Modified the API for lots of classes so that the number of...

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.

openmmapi/include/GBSAOBCForce.h

@@ -41,6 +41,12 @@ namespace OpenMM {
 /**
  * This class implements an implicit solvation force using the GBSA-OBC model.
  * <p>
+ * To use this class, create a GBSAOBCForce object, then call addParticle() once for each particle in the
+ * System to define its parameters.  The number of particles for which you define GBSA parameters must
+ * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
+ * try to create an OpenMMContext.  After a particle has been added, you can modify its force field parameters
+ * by calling setParticleParameters().
+ * <p>
  * If the System also contains a NonbondedForce, this force will use the cutoffs
  * and periodic boundary conditions specified in it.
  */
@@ -49,16 +55,23 @@ class OPENMM_EXPORT GBSAOBCForce : public Force {
 public:
     /*
      * Create a GBSAOBCForce.
-     * 
-     * @param numParticles    the number of particles in the system
      */
-    GBSAOBCForce(int numParticles);
+    GBSAOBCForce();
     /**
      * Get the number of particles in the system.
      */
     int getNumParticles() const {
         return particles.size();
     }
+    /**
+     * Add the GBSA parameters for a particle.  This should be called once for each particle
+     * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
+     *
+     * @param charge         the charge of the particle, measured in units of the proton charge
+     * @param radius         the GBSA radius of the particle, measured in nm
+     * @param scalingFactor  the OBC scaling factor for the particle
+     */
+    void addParticle(double charge, double radius, double scalingFactor);
     /**
      * Get the force field parameters for a particle.
      * 
@@ -129,6 +142,9 @@ public:
     ParticleInfo() {
         charge = radius = scalingFactor = 0.0;
     }
+    ParticleInfo(double charge, double radius, double scalingFactor) :
+        charge(charge), radius(radius), scalingFactor(scalingFactor) {
+    }
 };
 
 } // namespace OpenMM

openmmapi/include/GBVIForce.h

@@ -41,6 +41,12 @@ namespace OpenMM {
 /**
  * This class implements an implicit solvation force using the GB/VI model.
  * <p>
+ * To use this class, create a GBVIForce object, then call addParticle() once for each particle in the
+ * System to define its parameters.  The number of particles for which you define GB/VI parameters must
+ * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
+ * try to create an OpenMMContext.  After a particle has been added, you can modify its force field parameters
+ * by calling setParticleParameters().
+ * <p>
  * If the System also contains a NonbondedForce, this force will use the cutoffs
  * and periodic boundary conditions specified in it.
  */
@@ -49,16 +55,23 @@ class OPENMM_EXPORT GBVIForce : public Force {
 public:
     /*
      * Create a GBVIForce.
-     * 
-     * @param numParticles    the number of particles in the system
      */
-    GBVIForce(int numParticles);
+    GBVIForce();
     /**
      * Get the number of particles in the system.
      */
     int getNumParticles() const {
         return particles.size();
     }
+    /**
+     * Add the GB/VI parameters for a particle.  This should be called once for each particle
+     * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
+     *
+     * @param charge         the charge of the particle, measured in units of the proton charge
+     * @param radius         the GB/VI radius of the particle, measured in nm
+     * @param gamma          the gamma parameter
+     */
+    void addParticle(double charge, double radius, double gamma);
     /**
      * Get the force field parameters for a particle.
      * 
@@ -129,6 +142,9 @@ public:
     ParticleInfo() {
         charge = radius = gamma = 0.0;
     }
+    ParticleInfo(double charge, double radius, double gamma) :
+        charge(charge), radius(radius), gamma(gamma) {
+    }
 };
 
 } // namespace OpenMM

openmmapi/include/HarmonicAngleForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,24 +42,32 @@ namespace OpenMM {
 
 /**
  * This class implements an interaction between groups of three particles that varies harmonically with the angle
- * between them.  When creating a HarmonicAngleForce, you specify the number of angle as an argument to the
- * constructor, then loop over them and call setAngleParameters() to set the force field parameters for each one.
+ * between them.  To use it, create a HarmonicAngleForce object then call addAngle() once for each angle.  After
+ * an angle has been added, you can modify its force field parameters by calling setAngleParameters().
  */
 
 class OPENMM_EXPORT HarmonicAngleForce : public Force {
 public:
     /**
      * Create a HarmonicAngleForce.
-     * 
-     * @param numAngles           the number of harmonic bond angle terms in the potential function
      */
-    HarmonicAngleForce(int numAngles);
+    HarmonicAngleForce();
     /**
      * Get the number of harmonic bond angle terms in the potential function
      */
     int getNumAngles() const {
         return angles.size();
     }
+    /**
+     * Add an angle term to the force field.
+     *
+     * @param particle1 the index of the first particle forming the angle
+     * @param particle2 the index of the second particle forming the angle
+     * @param particle3 the index of the third particle forming the angle
+     * @param length    the equilibrium angle, measured in radians
+     * @param k         the harmonic force constant for the angle
+     */
+    void addAngle(int particle1, int particle2, int particle3, double angle, double k);
     /**
      * Get the force field parameters for an angle term.
      * 
@@ -109,6 +117,9 @@ public:
         particle1 = particle2 = particle3 = -1;
         angle = k = 0.0;
     }
+    AngleInfo(int particle1, int particle2, int particle3, double angle, double k) :
+        particle1(particle1), particle2(particle2), particle3(particle3), angle(angle), k(k) {
+    }
 };
 
 } // namespace OpenMM

openmmapi/include/HarmonicBondForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,24 +42,31 @@ namespace OpenMM {
 
 /**
  * This class implements an interaction between pairs of particles that varies harmonically with the distance
- * between them.  When creating a HarmonicBondForce, you specify the number of bonds as an argument to the
- * constructor, then loop over them and call setBondParameters() to set the force field parameters for each one.
+ * between them.  To use it, create a HarmonicBondForce object then call addBond() once for each bond.  After
+ * a bond has been added, you can modify its force field parameters by calling setBondParameters().
  */
 
 class OPENMM_EXPORT HarmonicBondForce : public Force {
 public:
     /**
      * Create a HarmonicBondForce.
-     * 
-     * @param numBonds            the number of harmonic bond stretch terms in the potential function
      */
-    HarmonicBondForce(int numBonds);
+    HarmonicBondForce();
     /**
      * Get the number of harmonic bond stretch terms in the potential function
      */
     int getNumBonds() const {
         return bonds.size();
     }
+    /**
+     * Add a bond term to the force field.
+     *
+     * @param particle1 the index of the first particle connected by the bond
+     * @param particle2 the index of the second particle connected by the bond
+     * @param length    the equilibrium length of the bond, measured in nm
+     * @param k         the harmonic force constant for the bond
+     */
+    void addBond(int particle1, int particle2, double length, double k);
     /**
      * Get the force field parameters for a bond term.
      * 
@@ -107,6 +114,9 @@ public:
         particle1 = particle2 = -1;
         length = k = 0.0;
     }
+    BondInfo(int particle1, int particle2, double length, double k) :
+        particle1(particle1), particle2(particle2), length(length), k(k) {
+    }
 };
 
 } // namespace OpenMM

openmmapi/include/PeriodicTorsionForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,24 +42,34 @@ namespace OpenMM {
 
 /**
  * This class implements an interaction between groups of four particles that varies periodically with the torsion angle
- * between them.  When creating a PeriodicTorsionForce, you specify the number of torsions as an argument to the
- * constructor, then loop over them and call setTorsionParameters() to set the force field parameters for each one.
+ * between them.  To use it, create a PeriodicTorsionForce object then call addTorsion() once for each torsion.  After
+ * a torsion has been added, you can modify its force field parameters by calling setTorsionParameters().
  */
 
 class OPENMM_EXPORT PeriodicTorsionForce : public Force {
 public:
     /**
      * Create a PeriodicTorsionForce.
-     * 
-     * @param numTorsions the number of periodic torsion terms in the potential function
      */
-    PeriodicTorsionForce(int numTorsions);
+    PeriodicTorsionForce();
     /**
      * Get the number of periodic torsion terms in the potential function
      */
     int getNumTorsions() const {
         return periodicTorsions.size();
     }
+    /**
+     * Add a periodic torsion term to the force field.
+     *
+     * @param particle1    the index of the first particle forming the torsion
+     * @param particle2    the index of the second particle forming the torsion
+     * @param particle3    the index of the third particle forming the torsion
+     * @param particle3    the index of the fourth particle forming the torsion
+     * @param periodicity  the periodicity of the torsion
+     * @param phase        the phase offset of the torsion, measured in radians
+     * @param k            the force constant for the torsion
+     */
+    void addTorsion(int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k);
     /**
      * Get the force field parameters for a periodic torsion term.
      * 
@@ -114,6 +124,9 @@ public:
         periodicity = 1;
         phase = k = 0.0;
     }
+    PeriodicTorsionInfo(int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k) :
+        particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4), periodicity(periodicity), phase(phase), k(k) {
+    }
 };
 
 } // namespace OpenMM

openmmapi/include/RBTorsionForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,25 +42,37 @@ namespace OpenMM {
 
 /**
  * This class implements an interaction between groups of four particles that varies with the torsion angle between them
- * according to the Ryckaert-Bellemans potential.  When creating an RBTorsionForce, you specify the number of torsions
- * as an argument to the constructor, then loop over them and call setTorsionParameters() to set the force field
- * parameters for each one.
+ * according to the Ryckaert-Bellemans potential.  To use it, create an RBTorsionForce object then call addTorsion() once
+ * for each torsion.  After a torsion has been added, you can modify its force field parameters by calling setTorsionParameters().
  */
 
 class OPENMM_EXPORT RBTorsionForce : public Force {
 public:
     /**
      * Create a RBTorsionForce.
-     * 
-     * @param numTorsions the number of torsion terms in the potential function
      */
-    RBTorsionForce(int numTorsions);
+    RBTorsionForce();
     /**
      * Get the number of Ryckaert-Bellemans torsion terms in the potential function
      */
     int getNumTorsions() const {
         return rbTorsions.size();
     }
+    /**
+     * Add a Ryckaert-Bellemans torsion term to the force field.
+     *
+     * @param particle1    the index of the first particle forming the torsion
+     * @param particle2    the index of the second particle forming the torsion
+     * @param particle3    the index of the third particle forming the torsion
+     * @param particle3    the index of the fourth particle forming the torsion
+     * @param c0           the coefficient of the constant term
+     * @param c1           the coefficient of the 1st order term
+     * @param c2           the coefficient of the 2nd order term
+     * @param c3           the coefficient of the 3rd order term
+     * @param c4           the coefficient of the 4th order term
+     * @param c5           the coefficient of the 5th order term
+     */
+    void addTorsion(int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5);
     /**
      * Get the force field parameters for a Ryckaert-Bellemans torsion term.
      * 
@@ -120,6 +132,15 @@ public:
         particle1 = particle2 = particle3 = particle4 = -1;
         c[0] = c[1] = c[2] = c[3] = c[4] = c[5] = 0.0;
     }
+    RBTorsionInfo(int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5) :
+            particle1(particle1), particle2(particle2), particle3(particle3), particle4(particle4) {
+        c[0] = c0;
+        c[1] = c1;
+        c[2] = c2;
+        c[3] = c3;
+        c[4] = c4;
+        c[5] = c5;
+    }
 };
 
 } // namespace OpenMM

openmmapi/include/System.h

@@ -49,20 +49,18 @@ class OPENMM_EXPORT Force;
  * <li>Pairs of particles whose separation should be constrained to a fixed value</li>
  * </ol>
  * 
- * The particles and constraints are defined directly by the System object.
- * The forces are defined by objects that extend the Force class.  The System
- * stores a list of Force objects that determine the motion of the particles.
+ * The particles and constraints are defined directly by the System object, while
+ * forces are defined by objects that extend the Force class.  After creating a
+ * System, call addParticle() once for each particle, addConstraint() for each constraint,
+ * and addForce() for each Force.
  */
 
 class OPENMM_EXPORT System {
 public:
     /**
      * Create a new System.
-     * 
-     * @param numParticles   the number of particles in the System
-     * @param numConstraints the number of distance constraints in the System.
      */
-    System(int numParticles, int numConstraints);
+    System();
     ~System();
     /**
      * Get the number of particles in this System.
@@ -70,6 +68,14 @@ public:
     int getNumParticles() const {
         return masses.size();
     }
+    /**
+     * Add a particle to the System.
+     *
+     * @param mass   the mass of the particle (in atomic mass units)
+     */
+    void addParticle(double mass) {
+        masses.push_back(mass);
+    }
     /**
      * Get the mass (in atomic mass units) of a particle.
      * 
@@ -93,6 +99,14 @@ public:
     int getNumConstraints() const {
         return constraints.size();
     }
+    /**
+     * Add a constraint to the System.
+     *
+     * @param particle1 the index of the first particle involved in the constraint
+     * @param particle2 the index of the second particle involved in the constraint
+     * @param distance  the required distance between the two particles, measured in nm
+     */
+    void addConstraint(int particle1, int particle2, double distance);
     /**
      * Get the parameters defining a distance constraint.
      * 
@@ -170,6 +184,9 @@ public:
         particle1 = particle2 = -1;
         distance = 0.0;
     }
+    ConstraintInfo(int particle1, int particle2, double distance) :
+        particle1(particle1), particle2(particle2), distance(distance) {
+    }
 };
 
 } // namespace OpenMM

openmmapi/src/GBSAOBCForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,11 @@
 
 using namespace OpenMM;
 
-GBSAOBCForce::GBSAOBCForce(int numParticles) : particles(numParticles), solventDielectric(78.3), soluteDielectric(1.0) {
+GBSAOBCForce::GBSAOBCForce() : solventDielectric(78.3), soluteDielectric(1.0) {
+}
+
+void GBSAOBCForce::addParticle(double charge, double radius, double scalingFactor) {
+    particles.push_back(ParticleInfo(charge, radius, scalingFactor));
 }
 
 void GBSAOBCForce::getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const {

openmmapi/src/GBSAOBCForceImpl.cpp

@@ -29,6 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "OpenMMException.h"
 #include "internal/GBSAOBCForceImpl.h"
 #include "internal/OpenMMContextImpl.h"
 #include "kernels.h"
@@ -42,6 +43,8 @@ GBSAOBCForceImpl::GBSAOBCForceImpl(GBSAOBCForce& owner) : owner(owner) {
 
 void GBSAOBCForceImpl::initialize(OpenMMContextImpl& context) {
     kernel = context.getPlatform().createKernel(CalcGBSAOBCForceKernel::Name(), context);
+    if (owner.getNumParticles() != context.getSystem().getNumParticles())
+        throw OpenMMException("GBSAOBCForce must have exactly as many particles as the System it belongs to.");
     dynamic_cast<CalcGBSAOBCForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 

openmmapi/src/GBVIForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,11 @@
 
 using namespace OpenMM;
 
-GBVIForce::GBVIForce(int numParticles) : particles(numParticles), solventDielectric(78.3), soluteDielectric(1.0) {
+GBVIForce::GBVIForce() : solventDielectric(78.3), soluteDielectric(1.0) {
+}
+
+void GBVIForce::addParticle(double charge, double radius, double gamma) {
+    particles.push_back(ParticleInfo(charge, radius, gamma));
 }
 
 void GBVIForce::getParticleParameters(int index, double& charge, double& radius, double& gamma) const {

openmmapi/src/GBVIForceImpl.cpp

@@ -44,6 +44,8 @@ GBVIForceImpl::GBVIForceImpl(GBVIForce& owner) : owner(owner) {
 
 void GBVIForceImpl::initialize(OpenMMContextImpl& context) {
     kernel = context.getPlatform().createKernel(CalcGBVIForceKernel::Name(), context);
+    if (owner.getNumParticles() != context.getSystem().getNumParticles())
+        throw OpenMMException("GBVIForce must have exactly as many particles as the System it belongs to.");
 
     // load 1-2 atom pairs along w/ bond distance using HarmonicBondForce & constraints
     

openmmapi/src/HarmonicAngleForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,11 @@
 
 using namespace OpenMM;
 
-HarmonicAngleForce::HarmonicAngleForce(int numAngles) : angles(numAngles) {
+HarmonicAngleForce::HarmonicAngleForce() {
+}
+
+void HarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double angle, double k) {
+    angles.push_back(AngleInfo(particle1, particle2, particle3, angle, k));
 }
 
 void HarmonicAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& angle, double& k) const {

openmmapi/src/HarmonicBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,11 @@
 
 using namespace OpenMM;
 
-HarmonicBondForce::HarmonicBondForce(int numBonds) : bonds(numBonds) {
+HarmonicBondForce::HarmonicBondForce() {
+}
+
+void HarmonicBondForce::addBond(int particle1, int particle2, double length, double k) {
+    bonds.push_back(BondInfo(particle1, particle2, length, k));
 }
 
 void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const {

openmmapi/src/PeriodicTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,11 @@
 
 using namespace OpenMM;
 
-PeriodicTorsionForce::PeriodicTorsionForce(int numTorsions) : periodicTorsions(numTorsions) {
+PeriodicTorsionForce::PeriodicTorsionForce() {
+}
+
+void PeriodicTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k) {
+    periodicTorsions.push_back(PeriodicTorsionInfo(particle1, particle2, particle3, particle4, periodicity, phase, k));
 }
 
 void PeriodicTorsionForce::getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& periodicity, double& phase, double& k) const {

openmmapi/src/RBTorsionForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,7 +36,11 @@
 
 using namespace OpenMM;
 
-RBTorsionForce::RBTorsionForce(int numTorsions) : rbTorsions(numTorsions) {
+RBTorsionForce::RBTorsionForce() {
+}
+
+void RBTorsionForce::addTorsion(int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5) {
+    rbTorsions.push_back(RBTorsionInfo(particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5));
 }
 
 void RBTorsionForce::getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& c0, double& c1, double& c2, double& c3, double& c4, double& c5) const {

openmmapi/src/System.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,9 +34,7 @@
 
 using namespace OpenMM;
 
-System::System(int numParticles, int numConstraints) : masses(numParticles), constraints(numConstraints), forces(0) {
-    for (int i = 0; i < numParticles; ++i)
-        masses[i] = 0.0;
+System::System() {
 }
 
 System::~System() {
@@ -44,6 +42,10 @@ System::~System() {
         delete forces[i];
 }
 
+void System::addConstraint(int particle1, int particle2, double distance) {
+    constraints.push_back(ConstraintInfo(particle1, particle2, distance));
+}
+
 void System::getConstraintParameters(int index, int& particle1, int& particle2, double& distance) const {
     particle1 = constraints[index].particle1;
     particle2 = constraints[index].particle2;

platforms/brook/tests/TestBrookAngleBondForce.cpp

@@ -69,16 +69,16 @@ void testBrookAngles( FILE* log ){
    }
 
    BrookPlatform platform( 32, "cal", log );
-   System system( numberOfParticles, 0 ); 
+   System system;
+   for (int i = 0; i < numberOfParticles; i++)
+       system.addParticle(1.0);
    LangevinIntegrator integrator( 0, 0.1, 0.01 );
 
-   // int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
+   HarmonicAngleForce* forceField = new HarmonicAngleForce();
 
-   HarmonicAngleForce* forceField = new HarmonicAngleForce(2);
-
-   // int index, int atom1, int atom2, int atom3, double angle, double k
-   forceField->setAngleParameters(0, 0, 1, 2, PI_M/3, 1.1);
-   forceField->setAngleParameters(1, 1, 2, 3, PI_M/2, 1.2);
+   // int atom1, int atom2, int atom3, double angle, double k
+   forceField->addAngle(0, 1, 2, PI_M/3, 1.1);
+   forceField->addAngle(1, 2, 3, PI_M/2, 1.2);
    system.addForce(forceField);
 
    OpenMMContext context(system, integrator, platform);

platforms/brook/tests/TestBrookCMMotionRemover.cpp

@@ -82,15 +82,15 @@ void testMotionRemoval( FILE* log ) {
    //ReferencePlatform platform;
    BrookPlatform platform( 32, "cal", log );
 
-   System system( numberOfParticles, 0 );
+   System system;
    VerletIntegrator integrator(0.001);
-   HarmonicBondForce* bonds = new HarmonicBondForce(1);
-   bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
+   HarmonicBondForce* bonds = new HarmonicBondForce();
+   bonds->addBond(2, 3, 2.0, 0.5);
    system.addForce(bonds);
 
    NonbondedForce* nonbonded = new NonbondedForce();
    for (int i = 0; i < numberOfParticles; ++i) {
-       system.setParticleMass(i, (double) (i+1) );
+       system.addParticle((double) (i+1) );
        nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(nonbonded);

platforms/brook/tests/TestBrookHarmonicBondForce.cpp

@@ -64,16 +64,18 @@ void testBrookBonds( FILE* log ){
    }
 
    BrookPlatform platform( 32, "cal", log );
-   System system( numberOfParticles, 0 ); 
+   System system;
+   for (int i = 0; i < numberOfParticles; i++)
+       system.addParticle(1.0);
    LangevinIntegrator integrator(0, 0.1, 0.01);
 
    // int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
 
-   HarmonicBondForce* forceField = new HarmonicBondForce( 2 ); 
+   HarmonicBondForce* forceField = new HarmonicBondForce(); 
 
    // ( index, atom1, atom2, length, k )
-   forceField->setBondParameters(0, 0, 1, 1.5, 0.8);
-   forceField->setBondParameters(1, 1, 2, 1.2, 0.7);
+   forceField->addBond(0, 1, 1.5, 0.8);
+   forceField->addBond(1, 2, 1.2, 0.7);
    system.addForce(forceField);
 
    OpenMMContext context(system, integrator, platform);

platforms/brook/tests/TestBrookLangevinIntegrator.cpp

@@ -79,17 +79,17 @@ static OpenMMContext* testLangevinSingleBondSetup( int brookContext, LangevinInt
       platform = new ReferencePlatform();
    }
 
-   System* system = new System( numberOfParticles, 0);
-   system->setParticleMass(0, mass );
-   system->setParticleMass(1, mass );
+   System* system = new System;
+   system->addParticle(mass);
+   system->addParticle(mass);
 
    // double temperature, double frictionCoeff, double stepSize
    LangevinIntegrator* integrator = new LangevinIntegrator(0, 0.1, 0.001);
    integrator->setConstraintTolerance(1e-5);
    *outIntegrator                 = integrator;
 
-   HarmonicBondForce* forceField  = new HarmonicBondForce(1);
-   forceField->setBondParameters(0, 0, 1, 1.5, 1);
+   HarmonicBondForce* forceField  = new HarmonicBondForce();
+   forceField->addBond(0, 1, 1.5, 1);
    system->addForce(forceField);
 
    OpenMMContext* context         = new OpenMMContext( *system, *integrator, *platform );
@@ -215,11 +215,11 @@ void testLangevinTemperature( FILE* log ){
    BrookPlatform platform( 32, "cal", log );
    //ReferencePlatform platform;
 
-   System system(numberOfParticles, 0);
+   System system;
    LangevinIntegrator integrator(temp, 0.2, 0.002);
    NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numberOfParticles; ++i){
-      system.setParticleMass(i, mass );
+      system.addParticle(mass);
       forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
@@ -312,16 +312,16 @@ void testLangevinConstraints( FILE* log ){
    const int numConstraints = 4;
    const double temp        = 100.0;
    // ReferencePlatform platform;
-   System system( numParticles, numConstraints );
+   System system;
    LangevinIntegrator integrator( temp, 2.0, 0.001 );
    integrator.setConstraintTolerance(1e-5);
    NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numParticles; ++i) {
-       system.setParticleMass(i, mass);
+       system.addParticle(mass);
        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
    }
    for (int i = 0; i < numConstraints; ++i){
-       system.setConstraintParameters(i, 2*i, 2*i+1, 1.0);
+       system.addConstraint(2*i, 2*i+1, 1.0);
    }
    system.addForce(forceField);