[IMP-dev] Minor patches

[Daniel Russel <>]

First, I changed vector so that it is get_magnitude rather than just 
magnitude to be consistent with the rest of IMP. I also added operator* 
for the dot product and operator- (and difference for python) since that 
is pretty standard and added a method to XYZDecorator to get a vector 
for the current position.

Second, I added a check for NaN derivative values in Particle.

Third, I added a comment about the internal checks in nonbonded list test.

Index: kernel/src/restraints/DihedralRestraint.cpp
===================================================================
--- kernel/src/restraints/DihedralRestraint.cpp	(revision 457)
+++ kernel/src/restraints/DihedralRestraint.cpp	(working copy)
@@ -58,7 +58,7 @@
   Vector3D v1 = rij.vector_product(rkj);
   Vector3D v2 = rkj.vector_product(rkl);
   Float scalar_product = v1.scalar_product(v2);
-  Float mag_product = v1.magnitude() * v2.magnitude();
+  Float mag_product = v1.get_magnitude() * v2.get_magnitude();
 
   // avoid division by zero
   Float cosangle = std::abs(mag_product) > 1e-12
@@ -86,9 +86,9 @@
     // J. Mol. Biol. 234, 751-762 (1993)
     Vector3D vijkj = rij.vector_product(rkj);
     Vector3D vkjkl = rkj.vector_product(rkl);
-    Float sijkj2 = vijkj.squared_magnitude();
-    Float skjkl2 = vkjkl.squared_magnitude();
-    Float skj = rkj.magnitude();
+    Float sijkj2 = vijkj.get_squared_magnitude();
+    Float skjkl2 = vkjkl.get_squared_magnitude();
+    Float skj = rkj.get_magnitude();
     Float rijkj = rij.scalar_product(rkj);
     Float rkjkl = rkj.scalar_product(rkl);
 
Index: kernel/include/IMP/decorators/XYZDecorator.h
===================================================================
--- kernel/include/IMP/decorators/XYZDecorator.h	(revision 457)
+++ kernel/include/IMP/decorators/XYZDecorator.h	(working copy)
@@ -82,6 +82,13 @@
                     b.get_coordinate(2) - get_coordinate(2));
   }
 
+  //! Convert it to a vector.
+  /** Somewhat suspect based on wanting a Point/Vector differentiation
+      but we don't have points*/
+  Vector3D get_vector() const {
+    return Vector3D(get_x(), get_y(), get_z());
+  }
+
   //! Get a vector containing the keys for x,y,z
   /** This is quite handy for initializing movers and things.
    */
Index: kernel/include/IMP/Vector3D.h
===================================================================
--- kernel/include/IMP/Vector3D.h	(revision 457)
+++ kernel/include/IMP/Vector3D.h	(working copy)
@@ -52,6 +52,11 @@
     return vec_[0] * vec2.vec_[0] + vec_[1] * vec2.vec_[1]
            + vec_[2] * vec2.vec_[2];
   }
+  
+  //! scalar product
+  Float operator*(const Vector3D &o) const {
+    return scalar_product(o);
+  }
 
   //! \return the vector product of two vectors.
   /** \param[in] vec2 The other vector to use in the product.
@@ -63,23 +68,33 @@
   }
 
   //! \return The square of the magnitude of this vector.
-  Float squared_magnitude() const {
+  Float get_squared_magnitude() const {
     return vec_[0] * vec_[0] + vec_[1] * vec_[1] + vec_[2] * vec_[2];
   }
 
   //! \return The magnitude of this vector.
-  Float magnitude() const {
-    return std::sqrt(squared_magnitude());
+  Float get_magnitude() const {
+    return std::sqrt(get_squared_magnitude());
   }
 
   //! \return This vector normalized to unit length.
   Vector3D get_unit_vector() const {
-    Float mag = magnitude();
+    Float mag = get_magnitude();
     // avoid division by zero
     mag = std::max(mag, static_cast<Float>(1e-12));
     return Vector3D(vec_[0] / mag, vec_[1] / mag, vec_[2] / mag);
   }
 
+  //! for C++
+  Vector3D operator-(const Vector3D &o) const {
+    return Vector3D(operator[](0)-o[0],
+                    operator[](1)-o[1],
+                    operator[](2)-o[2]);
+  }
+  //! for python
+  Vector3D difference(const Vector3D &o) const {
+    return operator-(o);
+  }
 private:
   Float vec_[3];
 };

Index: kernel/include/IMP/Particle.h
===================================================================
--- kernel/include/IMP/Particle.h	(revision 457)
+++ kernel/include/IMP/Particle.h	(working copy)
@@ -336,6 +336,7 @@
 {
   IMP_check(get_is_active(), "Do not touch inactive particles",
             InactiveParticleException());
+  IMP_assert(value==value, "Can't add NaN to derivative");
   float_indexes_.get_value(name).derivative+= da(value);
 }
 

Index: kernel/test/states/test_nonbonded_list.py
===================================================================
--- kernel/test/states/test_nonbonded_list.py	(revision 457)
+++ kernel/test/states/test_nonbonded_list.py	(working copy)
@@ -119,6 +119,8 @@
         self.assertEqual(score, 25, "Wrong score")
     def test_spheres2(self):
         """Test the nonbonded list of spheres (num pairs)"""
+        # This uses the internal checks of the nonbonded list to 
+        # verify correctness
         m= IMP.Model()
         rk= IMP.FloatKey("radius")
         for i in range(0,100):