- self.rsrs = []
-
- self.t = self.env.edat.energy_terms
- self.t.append(IMP.modeller_intf.IMPRestraints(self.imp_model,
- self.particles))
-
- self.modeller_model = IMP.modeller_intf.create_particles(6, self.env,
- self.imp_model,
- self.particles)
- p1 = self.particles[0]
- p1.add_attribute(radius, 2.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 1)
-
- p1 = self.particles[1]
- p1.add_attribute(radius, 2.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 2)
-
- p1 = self.particles[2]
- p1.add_attribute(radius, 1.5, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 3)
-
- p1 = self.particles[3]
- p1.add_attribute(radius, 1.5, False)
- p1.add_attribute(IMP.IntKey("protein"), 2)
- p1.add_attribute(IMP.IntKey("id"), 4)
-
- p1 = self.particles[4]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 3)
- p1.add_attribute(IMP.IntKey("id"), 5)
-
- p1 = self.particles[5]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 3)
- p1.add_attribute(IMP.IntKey("id"), 6)
-
- self.atmsel = modeller.selection(self.modeller_model)
-
- self.opt = modeller.optimizers.conjugate_gradients()
-
-
- def test_proximity(self):
- """Test proximity restraints using Modeller optimizers"""
- self.atmsel.randomize_xyz(deviation=100.0)
-
- self.restraint_sets.append(IMP.RestraintSet("proximity"))
- rs = self.restraint_sets[len(self.restraint_sets)-1]
- self.imp_model.add_restraint(rs)
-
- # add proximity restraints
-
- particle_indexes = IMP.Ints()
- rsrs = []
-
- # set up exclusion volumes
- IMP.utils.set_up_exclusion_volumes(self.imp_model, self.particles,
- radius, rsrs)
-
- max_distance = 10.0
-
- # set max distance for two most distant particles together
- particle_indexes.clear()
- for i in range(6):
- particle_indexes.push_back(i)
-
- score_func_params = IMP.BasicScoreFuncParams("harmonic_upper_bound", 0.0, 0.1)
- rsrs.append(IMP.ProximityRestraint(self.imp_model, particle_indexes,
- radius, max_distance,
- score_func_params))
-
- # add restraints
- for i in range(len(rsrs)):
- rs.add_restraint(rsrs[i])
-
- self.atmsel.randomize_xyz(deviation=100.0)
- new_mdl = self.opt.optimize (self.atmsel, max_iterations=1800, actions=None)
- self.modeller_model.write (file='out_proximity.pdb', model_format='PDB')
-
- coords = self.load_coordinates('out_proximity.pdb')
- os.unlink('out_proximity.pdb')
-
- # min distances
- for i in range(len(coords)):
- irad = self.particles[i].get_value(radius)
- for j in range(i+1,len(coords)):
- jrad = self.particles[j].get_value(radius)
- self.assert_(self.check_min_distance(coords[i], coords[j], irad + jrad - 0.1), "min distance for any pair condition (" + str(i) + ", " + str(j) + ")")
-
- # max distances
- for i in range(len(coords)):
- irad = self.particles[i].get_value(radius)
- for j in range(i+1,len(coords)):
- jrad = self.particles[j].get_value(radius)
- self.assert_(self.check_max_distance(coords[i], coords[j], max_distance - irad - jrad + 0.1), "max distance for any pair condition (" + str(i) + ", " + str(j) + ")")
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/test/modeller/test_easy_proximity.py
===================================================================
--- kernel/test/modeller/test_easy_proximity.py (revision 441)
+++ kernel/test/modeller/test_easy_proximity.py (working copy)
@@ -1,111 +0,0 @@
-import modeller, unittest
-import modeller.optimizers
-import os
-import IMP
-import IMP.modeller_intf
-import IMP.utils
-import IMP.test
-
-radius = IMP.FloatKey("radius")
-
-class ProximityRestraintTests(IMP.test.TestCase):
- """Test proximity restraints"""
-
- def setUp(self):
- """set up Modeller with proximity restraints """
- modeller.log.level(0,0,0,0,0)
-
- self.env = modeller.environ()
- self.env.io.atom_files_directory = '../data/'
- self.env.edat.dynamic_sphere = False
- self.env.libs.topology.read(file='$(LIB)/top_heav.lib')
- self.env.libs.parameters.read(file='$(LIB)/par.lib')
-
- self.imp_model = IMP.Model()
- self.particles = []
- self.restraint_sets = []
- self.rsrs = []
-
- self.t = self.env.edat.energy_terms
- self.t.append(IMP.modeller_intf.IMPRestraints(self.imp_model,
- self.particles))
-
- self.modeller_model = IMP.modeller_intf.create_particles(4, self.env,
- self.imp_model,
- self.particles)
- p1 = self.particles[0]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 1)
-
- p1 = self.particles[1]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 2)
-
- p1 = self.particles[2]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 3)
-
- p1 = self.particles[3]
- p1.add_attribute(radius, 1.0, False)
- p1.add_attribute(IMP.IntKey("protein"), 1)
- p1.add_attribute(IMP.IntKey("id"), 4)
-
- self.atmsel = modeller.selection(self.modeller_model)
-
- self.opt = modeller.optimizers.conjugate_gradients()
-
-
- # proximity
- def test_proximity(self):
- """All particles should be within a given max distance of each other"""
- self.atmsel.randomize_xyz(deviation=100.0)
-
- self.restraint_sets.append(IMP.RestraintSet("proximity"))
- rs = self.restraint_sets[len(self.restraint_sets)-1]
- self.imp_model.add_restraint(rs)
-
- # add proximity restraints
-
- particle_indexes = IMP.Ints()
- rsrs = []
-
- # set up exclusion volumes
- IMP.utils.set_up_exclusion_volumes(self.imp_model, self.particles,
- radius, rsrs, 0.1)
- max_distance = 4.0
-
- # set max distance for two most distant particles together
- particle_indexes.clear()
- for i in range(4):
- particle_indexes.push_back(i)
- score_func_params_ub = IMP.BasicScoreFuncParams("harmonic_upper_bound", 0.0, 0.1)
- rsrs.append(IMP.ProximityRestraint(self.imp_model, particle_indexes,
- radius, max_distance,
- score_func_params_ub))
-
- # add restraints
- for i in range(len(rsrs)):
- rs.add_restraint(rsrs[i])
-
- self.atmsel.randomize_xyz(deviation=100.0)
- new_mdl = self.opt.optimize (self.atmsel, max_iterations=155, actions=None)
- self.modeller_model.write (file='out_proximity.pdb', model_format='PDB')
-
- coords = self.load_coordinates('out_proximity.pdb')
- os.unlink('out_proximity.pdb')
-
- # min distances
- for i in range(len(coords)):
- for j in range(i+1,len(coords)):
- self.assert_(self.check_min_distance(coords[i], coords[j], self.particles[i].get_value(radius) + self.particles[j].get_value(radius) - 0.1), "min distance for any pair condition (" + str(i) + ", " + str(j) + ")")
-
- # max distances
- for i in range(len(coords)):
- for j in range(i+1,len(coords)):
- self.assert_(self.check_max_distance(coords[i], coords[j], max_distance - self.particles[i].get_value(radius) - self.particles[j].get_value(radius) + 0.1), "max distance for any pair condition (" + str(i) + ", " + str(j) + ")")
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/test/torus/test_torus.py
===================================================================
--- kernel/test/torus/test_torus.py (revision 441)
+++ kernel/test/torus/test_torus.py (working copy)
@@ -1,46 +0,0 @@
-import unittest
-import os
-import IMP
-import IMP.test
-import IMP.utils
-
-class TorusRestraintTests(IMP.test.TestCase):
- """Class to test torus restraints"""
-
- def setUp(self):
- """Build test model and optimizer"""
- self.imp_model = IMP.Model()
- self.particles = []
- self.restraint_sets = []
- self.rsrs = []
-
- for p in range(12):
- self.particles.append(IMP.utils.XYZParticle(self.imp_model,
- 0., 0., 0.))
- self.opt = IMP.ConjugateGradients()
- self.opt.set_model(self.imp_model);
- self.opt.set_threshold(1e-4)
-
-
- def test_torus(self):
- """All particles should be inside the specified torus"""
- rs = IMP.RestraintSet("torus")
- self.restraint_sets.append(rs)
- self.imp_model.add_restraint(rs)
-
- for p in self.imp_model.get_particles():
- r = IMP.TorusRestraint(p, 50, 10, IMP.HarmonicUpperBound(0.0, 0.1))
- self.rsrs.append(r)
- rs.add_restraint(r)
-
- # Randomize particle coordinates
- self.randomize_particles(self.particles, 50.0)
-
- self.opt.optimize(50)
- for p in self.particles:
- coord = (p.x(), p.y(), p.z())
- self.assert_(self.check_in_torus(coord, 50, 10.001),
- "in torus condition")
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/test/torus/test_torus.py
===================================================================
--- kernel/test/torus/test_torus.py (revision 441)
+++ kernel/test/torus/test_torus.py (working copy)
@@ -1,46 +0,0 @@
-import unittest
-import os
-import IMP
-import IMP.test
-import IMP.utils
-
-class TorusRestraintTests(IMP.test.TestCase):
- """Class to test torus restraints"""
-
- def setUp(self):
- """Build test model and optimizer"""
- self.imp_model = IMP.Model()
- self.particles = []
- self.restraint_sets = []
- self.rsrs = []
-
- for p in range(12):
- self.particles.append(IMP.utils.XYZParticle(self.imp_model,
- 0., 0., 0.))
- self.opt = IMP.ConjugateGradients()
- self.opt.set_model(self.imp_model);
- self.opt.set_threshold(1e-4)
-
-
- def test_torus(self):
- """All particles should be inside the specified torus"""
- rs = IMP.RestraintSet("torus")
- self.restraint_sets.append(rs)
- self.imp_model.add_restraint(rs)
-
- for p in self.imp_model.get_particles():
- r = IMP.TorusRestraint(p, 50, 10, IMP.HarmonicUpperBound(0.0, 0.1))
- self.rsrs.append(r)
- rs.add_restraint(r)
-
- # Randomize particle coordinates
- self.randomize_particles(self.particles, 50.0)
-
- self.opt.optimize(50)
- for p in self.particles:
- coord = (p.x(), p.y(), p.z())
- self.assert_(self.check_in_torus(coord, 50, 10.001),
- "in torus condition")
-
-if __name__ == '__main__':
- unittest.main()
Index: kernel/include/IMP/ScoreFuncParams.h
===================================================================
--- kernel/include/IMP/ScoreFuncParams.h (revision 441)
+++ kernel/include/IMP/ScoreFuncParams.h (working copy)
@@ -1,66 +0,0 @@
-/**
- * \file ScoreFuncParams.h \brief Factory for creating UnaryFunctions.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- */
-
-#ifndef __IMP_SCORE_FUNC_PARAMS_H
-#define __IMP_SCORE_FUNC_PARAMS_H
-
-#include "IMP_config.h"
-#include "base_types.h"
-#include "UnaryFunction.h"
-
-namespace IMP
-{
-
-//! Abstract class containing parameters for creating UnaryFunction instances.
-/** Also has factory method for creating those instances.
- */
-class IMPDLLEXPORT ScoreFuncParams
-{
-public:
- ScoreFuncParams() {}
- virtual ~ScoreFuncParams() {}
- virtual UnaryFunction* create_score_func() = 0;
-};
-
-
-//! Basic mean+standard deviation parameter class for making UnaryFunctions.
-class IMPDLLEXPORT BasicScoreFuncParams : public ScoreFuncParams
-{
-public:
- BasicScoreFuncParams(std::string score_func_type = "harmonic",
- Float mean = 1.0, Float sd = 0.1);
- virtual ~BasicScoreFuncParams();
-
- //! Create a new score function with the current set of parameters.
- /** \return pointer to score function.
- */
- virtual UnaryFunction* create_score_func();
-
- //! Set the mean to use in calculating this score function.
- /** \param[in] mean Value for the mean.
- */
- void set_mean(Float mean);
-
- //! Set the standard deviation to use in calculating this score function.
- /** \param[in] sd Value for the standard deviation.
- */
- void set_sd(Float sd);
-
- //! Set the type of score function to use.
- /** \param[in] score_func_type Name of the score function type
- */
- void set_score_func_type(std::string score_func_type);
-
-protected:
- Float mean_;
- Float sd_;
- std::string score_func_type_;
-};
-
-
-} // namespace IMP
-
-#endif /* __IMP_SCORE_FUNC_PARAMS_H */
Index: kernel/include/IMP/restraints/ExclusionVolumeRestraint.h
===================================================================
--- kernel/include/IMP/restraints/ExclusionVolumeRestraint.h (revision 441)
+++ kernel/include/IMP/restraints/ExclusionVolumeRestraint.h (working copy)
@@ -1,70 +0,0 @@
-/**
- * \file ExclusionVolumeRestraint.h \brief Excluded volume restraint.
- *
- * Prevent particles from getting too close together, by restricting the
- * minimum distance between all pairs of particles formed from one or two
- * sets of particles.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_EXCLUSION_VOLUME_RESTRAINT_H
-#define __IMP_EXCLUSION_VOLUME_RESTRAINT_H
-
-#include <list>
-
-#include "../IMP_config.h"
-#include "../Restraint.h"
-#include "../ScoreFuncParams.h"
-#include "../internal/kernel_version_info.h"
-#include "DistanceRestraint.h"
-
-namespace IMP
-{
-
-//! Apply restraints that prevent particles from getting too close together.
-/** Restrict min distance between all pairs of particles formed from one or
- two sets of particles. If two sets of particles are passed, it assumes
- that the two sets of particles have no overlap (otherwise, you will get
- repeats).
-
- Calculate the distance restraints for the given particles. Use the
- smallest restraints that will connect one particle of each type
- together (i.e. a minimum spanning tree with nodes corresponding to
- particle types and the edge weights corresponding to restraint
- violation scores).
- */
-class IMPDLLEXPORT ExclusionVolumeRestraint : public Restraint
-{
-public:
- ExclusionVolumeRestraint(Model* model, std::vector<int>& particle1_indexes,
- std::vector<int>& particle2_indexes,
- FloatKey attr_name,
- BasicScoreFuncParams* score_func_params);
-
- ExclusionVolumeRestraint(Model* model, std::vector<int>& particle_indexes,
- FloatKey attr_name,
- BasicScoreFuncParams* score_func_params);
-
- virtual ~ExclusionVolumeRestraint();
-
- IMP_RESTRAINT(internal::kernel_version_info)
-
-protected:
- //! number of particles all together
- int num_particles_;
- //! number of particles in vector 1
- int num_particles1_;
- //! number of particles in vector 2
- int num_particles2_;
-
- //! total number of restraints
- int num_restraints_;
- //! restraints and their scores
- std::vector<DistanceRestraint*> dist_rsrs_;
-};
-
-} // namespace IMP
-
-#endif /* __IMP_EXCLUSION_VOLUME_RESTRAINT_H */
Index: kernel/include/IMP/restraints/ProximityRestraint.h
===================================================================
--- kernel/include/IMP/restraints/ProximityRestraint.h (revision 441)
+++ kernel/include/IMP/restraints/ProximityRestraint.h (working copy)
@@ -1,74 +0,0 @@
-/**
- * \file ProximityRestraint.h \brief Proximity restraint.
- *
- * Restrict maximum distance between any two particles.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_PROXIMITY_RESTRAINT_H
-#define __IMP_PROXIMITY_RESTRAINT_H
-
-#include <list>
-#include <vector>
-
-#include "../IMP_config.h"
-#include "../Restraint.h"
-#include "../ScoreFuncParams.h"
-#include "../internal/kernel_version_info.h"
-#include "DistanceRestraint.h"
-
-namespace IMP
-{
-
-//! Restrict maximum distance between any two particles
-/** Given a list of particles, this restraint calculates the distance
- restraints between all pairs of particles, and then applies the
- one restraint with the greatest score.
-
- Calculate the distance restraints for the given particles. Use the
- smallest restraints that will connect one particle of each type together
- (i.e. a minimum spanning tree with nodes corresponding to particle
- types and the edge weights corresponding to restraint violation score
- values).
- */
-class IMPDLLEXPORT ProximityRestraint : public Restraint
-{
-public:
- ProximityRestraint(Model* model, std::vector<int>& particle_indexes,
- const Float distance,
- BasicScoreFuncParams* score_func_params);
-
- ProximityRestraint(Model* model, std::vector<int>& particle_indexes,
- FloatKey attr_name, const Float distance,
- BasicScoreFuncParams* score_func_params);
-
- virtual ~ProximityRestraint();
-
- IMP_RESTRAINT(internal::kernel_version_info)
-
-protected:
- //! Internal set up for the constructors.
- /** \param[in] model Pointer to the model.
- \param[in] particle_indexes Vector of indexes of particles in the
- restraint.
- */
- void set_up(Model* model, std::vector<int>& particle_indexes);
-
- //! number of particles in the restraint
- int num_particles_;
-
- //! total number of restraints being tested
- int num_restraints_;
- //! calculated restraint scores
- std::vector<Float> scores_;
- //! indexes of local indexes sorted by energies
- std::vector<int> rsr_idx_;
- //! the distance restraints
- std::vector<DistanceRestraint*> dist_rsrs_;
-};
-
-} // namespace IMP
-
-#endif /* __IMP_PROXIMITY_RESTRAINT_H */
Index: kernel/include/IMP/restraints/TorusRestraint.h
===================================================================
--- kernel/include/IMP/restraints/TorusRestraint.h (revision 441)
+++ kernel/include/IMP/restraints/TorusRestraint.h (working copy)
@@ -1,52 +0,0 @@
-/**
- * \file TorusRestraint.h \brief Score based on distance from torus interior
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_TORUS_RESTRAINT_H
-#define __IMP_TORUS_RESTRAINT_H
-
-#include <list>
-
-#include "../IMP_config.h"
-#include "../ScoreFuncParams.h"
-#include "../Restraint.h"
-#include "../internal/kernel_version_info.h"
-
-namespace IMP
-{
-
-//! Restrict particle position to interior of a torus
-class IMPDLLEXPORT TorusRestraint : public Restraint
-{
-public:
- /** \param[in] p1 Pointer to particle of the restraint.
- \param[in] main_radius The main radius from the origin to the midline
- of the tube.
- \param[in] tube_radius The tube radius is min distance from the tube
- midline to the tube surface.
- \param[in] score_func Scoring function for the torus feature (distance
- of the particle from the torus surface)
- */
- TorusRestraint(Particle* p1, const Float main_radius,
- const Float tube_radius, UnaryFunction* score_func);
- virtual ~TorusRestraint();
-
- IMP_RESTRAINT(internal::kernel_version_info)
-
-protected:
- //! variables used to determine the distance
- FloatKey x_, y_, z_;
- //! main radius of the torus
- Float main_radius_;
- //! radius of the torus tube
- Float tube_radius_;
- //! math form for this restraint (typically one of the harmonics)
- UnaryFunction* score_func_;
-};
-
-} // namespace IMP
-
-#endif /* __IMP_TORUS_RESTRAINT_H */
Index: kernel/include/IMP/restraints/PairConnectivityRestraint.h
===================================================================
--- kernel/include/IMP/restraints/PairConnectivityRestraint.h (revision 441)
+++ kernel/include/IMP/restraints/PairConnectivityRestraint.h (working copy)
@@ -1,116 +0,0 @@
-/**
- * \file PairConnectivityRestraint.h \brief Pair connectivity restraint.
- *
- * Restrict max distance between one or more pair of particles of any
- * two sets of particles (e.g. rigid bodies).
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_PAIR_CONNECTIVITY_RESTRAINT_H
-#define __IMP_PAIR_CONNECTIVITY_RESTRAINT_H
-
-#include <list>
-
-#include "../IMP_config.h"
-#include "../Restraint.h"
-#include "../ScoreFuncParams.h"
-#include "../internal/kernel_version_info.h"
-#include "DistanceRestraint.h"
-
-namespace IMP
-{
-
-//! Pair connectivity restraint.
-/** Restrict max distance between one or more pair of particles of any
- two sets of particles (e.g. rigid bodies).
-
- Calculate the distance restraints for the given particles. Use the
- smallest restraints that will connect one particle of each type together
- (i.e. a minimum spanning tree with nodes corresponding to particle
- types and the edge weights corresponding to restraint violation scores).
-
- There is a potential when using this restraint for two large rigid bodies
- to maintain its own exclusion volume restraints. These could be calculated
- only for the particles in the neighborhoods of the particles involved in
- the activated restraints rather than between all particles in the two
- bodies. Since once restraints are activated, they tend to be activated
- over and over, the exclusion volume restraint sets should only be reset
- whenever on rare occasion the neighborhoods actually change.
-
- */
-class IMPDLLEXPORT PairConnectivityRestraint : public Restraint
-{
-public:
- PairConnectivityRestraint(Model *m, std::vector<int>& particle1_indexes,
- std::vector<int>& particle2_indexes,
- BasicScoreFuncParams* score_func_params,
- const int num_to_apply = 1,
- const bool particle_reuse = false);
-
- PairConnectivityRestraint(Model *m, std::vector<int>& particle1_indexes,
- std::vector<int>& particle2_indexes,
- FloatKey attr_name,
- BasicScoreFuncParams* score_func_params,
- const int num_to_apply,
- const bool particle_reuse = false);
-
- virtual ~PairConnectivityRestraint();
-
- IMP_RESTRAINT(internal::kernel_version_info)
-
-protected:
- class RestraintScore
- {
- public:
- RestraintScore() {}
- ~RestraintScore() {}
- void evaluate() {
- score_ = rsr_->evaluate(false);
- }
- bool operator<(const RestraintScore& rs) const {
- return score_ < rs.score_;
- }
-
- int part1_idx_;
- int part2_idx_;
- DistanceRestraint* rsr_;
- Float score_;
- };
-
- //! Internal set up for the constructors.
- /** \param[in] model Pointer to the model.
- \param[in] particle1_indexes Vector of indexes of particles in first body
- of the restraint.
- \param[in] particle2_indexes Vector of indexes of particles in second body
- of the restraint.
- */
- void set_up(Model* model, std::vector<int>& particle1_indexes,
- std::vector<int>& particle2_indexes);
-
- //! variables to determine the particle type
- IntKey type_;
-
- //! number of particles all together
- int num_particles_;
- //! number of particles in vector 1
- int num_particles1_;
- //! number of particles in vector 2
- int num_particles2_;
- //! total number of restraints to apply
- int num_to_apply_;
- //! true if a particle can be involved in more than one restraint
- int particle_reuse_;
- //! which of particles have already been used
- std::vector<bool> used_;
-
- //! total number of restraints being tested
- int num_restraints_;
- //! restraints and their scores
- std::list<RestraintScore> rsr_scores_;
-};
-
-} // namespace IMP
-
-#endif /* __IMP_PAIR_CONNECTIVITY_RESTRAINT_H */
Index: kernel/src/restraints/ProximityRestraint.cpp
===================================================================
--- kernel/src/restraints/ProximityRestraint.cpp (revision 441)
+++ kernel/src/restraints/ProximityRestraint.cpp (working copy)
@@ -1,229 +0,0 @@
-/**
- * \file ProximityRestraint.cpp \brief Proximity restraint.
- *
- * Restrict maximum distance between any two particles.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include <cmath>
-
-#include "IMP/Model.h"
-#include "IMP/Particle.h"
-#include "IMP/log.h"
-#include "IMP/restraints/ProximityRestraint.h"
-
-namespace IMP
-{
-
-//! Constructor - set up the restraint for point-like particles.
-/** \param[in] model Pointer to the model.
- \param[in] particle_indexes Vector of indexes of particles
- \param[in] distance Maximum length allowable between any two particles.
- \param[in] score_func_params Parameters for creating a score function.
- */
-ProximityRestraint::ProximityRestraint(Model* model,
- std::vector<int>& particle_indexes,
- const Float distance,
- BasicScoreFuncParams* score_func_params)
-{
- set_up(model, particle_indexes);
-
- // get the indexes associated with the restraints
- int idx = 0;
- score_func_params->set_mean(distance);
- score_func_params->set_score_func_type("harmonic_upper_bound");
- for (int i = 0; i < num_particles_ - 1; i++) {
- for (int j = i + 1; j < num_particles_; j++) {
- // create the restraint
-
- UnaryFunction *sf = score_func_params->create_score_func();
- dist_rsrs_[idx] = new DistanceRestraint(get_particle(i),
- get_particle(j),
- sf);
- idx++;
- }
- }
-
- IMP_LOG(VERBOSE,
- "Number of restraints: " << num_restraints_
- << " number of particles: " << num_particles_ << std::endl);
-}
-
-
-//! Constructor - set up the restraint for particles with radii.
-/** \param[in] model Pointer to the model.
- \param[in] particle_indexes Vector of indexes of particles
- \param[in] attr_name Name to get radii to calculate the mean distance.
- \param[in] distance Maximum length allowable between any two particles.
- \param[in] score_func_params Parameters for creating a score function.
- */
-ProximityRestraint::ProximityRestraint(Model* model,
- std::vector<int>& particle_indexes,
- FloatKey attr_name,
- const Float distance,
- BasicScoreFuncParams* score_func_params)
-{
- // Use those radii to calculate the expected distance
- set_up(model, particle_indexes);
-
- // get the indexes associated with the restraints
- int idx = 0;
- Float actual_mean;
- score_func_params->set_score_func_type("harmonic_upper_bound");
- for (int i = 0; i < num_particles_ - 1; i++) {
- for (int j = i + 1; j < num_particles_; j++) {
- // Use those radii to calculate the expected distance between centers
- Float attri, attrj;
- attri = get_particle(i)->get_value(attr_name);
- attrj = get_particle(j)->get_value(attr_name);
- actual_mean = distance - attri - attrj;
-
- // create the restraint
- IMP_LOG(VERBOSE, i << " " << j << " add distance: " << actual_mean);
- score_func_params->set_mean(actual_mean);
- UnaryFunction *sf = score_func_params->create_score_func();
- dist_rsrs_[idx] = new DistanceRestraint(get_particle(i),
- get_particle(j),
- sf);
- idx++;
- }
- }
-}
-
-
-//! Internal set up for the constructors.
-/** \param[in] model Pointer to the model.
- \param[in] particle_indexes Vector of indexes of particles in the restraint.
- */
-void ProximityRestraint::set_up(Model* model,
- std::vector<int>& particle_indexes)
-{
- IMP_LOG(VERBOSE, "init ConnectivityRestraint");
-
- /** number of particles in the restraint */
- num_particles_ = particle_indexes.size();
-
- // set up the particles, their position indexes, and their type indexes
- Particle* p1;
- for (int i = 0; i < num_particles_; i++) {
- p1 = model->get_particle(particle_indexes[i]);
- add_particle(p1);
- }
-
- // figure out how many restraints there are
- num_restraints_ = num_particles_ * (num_particles_ - 1) / 2;
-
- // use number of restraints and number of types to set up some of the
- // ... main arrays
- dist_rsrs_.resize(num_restraints_);
- scores_.resize(num_restraints_);
- rsr_idx_.resize(num_restraints_);
-}
-
-
-//! Destructor
-ProximityRestraint::~ProximityRestraint()
-{
- for (int i = 0; i < num_restraints_; i++) {
- delete dist_rsrs_[i];
- }
-}
-
-
-//! Evaluate the score for the model.
-/** Calculate the distance restraints for the given particles. Use the smallest
- restraints that will connect one particle of each type together (i.e. a
- minimum spanning tree with nodes corresponding to particle types and the
- edge weights corresponding to restraint violation score values).
-
- \param[in] accum If not NULL, use this object to accumulate partial first
- derivatives.
- \return score associated with this restraint for the given state of
- the model.
- */
-Float ProximityRestraint::evaluate(DerivativeAccumulator *accum)
-{
- int idx;
-
- IMP_LOG(VERBOSE, "evaluate ProximityRestraint");
-
- // calculate the scores for all of the restraints
- /*
- There is a problem with using just the largest violation restraint
- in that it causes an inherent unsmoothness in the optimization process.
- I.e. when one pair becomes more distant in another, there is a complete
- switch to an orthogonal direction.
-
- LogMsg(VERBOSE, "calculate restraint scores");
- for (int i = 0; i < num_restraints_; i++)
- {
- scores_[i] = dist_rsrs_[i]->evaluate(false);
- }
- */
-
- // dumb bubble sort of indexes by scores.
- // /rsr_idx[]/ holds the sorted indexes so that all other arrays
- // associated with the particles can be left as they are.
-
- /*
- LogMsg(VERBOSE, "sort scores");
- for (int i = 0; i < num_restraints_; i++)
- {
- rsr_idx_[i] = i;
- }
-
- for (int i = 0; i < num_restraints_ - 1; i++)
- {
- // move the next highest score index to the left most position of the
- // remaining unsorted list.
- for (int j = num_restraints_ - 1; j > i; j--)
- {
- if (scores_[rsr_idx_[j - 1]] < scores_[rsr_idx_[j]])
- {
- idx = rsr_idx_[j - 1];
- rsr_idx_[j - 1] = rsr_idx_[j];
- rsr_idx_[j] = idx;
- }
- }
- }
- */
-
- // apply the restraints corresponding the highest score restraints
- int num_restraints_to_use = 1; // mod later if it should be more than one
-
- // switching back and forth seems to be less smooth
- // just apply all of the restraints every time (also faster)
- num_restraints_to_use = num_restraints_;
- Float score = 0.0;
- for (int i = 0; i < num_restraints_to_use; i++) {
- // idx = rsr_idx_[i];
- idx = i;
-
- score += dist_rsrs_[idx]->evaluate(accum);
- IMP_LOG(VERBOSE,
- " " << i << " Applying Restraint: score: "
- << score << std::endl);
- }
-
- return score;
-}
-
-
-//! Show the current restraint.
-/** \param[in] out Stream to send restraint description to.
- */
-void ProximityRestraint::show(std::ostream& out) const
-{
- if (get_is_active()) {
- out << "proximity restraint (active):" << std::endl;
- } else {
- out << "proximity restraint (inactive):" << std::endl;
- }
-
- get_version_info().show(out);
- out << " num particles:" << num_particles_;
-}
-
-} // namespace IMP
Index: kernel/src/restraints/TorusRestraint.cpp
===================================================================
--- kernel/src/restraints/TorusRestraint.cpp (revision 441)
+++ kernel/src/restraints/TorusRestraint.cpp (working copy)
@@ -1,135 +0,0 @@
-/**
- * \file TorusRestraint.cpp \brief Score based on distance from torus interior
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include <cmath>
-
-#include "IMP/Model.h"
-#include "IMP/Particle.h"
-#include "IMP/log.h"
-#include "IMP/restraints/TorusRestraint.h"
-
-namespace IMP
-{
-
-TorusRestraint::TorusRestraint(Particle* p1, const Float main_radius,
- const Float tube_radius,
- UnaryFunction* score_func)
-{
- add_particle(p1);
- x_ = FloatKey("x");
- y_ = FloatKey("y");
- z_ = FloatKey("z");
-
- main_radius_ = main_radius;
- tube_radius_ = tube_radius;
- score_func_ = score_func;
-}
-
-
-//! Destructor
-TorusRestraint::~TorusRestraint()
-{
- delete score_func_;
-}
-
-
-//! Calculate the score for this restraint for the current model state.
-/** \param[in] accum If not NULL, use this object to accumulate partial first
- derivatives.
- \return Current score.
- */
-Float TorusRestraint::evaluate(DerivativeAccumulator *accum)
-{
- IMP_CHECK_OBJECT(score_func_);
-
- Float tube_center_x, tube_center_y;
- Float xy_distance_from_center;
- Float distance_from_tube_center;
- Float torus_feature;
- Float score, deriv;
- Float x, y, z;
- Float dx, dy, dz;
-
- IMP_LOG(VERBOSE, "... evaluating torus restraint.");
- // get current position of particle
- x = get_particle(0)->get_value(x_);
- y = get_particle(0)->get_value(y_);
- z = get_particle(0)->get_value(z_);
-
- // get the x, y distance from the origin
- xy_distance_from_center = sqrt(x * x + y * y);
- if (xy_distance_from_center == 0.0) {
- // if no direction is favored,
- // ... pick some arbitrary direction to head towards the
- // ... torus interior
- xy_distance_from_center = 0.001;
- x = 0.001;
- }
-
- // calculate the cross-section_center (large radius away from origin with z=0)
- tube_center_x = x * main_radius_ / xy_distance_from_center;
- tube_center_y = y * main_radius_ / xy_distance_from_center;
- // by definition: tube_center_z = 0;
-
- // translate to cross-section center
- x -= tube_center_x;
- y -= tube_center_y;
-
- // calculate the distance from the cross-section_center
- distance_from_tube_center = sqrt(x * x + y * y + z * z);
-
- // subtract the small radius of the torus so that if the point is within the
- // ... torus the value is negative
- torus_feature = distance_from_tube_center - tube_radius_;
-
- // if in the torus, partials should be zero
- if (torus_feature <= 0) {
- score = 0.0;
- deriv = 0.0;
- }
-
- // otherwise, derivatives should reduce feature as torus is neared
- // the derivative vector stays constant independent of distance from torus
- // i.e. a unit vector
- else {
- score = (*score_func_)(torus_feature, deriv);
- }
-
- // if needed, use the partial derivatives
- if (accum) {
- dx = deriv * x / distance_from_tube_center;
- dy = deriv * y / distance_from_tube_center;
- dz = deriv * z / distance_from_tube_center;
-
- get_particle(0)->add_to_derivative(x_, dx, *accum);
- get_particle(0)->add_to_derivative(y_, dy, *accum);
- get_particle(0)->add_to_derivative(z_, dz, *accum);
- }
-
- return score;
-}
-
-
-//! Show the current restraint.
-/** \param[in] out Stream to send restraint description to.
- */
-void TorusRestraint::show(std::ostream& out) const
-{
- if (get_is_active()) {
- out << "torus restraint (active):" << std::endl;
- } else {
- out << "torus restraint (inactive):" << std::endl;
- }
-
- get_version_info().show(out);
- out << " particle: " << get_particle(0)->get_index() << " ";
-
- out << " main radius:" << main_radius_;
- out << " tube radius:" << tube_radius_;
-}
-
-} // namespace IMP
Index: kernel/src/restraints/PairConnectivityRestraint.cpp
===================================================================
--- kernel/src/restraints/PairConnectivityRestraint.cpp (revision 441)
+++ kernel/src/restraints/PairConnectivityRestraint.cpp (working copy)
@@ -1,276 +0,0 @@
-/**
- * \file PairConnectivityRestraint.cpp \brief Pair connectivity restraint.
- *
- * Restrict max distance between one or more pair of particles of any
- * two sets of particles (e.g. rigid bodies).
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include <cmath>
-
-#include "IMP/Model.h"
-#include "IMP/Particle.h"
-#include "IMP/log.h"
-#include "IMP/restraints/PairConnectivityRestraint.h"
-
-namespace IMP
-{
-
-//! Set up a restraint using the given mean for particle-particle distance.
-/** \param[in] model Pointer to the model.
- \param[in] particle1_indexes Vector of indexes of particles of first body.
- \param[in] particle2_indexes Vector of indexes of particles of second body.
- \param[in] score_func_params Parameters for creating a score function.
- \param[in] num_to_apply Number of minimum restraints to apply.
- \param[in] particle_reuse Allow minimum restraints to use particle
- more than once.
- */
-PairConnectivityRestraint::PairConnectivityRestraint(Model* model,
- std::vector<int>& particle1_indexes, std::vector<int>& particle2_indexes,
- BasicScoreFuncParams* score_func_params, const int num_to_apply,
- const bool particle_reuse)
-{
- particle_reuse_ = particle_reuse;
- num_to_apply_ = num_to_apply;
- set_up(model, particle1_indexes, particle2_indexes);
-
-
- // get the indexes associated with the restraints
- int idx = 0;
- // use iterator to move through each predefined position in the
- // restraint/score list
- std::list<PairConnectivityRestraint::RestraintScore>::iterator rs_iter;
- rs_iter = rsr_scores_.begin();
- for (int i = 0; i < num_particles1_; i++) {
- for (int j = num_particles1_; j < num_particles1_ + num_particles2_; j++) {
- // create the restraint
- if (rs_iter == rsr_scores_.end()) {
- IMP_failure("Reached end of rsr_scores too early.",
- ValueException("Reached end of rsr_scores too early"));
- } else {
- IMP_LOG(VERBOSE, "Adding possible restraint: " << i << " " << j);
- UnaryFunction *sf = score_func_params->create_score_func();
- rs_iter->rsr_ = new DistanceRestraint(get_particle(i),
- get_particle(j),
- sf);
-
- rs_iter->part1_idx_ = i;
- rs_iter->part2_idx_ = j;
- }
-
- ++rs_iter;
- }
- }
-
- IMP_LOG(VERBOSE, idx <<
- " num_restraints_: " << num_restraints_ << " num_particles1_: " <<
- num_particles1_ << " num_particles2_:" << num_particles2_
- << std::endl);
-}
-
-//! Set up a restraint using the given attribute for particle-particle distance.
-/** \param[in] model Pointer to the model.
- \param[in] particle1_indexes Vector of indexes of particles of first body.
- \param[in] particle2_indexes Vector of indexes of particles of second body.
- \param[in] attr_name Name to get radii to calculate the mean distance.
- \param[in] score_func_params Parameters for creating a score function.
- \param[in] num_to_apply Number of minimum restraints to apply.
- \param[in] particle_reuse Allow minimum restraints to use particle
- more than once.
- */
-PairConnectivityRestraint::PairConnectivityRestraint(Model* model,
- std::vector<int>& particle1_indexes, std::vector<int>& particle2_indexes,
- FloatKey attr_name, BasicScoreFuncParams* score_func_params,
- const int num_to_apply, const bool particle_reuse)
-{
- particle_reuse_ = particle_reuse;
- num_to_apply_ = num_to_apply;
- set_up(model, particle1_indexes, particle2_indexes);
-
- // get the indexes associated with the restraints
- int idx = 0;
- Float actual_mean;
-
- // use iterator to move through each predefined position in the
- // restraint/score list
- std::list<PairConnectivityRestraint::RestraintScore>::iterator rs_iter;
- rs_iter = rsr_scores_.begin();
- // particles from list 1
- for (int i = 0; i < num_particles1_; i++) {
- // particles from list 2
- for (int j = num_particles1_; j < num_particles_; j++) {
- // Use those radii to calculate the expected distance
- Float attri, attrj;
- attri = get_particle(i)->get_value(attr_name);
- attrj = get_particle(j)->get_value(attr_name);
- actual_mean = attri + attrj;
-
- score_func_params->set_mean(actual_mean);
-
- // create the restraint
- if (rs_iter == rsr_scores_.end()) {
- IMP_failure("Reached end of rsr_scores too early.",
- ValueException("Reached end of rsr_scores too early"));
- } else {
- IMP_LOG(VERBOSE, "Adding possible restraint: " << i << " " << j);
- UnaryFunction *sf = score_func_params->create_score_func();
- rs_iter->rsr_ = new DistanceRestraint(get_particle(i),
- get_particle(j),
- sf);
-
- rs_iter->part1_idx_ = i;
- rs_iter->part2_idx_ = j;
- }
-
- ++rs_iter;
- }
- }
-
- IMP_LOG(VERBOSE, idx <<
- " num_restraints_: " << num_restraints_ << " num_particles1_: " <<
- num_particles1_ << " num_particles2_:" << num_particles2_
- << std::endl);
-}
-
-
-//! Internal set up for the constructors.
-/** \param[in] model Pointer to the model.
- \param[in] particle1_indexes Vector of indexes of particles in first body
- of the restraint.
- \param[in] particle2_indexes Vector of indexes of particles in second body
- of the restraint.
- */
-void PairConnectivityRestraint::set_up(Model* model,
- std::vector<int>& particle1_indexes,
- std::vector<int>& particle2_indexes)
-{
- Particle* p1;
-
- IMP_LOG(VERBOSE, "init ConnectivityRestraint");
-
- //model_data_ = model.get_model_data();
-
- /** number of particles in the restraint */
- num_particles1_ = particle1_indexes.size();
- num_particles2_ = particle2_indexes.size();
- num_particles_ = num_particles1_ + num_particles2_;
-
- IMP_LOG(VERBOSE, "set up particle types");
- // set up the particles, their position indexes, and their type indexes
- for (int i = 0; i < num_particles1_; i++) {
- p1 = model->get_particle(particle1_indexes[i]);
- add_particle(p1);
- }
-
- for (int i = 0; i < num_particles2_; i++) {
- p1 = model->get_particle(particle2_indexes[i]);
- add_particle(p1);
- }
-
- // figure out how many restraints there are
- num_restraints_ = num_particles1_ * num_particles2_;
-
- // use number of restraints and number of types to set up some of the
- // ... main arrays
- used_.resize(num_particles_);
- rsr_scores_.resize(num_restraints_);
-}
-
-//! Destructor
-PairConnectivityRestraint::~PairConnectivityRestraint()
-{
- std::list<PairConnectivityRestraint::RestraintScore>::iterator rs_iter;
-
- for (rs_iter = rsr_scores_.begin(); rs_iter != rsr_scores_.end(); ++rs_iter) {
- delete(rs_iter->rsr_);
- }
-}
-
-
-//! Evaluate the restraint for the current model state.
-/** Calculate the distance restraints for the given particles. Use the smallest
- restraints that will connect one particle of each type together (i.e. a
- minimum spanning tree with nodes corresponding to particle types and the
- edge weights corresponding to restraint violation scores).
-
- There is a potential when using this restraint for two large rigid bodies
- to maintain its own exclusion volume restraints. These could be calculated
- only for the particles in the neighborhoods of the particles involved in the
- activated restraints rather than between all particles in the two bodies.
- Since once restraints are activated, they tend to be activated over and
- over, the exclusion volume restraint sets should only be reset whenever
- on rare occasion the neighborhoods actually change.
-
- \param[in] accum If not NULL, use this object to accumulate partial first
- derivatives.
- \return score associated with this restraint for the given state of
- the model.
- */
-Float PairConnectivityRestraint::evaluate(DerivativeAccumulator *accum)
-{
- std::list<PairConnectivityRestraint::RestraintScore>::iterator rs_iter;
-
- IMP_LOG(VERBOSE, "evaluate PairConnectivityRestraint");
-
- // only use a particle at most once in set of restraints
- for (int i = 0; i < num_particles_; i++)
- used_[i] = false;
-
- // calculate the scores for all of the restraints
- IMP_LOG(VERBOSE, "calculate restraint scores");
- int j = 0;
- for (rs_iter = rsr_scores_.begin(); rs_iter != rsr_scores_.end(); ++rs_iter) {
- rs_iter->evaluate();
- IMP_LOG(VERBOSE, j++ << " score: " << rs_iter->score_);
- }
-
- // sort by the scores
- rsr_scores_.sort();
-
- IMP_LOG(VERBOSE, "sorted");
- j = 0;
- for (rs_iter = rsr_scores_.begin(); rs_iter != rsr_scores_.end(); ++rs_iter) {
- IMP_LOG(VERBOSE, j++ << " score: " << rs_iter->score_);
- }
-
- Float score = 0.0;
- rs_iter = rsr_scores_.begin();
- int num_applied = 0;
- for (int i = 0; num_applied < num_to_apply_ && rs_iter != rsr_scores_.end();
- ++i) {
- if (particle_reuse_ || (!used_[rs_iter->part1_idx_]
- && !used_[rs_iter->part2_idx_])) {
- used_[rs_iter->part1_idx_] = true;
- used_[rs_iter->part2_idx_] = true;
- score += rs_iter->rsr_->evaluate(accum);
- num_applied++;
- }
-
- ++rs_iter;
- }
-
- return score;
-}
-
-
-//! Show the current restraint.
-/** \param[in] out Stream to send restraint description to.
- */
-void PairConnectivityRestraint::show(std::ostream& out) const
-{
- if (get_is_active()) {
- out << "pair connectivity restraint (active):" << std::endl;
- } else {
- out << "pair connectivity restraint (inactive):" << std::endl;
- }
-
- get_version_info().show(out);
- out << " num particles1:" << num_particles1_;
- out << " num particles2:" << num_particles2_;
- out << " num restraints:" << num_restraints_;
- out << " num restraints to apply:" << num_to_apply_;
-}
-
-} // namespace IMP
Index: kernel/src/restraints/ExclusionVolumeRestraint.cpp
===================================================================
--- kernel/src/restraints/ExclusionVolumeRestraint.cpp (revision 441)
+++ kernel/src/restraints/ExclusionVolumeRestraint.cpp (working copy)
@@ -1,193 +0,0 @@
-/**
- * \file ExclusionVolumeRestraint.cpp \brief Excluded volume restraint.
- *
- * Prevent particles from getting too close together, by restricting the
- * minimum distance between all pairs of particles formed from one or two
- * sets of particles.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include <cmath>
-
-#include "IMP/Model.h"
-#include "IMP/Particle.h"
-#include "IMP/log.h"
-#include "IMP/restraints/ExclusionVolumeRestraint.h"
-
-namespace IMP
-{
-
-//! Set up restraint using two sets of particles.
-/** Uses the attr_name to access the radii for the minimum distance between
- any two particles. Assumes that there is no overlap between the two
- particle lists. Create restraints for all possible pairs between the
- two lists.
-
- \param[in] model Pointer to the model.
- \param[in] particle1_indexes Vector of indexes of particles of the
- first body.
- \param[in] particle2_indexes Vector of indexes of particles of the
- second body.
- \param[in] attr_name The attribute used to determine the radius of
- each particle.
- \param[in] score_func_params Scoring function parameters.
- */
-ExclusionVolumeRestraint::ExclusionVolumeRestraint(Model* model,
- std::vector<int>& particle1_indexes, std::vector<int>& particle2_indexes,
- FloatKey attr_name, BasicScoreFuncParams* score_func_params)
-{
- Particle* p1;
-
- num_particles1_ = particle1_indexes.size();
- num_particles2_ = particle2_indexes.size();
- num_particles_ = num_particles1_ + num_particles2_;
- for (int i = 0; i < num_particles1_; i++) {
- p1 = model->get_particle(particle1_indexes[i]);
- add_particle(p1);
- }
-
- for (int i = 0; i < num_particles2_; i++) {
- p1 = model->get_particle(particle2_indexes[i]);
- add_particle(p1);
- }
-
- num_restraints_ = num_particles1_ * num_particles2_;
-
- // get the indexes associated with the restraints
- Float actual_mean;
- IMP_LOG(VERBOSE, "Add inter-body exclusion volume restraints "
- << num_restraints_);
-
- // particle 1 indexes
- for (int i = 0; i < num_particles1_; i++) {
- // particle 2 indexes
- for (int j = num_particles1_; j < num_particles_; j++) {
- // Use those radii to calculate the expected distance
- Float attri, attrj;
- attri = get_particle(i)->get_value(attr_name);
- attrj = get_particle(j)->get_value(attr_name);
- actual_mean = attri + attrj;
-
- score_func_params->set_mean(actual_mean);
-
- // create the restraint
- UnaryFunction *sf = score_func_params->create_score_func();
- dist_rsrs_.push_back(new DistanceRestraint(get_particle(i),
- get_particle(j),
- sf));
- }
- }
-}
-
-
-//! Set up restraint using one set of particles.
-/** Uses the attr_name to access the radii for the minimum distance between
- any two particles. Create restraints for all possible pairs of particles
- in the list.
-
- \param[in] model Pointer to the model.
- \param[in] particle_indexes Vector of indexes of particles
- \param[in] attr_name The attribute used to determine the radius of
- each particle.
- \param[in] score_func_params Scoring function parameters.
- */
-ExclusionVolumeRestraint::ExclusionVolumeRestraint(Model* model,
- std::vector<int>& particle_indexes, FloatKey attr_name,
- BasicScoreFuncParams* score_func_params)
-{
- Particle* p1;
-
- num_particles_ = particle_indexes.size();
- for (int i = 0; i < num_particles_; i++) {
- p1 = model->get_particle(particle_indexes[i]);
- add_particle(p1);
- }
-
- num_restraints_ = num_particles_ * (num_particles_ - 1) / 2;
-
- // get the indexes associated with the restraints
- int idx = 0;
- Float actual_mean;
- IMP_LOG(VERBOSE, "Add intra-body exclusion volume restraints "
- << num_restraints_);
-
- // particle 1 indexes
- for (int i = 0; i < num_particles_ - 1; i++) {
- // particle 2 indexes (avoid duplicates and particle with itself)
- for (int j = i + 1; j < num_particles_; j++) {
- // Use those radii to calculate the expected distance
- Float attri, attrj;
- attri = get_particle(i)->get_value(attr_name);
- attrj = get_particle(j)->get_value(attr_name);
- actual_mean = attri + attrj;
-
- score_func_params->set_mean(actual_mean);
-
- // create the restraint
- UnaryFunction *sf = score_func_params->create_score_func();
- dist_rsrs_.push_back(new DistanceRestraint(get_particle(i),
- get_particle(j),
- sf));
- idx++;
- }
- }
-}
-
-
-//! Destructor
-ExclusionVolumeRestraint::~ExclusionVolumeRestraint()
-{
- std::vector<DistanceRestraint*>::iterator rsr_iter;
-
- for (rsr_iter = dist_rsrs_.begin(); rsr_iter != dist_rsrs_.end();
- ++rsr_iter) {
- delete(*rsr_iter);
- }
-}
-
-
-//! Get the score of the restraint for the model.
-/** Calculate the distance restraints for the given particles. Use the smallest
- restraints that will connect one particle of each type together (i.e. a
- minimum spanning tree with nodes corresponding to particle types and the
- edge weights corresponding to restraint violation scores).
-
- \param[in] accum If not NULL, use this object to accumulate partial first
- derivatives.
- \return score associated with this restraint for the given state of
- the model.
- */
-Float ExclusionVolumeRestraint::evaluate(DerivativeAccumulator *accum)
-{
- std::vector<DistanceRestraint*>::iterator rsr_iter;
-
- Float score = 0.0;
-
- // until this is smarter, just calculate them all
- for (rsr_iter = dist_rsrs_.begin(); rsr_iter != dist_rsrs_.end();
- ++rsr_iter) {
- score += (*rsr_iter)->evaluate(accum);
- }
-
- return score;
-}
-
-
-//! Show the current restraint.
-/** \param[in] out Stream to send restraint description to.
- */
-void ExclusionVolumeRestraint::show(std::ostream& out) const
-{
- if (get_is_active()) {
- out << "exclusion volume restraint (active):" << std::endl;
- } else {
- out << "exclusion volume restraint (inactive):" << std::endl;
- }
-
- get_version_info().show(out);
- out << " num particles:" << num_particles_;
-}
-
-} // namespace IMP
Index: kernel/src/BasicScoreFuncParams.cpp
===================================================================
--- kernel/src/BasicScoreFuncParams.cpp (revision 441)
+++ kernel/src/BasicScoreFuncParams.cpp (working copy)
@@ -1,76 +0,0 @@
-/**
- * \file BasicScoreFuncParams.cpp \brief Factory for creating UnaryFunctions.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include "IMP/ScoreFuncParams.h"
-#include "IMP/unary_functions/Harmonic.h"
-#include "IMP/unary_functions/HarmonicLowerBound.h"
-#include "IMP/unary_functions/HarmonicUpperBound.h"
-#include "IMP/log.h"
-
-namespace IMP
-{
-
-//! Constructor
-BasicScoreFuncParams::BasicScoreFuncParams(std::string score_func_type,
- Float mean, Float sd)
-{
- mean_ = mean;
- sd_ = sd;
- score_func_type_ = score_func_type;
-}
-
-
-//! Destructor
-BasicScoreFuncParams::~BasicScoreFuncParams()
-{
-}
-
-
-//! Set the mean to use in calculating this score function.
-/** \param[in] mean Value for the mean.
- */
-void BasicScoreFuncParams::set_mean(Float mean)
-{
- mean_ = mean;
-}
-
-//! Set the standard deviation to use in calculating this score function.
-/** \param[in] sd Value for the standard deviation.
- */
-void BasicScoreFuncParams::set_sd(Float sd)
-{
- sd_ = sd;
-}
-
-//! Set the type of score function to use.
-/** \param[in] score_func_type Name of the score function type
- */
-void BasicScoreFuncParams::set_score_func_type(std::string score_func_type)
-{
- score_func_type_ = score_func_type;
-}
-
-
-//! Create a new score function with the current set of parameters.
-/** \return pointer to score function.
- */
-UnaryFunction* BasicScoreFuncParams::create_score_func()
-{
- if (score_func_type_ == "harmonic") {
- return new Harmonic(mean_, sd_);
- } else if (score_func_type_ == "harmonic_lower_bound") {
- return new HarmonicLowerBound(mean_, sd_);
- } else if (score_func_type_ == "harmonic_upper_bound") {
- return new HarmonicUpperBound(mean_, sd_);
- }
-
- IMP_check(0, "Unknown score function: " << score_func_type_,
- ValueException("Unknown score function"));
- return NULL;
-}
-
-} // namespace IMP
Index: kernel/pyext/IMP/xml_loader.py
===================================================================
--- kernel/pyext/IMP/xml_loader.py (revision 441)
+++ kernel/pyext/IMP/xml_loader.py (working copy)
@@ -1,542 +0,0 @@
-import xml.dom.minidom
-import IMP
-import IMP.utils
-
-class MalformedError(Exception):
- """Exception class for malformed XML data"""
- pass
-
-def load_imp_model(model, xml_file_path, base_particle = 0):
- """ Load imp model from given xml file """
- doc = xml.dom.minidom.parse(xml_file_path)
-
- # there should only be a single imp node, but just in case ...
- for head in doc.childNodes:
- if (head.nodeName == 'imp'):
- for n in head.childNodes:
- # process particle set nodes
- if n.nodeName == 'particles':
- load_particles(model, n, base_particle)
-
- # process restraint set nodes
- elif n.nodeName == 'restraint_set':
- load_restraint_set(model, n, base_particle)
-
- return doc
-
-
-def load_particles(model, particles_node, base_particle):
- """ Load particles from the DOM """
- # save particle pointers to prevent destructors from running
- try:
- model.particles
- except AttributeError:
- model.particles = []
- model.num_particles = 0
-
- # process individual particle nodes
- for part in particles_node.childNodes:
- if (part.nodeName == 'particle'):
- load_particle(model, part, base_particle)
-
-
-def load_particle(model, particle_node, base_particle):
- """ Load particle from the DOM """
- id = particle_node.getAttribute('id')
- model.particles.append(IMP.utils.XYZParticle(model))
- p_idx = len(model.particles)-1
-
- # process particle attributes
- for attr in particle_node.childNodes:
- if attr.nodeName == 'float':
- load_float(model, p_idx, attr)
-
- elif attr.nodeName == 'int':
- load_int(model, p_idx, attr)
-
- elif attr.nodeName == 'string':
- load_string(model, p_idx, attr)
-
-
-def load_float(model, p_idx, attr_node):
- """ Load float attribute from the DOM and add it to the particle """
- name = attr_node.getAttribute('name')
- p = model.particles[p_idx]
-
- # defaults
- optimize = True
- value = 0.0
- for n in attr_node.childNodes:
- if n.nodeName == 'optimize':
- optimize = (n.childNodes[0].nodeValue == 'T')
-
- if n.nodeName == 'value':
- value = n.childNodes[0].nodeValue
-
- p.add_attribute(IMP.FloatKey(str(name)), float(value), bool(optimize))
-
-
-def load_int(model, p_idx, attr_node):
- """ Load int attribute from the DOM and add it to the particle """
- name = attr_node.getAttribute('name')
- p = model.particles[p_idx]
-
- # defaults
- value = 0
- for n in attr_node.childNodes:
- if n.nodeName == 'value':
- value = n.childNodes[0].nodeValue
- p.add_attribute(IMP.IntKey(str(name)), int(value))
-
-
-def load_string(model, p_idx, attr_node):
- """ Load string attribute from the DOM and add it to the particle """
- name = attr_node.getAttribute('name')
- p = model.particles[p_idx]
-
- # defaults
- value = ""
- for n in attr_node.childNodes:
- if n.nodeName == 'value':
- value = n.childNodes[0].nodeValue
-
- p.add_attribute(IMP.StringKey(name), str(value))
-
-
-def load_restraint_set(model, restraint_set_node, base_particle):
- """ Load restraint set from the DOM """
-
- # save pointers to prevent destructors from running
- try:
- model.restraint_sets
- except AttributeError:
- model.restraint_sets = []
-
- try:
- model.restraints
- except AttributeError:
- model.restraints = []
-
- try:
- model.score_funcs
- except AttributeError:
- model.score_funcs = {}
-
- # get restraint set parameters
- name = str(restraint_set_node.getAttribute('name'))
- model.restraint_sets.append(IMP.RestraintSet(name))
- rs_idx = len(model.restraint_sets) - 1
- model.add_restraint(model.restraint_sets[rs_idx])
-
- # process restraints in subnodes
- for r in restraint_set_node.childNodes:
- if (r.nodeName == 'distance_restraint'):
- load_rsr_distance(model, rs_idx, r, base_particle)
-
- elif (r.nodeName == 'torus_restraint'):
- load_rsr_torus(model, rs_idx, r, base_particle)
-
- elif (r.nodeName == 'coordinate_restraint'):
- load_rsr_coordinate(model, rs_idx, r, base_particle)
-
- elif (r.nodeName == 'connectivity_restraint'):
- load_rsr_connectivity(model, rs_idx, r, base_particle)
-
- elif (r.nodeName == 'pair_connectivity_restraint'):
- load_rsr_pair_connectivity(model, rs_idx, r, base_particle)
-
- elif (r.nodeName == 'proximity_restraint'):
- load_rsr_proximity(model, rs_idx, r, base_particle)
-
- elif (r.nodeName == 'exclusion_volume_restraint'):
- load_rsr_exclusion_volume(model, rs_idx, r, base_particle)
-
- elif (r.nodeName == 'exclusion_volume_restraint'):
- load_rsr_exclusion_volume(model, rs_idx, r, base_particle)
-
-
-def load_rsr_distance(model, rs_idx, rsr, base_particle):
- """Load distance restraint from the DOM"""
-
- # process restraint parameters
-
- # defaults
- distance_attribute = ''
- distance = None
- sd = 0.1
- score_func_str = None
-
- # get the parameters
- for param in rsr.childNodes:
- if param.nodeName == 'particle_pairs':
- particle_pairs = _get_particle_pairs(param)
-
- elif param.nodeName == 'distance':
- distance = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'sd':
- sd = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'distance_attribute':
- distance_attribute = str(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'score_func':
- score_func_str = str(param.childNodes[0].nodeValue)
-
- # make sure we have the needed parameters
- if score_func_str == None:
- raise MalformedError("No score function specified.")
-
- if distance == None and distance_attribute == '':
- raise MalformedError("No distance specified.")
-
- # add restraint for each particle pair in the list
- for pair in particle_pairs:
- p1 = model.particles[int(pair[0])]
- p2 = model.particles[int(pair[1])]
- if distance_attribute != '':
- distance = p1.get_value(IMP.FloatKey(distance_attribute)) \
- + p2.get_value(IMP.FloatKey(distance_attribute))
-
- score_func_params = get_basic_score_func_params(score_func_str, distance, sd)
- sf = score_func_params.create_score_func()
- model.restraints.append(IMP.DistanceRestraint(p1, p2, sf))
- model.restraint_sets[rs_idx].add_restraint(model.restraints[-1])
-
-
-def load_rsr_torus(model, rs_idx, rsr, base_particle):
- """Load torus restraint from the DOM"""
-
- # process restraint parameters
-
- # defaults
- distance_attribute = ''
- sd = 0.1
- tube_radius = 5.0
- main_radius = 20.0
- score_func_str = None
-
- # get the parameters
- for param in rsr.childNodes:
- if param.nodeName == 'particle_list':
- particle_list = _get_particle_list(param)
-
- elif param.nodeName == 'main_radius':
- main_radius = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'tube_radius':
- tube_radius = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'sd':
- sd = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'score_func':
- score_func_str = str(param.childNodes[0].nodeValue)
-
- # make sure we have the needed parameters
- if score_func_str == None:
- raise MalformedError("No score function specified.")
-
- # add restraint for each particle in the list
- for p_idx in particle_list:
- p = model.particles[int(p_idx)]
- score_func_params = get_basic_score_func_params(score_func_str, 0.0, sd)
- sf = score_func_params.create_score_func()
- model.restraints.append(IMP.TorusRestraint(p, main_radius,
- tube_radius, sf))
- model.restraint_sets[rs_idx].add_restraint(model.restraints[-1])
-
-
-def load_rsr_coordinate(model, rs_idx, rsr, base_particle):
- """Load coordinate restraint from the DOM"""
- print "Load coordinate restraint"
-
- # process restraint parameters
-
- # defaults
- axis = 'X_AXIS'
- sd = 0.1
- distance = 10.0
- score_func_str = None
-
- # get the parameters
- for param in rsr.childNodes:
- if param.nodeName == 'particle_list':
- particle_list = _get_particle_list(param)
-
- elif param.nodeName == 'axis_type':
- axis = str(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'distance':
- distance = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'sd':
- sd = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'score_func':
- score_func_str = str(param.childNodes[0].nodeValue)
-
- # make sure we have the needed parameters
- if score_func_str == None:
- raise MalformedError("No score function specified.")
-
- # add restraint for each particle in the list
- for p_idx in particle_list:
- p = model.particles[int(p_idx)]
- score_func_params = get_basic_score_func_params(score_func_str, distance, sd)
- model.restraints.append(IMP.CoordinateRestraint(model, p, axis, score_func_params))
- model.restraint_sets[rs_idx].add_restraint(model.restraints[-1])
-
-
-def load_rsr_connectivity(model, rs_idx, rsr, base_particle):
- """Load connectivity restraint from the DOM"""
- print "Load connectivity restraint"
-
- # process restraint parameters
-
- # defaults
- distance_attribute = ''
- type_attribute = 'protein'
- distance = None
- sd = 0.1
- score_func_str = None
-
- # get the parameters
- for param in rsr.childNodes:
- if param.nodeName == 'particle_list':
- particle_list = _get_particle_list(param)
-
- elif param.nodeName == 'distance':
- distance = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'sd':
- sd = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'distance_attribute':
- distance_attribute = str(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'type_attribute':
- type_attribute = str(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'score_func':
- score_func_str = str(param.childNodes[0].nodeValue)
-
- # make sure we have the needed parameters
- if score_func_str == None:
- raise MalformedError("No score function specified.")
-
- # make sure we have the needed parameters
- if distance == None and distance_attribute == '':
- raise MalformedError("No distance specified.")
-
- # create a vector of particle indexes
- particle_indexes = IMP.Ints()
- for p_idx in particle_list:
- particle_indexes.push_back(int(p_idx))
-
- # add restraint for for vector of particles
- if distance_attribute:
- score_func_params = get_basic_score_func_params(score_func_str, 0.0, sd)
- model.restraints.append(IMP.ConnectivityRestraint(model, particle_indexes, type_attribute, distance_attribute, score_func_params))
- model.restraint_sets[rs_idx].add_restraint(model.restraints[-1])
- else:
- score_func_params = get_basic_score_func_params(score_func_str, distance, sd)
- model.restraints.append(IMP.ConnectivityRestraint(model, particle_indexes, type_attribute, score_func_params))
- model.restraint_sets[rs_idx].add_restraint(model.restraints[-1])
-
-
-def load_rsr_pair_connectivity(model, rs_idx, rsr, base_particle):
- """Load pair connectivity restraint from the DOM"""
- print "Load pair connectivity restraint"
-
- # process restraint parameters
-
- # defaults
- distance_attribute = ''
- distance = None
- sd = 0.1
- score_func_str = None
- num_lists = 0
- number_of_connects = 1
-
- # get the parameters
- for param in rsr.childNodes:
- if num_lists == 0 and param.nodeName == 'particle_list':
- particle_list1 = _get_particle_list(param)
- num_lists = 1
-
- elif param.nodeName == 'particle_list':
- particle_list2 = _get_particle_list(param)
-
- elif param.nodeName == 'distance':
- distance = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'sd':
- sd = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'distance_attribute':
- distance_attribute = str(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'score_func':
- score_func_str = str(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'number_of_connects':
- number_of_connects = int(param.childNodes[0].nodeValue)
-
- # make sure we have the needed parameters
- if distance == None and distance_attribute == '':
- raise MalformedError("No distance specified.")
-
- # make sure we have the needed parameters
- if score_func_str == None:
- raise MalformedError("No score function specified.")
-
- # create a vector of particle indexes
- particle_indexes1 = IMP.Ints()
- particle_indexes1.clear()
- for p_idx in particle_list1:
- particle_indexes1.push_back(int(p_idx))
-
- particle_indexes2 = IMP.Ints()
- particle_indexes2.clear()
- for p_idx in particle_list2:
- particle_indexes2.push_back(int(p_idx))
-
- # add restraint for for vector of particles
- if distance_attribute:
- score_func_params = get_basic_score_func_params(score_func_str, 0.0, sd)
- r = IMP.PairConnectivityRestraint(model, particle_indexes1, particle_indexes2, distance_attribute, score_func_params, number_of_connects)
- model.restraints.append(r)
- model.restraint_sets[rs_idx].add_restraint(r)
- else:
- score_func_params = get_basic_score_func_params(score_func_str, distance, sd)
- r = IMP.PairConnectivityRestraint(model, particle_indexes1, particle_indexes2, score_func_params, number_of_connects)
- model.restraints.append(r)
- model.restraint_sets[rs_idx].add_restraint(r)
-
-
-def load_rsr_proximity(model, rs_idx, rsr, base_particle):
- """Load proximity restraint from the DOM"""
- print "Load proximity restraint"
-
- # process restraint parameters
-
- # defaults
- distance = 5.0
- sd = 0.1
- score_func_str = None
-
- # get the parameters
- for param in rsr.childNodes:
- if param.nodeName == 'particle_list':
- particle_list = _get_particle_list(param)
-
- elif param.nodeName == 'distance':
- distance = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'sd':
- sd = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'score_func':
- score_func_str = str(param.childNodes[0].nodeValue)
-
- # make sure we have the needed parameters
- if score_func_str == None:
- raise MalformedError("No score function specified.")
-
- # create a vector of particle indexes
- particle_indexes = IMP.Ints()
- for p_idx in particle_list:
- particle_indexes.push_back(int(p_idx))
-
- # add restraint for for vector of particles
- score_func_params = get_basic_score_func_params(score_func_str, 0.0, sd)
- model.restraints.append(IMP.ProximityRestraint(model, particle_indexes, distance, score_func_params))
- model.restraint_sets[rs_idx].add_restraint(model.restraints[-1])
-
-
-
-def load_rsr_exclusion_volume(model, rs_idx, rsr, base_particle):
- """Load exclusion volume restraint from the DOM"""
- print "Load exclusion volume restraint"
-
- # defaults
- distance_attribute = ''
- sd = 0.1
- num_lists = 0
-
- # get the parameters
- for param in rsr.childNodes:
- if num_lists == 0 and param.nodeName == 'particle_list':
- particle_list1 = _get_particle_list(param)
- num_lists = 1
-
- elif param.nodeName == 'particle_list':
- particle_list2 = _get_particle_list(param)
- num_lists = 2
-
- elif param.nodeName == 'sd':
- sd = float(param.childNodes[0].nodeValue)
-
- elif param.nodeName == 'distance_attribute':
- distance_attribute = str(param.childNodes[0].nodeValue)
-
- # make sure we have the needed parameters
- if distance_attribute == '':
- raise MalformedError("No distance specified.")
-
- # create a vector of particle indexes
- particle_indexes1 = IMP.Ints()
- particle_indexes1.clear()
- for p_idx in particle_list1:
- particle_indexes1.push_back(int(p_idx))
-
- score_func_params = get_basic_score_func_params("harmonic_lower_bound", 0.0, sd)
- if (num_lists == 2):
- particle_indexes2 = IMP.Ints()
- particle_indexes2.clear()
- for p_idx in particle_list2:
- particle_indexes2.push_back(int(p_idx))
-
- print "adding inter particle exclusion volumes for two bodies: ", model, particle_indexes1, particle_indexes2, distance_attribute, sd
- r = IMP.ExclusionVolumeRestraint(model, particle_indexes1, particle_indexes2, distance_attribute, score_func_params)
- model.restraints.append(r)
- model.restraint_sets[rs_idx].add_restraint(r)
- else:
- print "adding intra particle exclusion volumes for one body: ", model, particle_indexes1, distance_attribute, sd
- r = IMP.ExclusionVolumeRestraint(model, particle_indexes1, distance_attribute, score_func_params)
- model.restraints.append(r)
- model.restraint_sets[rs_idx].add_restraint(r)
-
-
-
-def get_basic_score_func_params(score_func_str, mean=0.0, sd=0.1):
- """ Get score function params corresponding to the given name """
- return IMP.BasicScoreFuncParams(score_func_str, mean, sd)
-
-
-# support different ways of specifying particle pairs in the XML.
-# <pair>1 3</pair> direct entering of particle pair indexes:
-# (1, 3)
-# <all_pairs>3 4 5 6</all_pairs> all possible pairs from a list
-# (3, 4) (3, 5) (3, 6) (4, 5) (4, 6) (5, 6)
-def _get_particle_pairs(pairs_node):
- """ Get a list of all particle pairs specified by the given node """
- pairs = []
- for pair_node in pairs_node.childNodes:
- if pair_node.nodeName == 'pair':
- pairs.append(str(pair_node.childNodes[0].nodeValue).split())
-
- if pair_node.nodeName == 'all_pairs':
- list = _get_particle_list(pair_node)
- for i in range(0, len(list)-1):
- for j in range(i+1, len(list)):
- pairs.append((i, j))
-
- return pairs
-
-
-# <particle_list>3 4 5 6</particle_list> list (3, 4, 5, 6)
-def _get_particle_list(particle_list_node):
- """ Get a list of all particles specified by the given node """
- return str(particle_list_node.childNodes[0].nodeValue).split()