Merge pull request #1252 from peastman/localcoords

Added missing support for LocalCoordinatesSite

wrappers/python/simtk/openmm/app/modeller.py

@@ -1007,6 +1007,15 @@ class Modeller(object):
                                         v2 = templateAtomPositions[site.atoms[2]] - templateAtomPositions[site.atoms[0]]
                                         cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0])
                                         position = templateAtomPositions[site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
+                                    elif site.type == 'localCoords':
+                                        origin = templateAtomPositions[site.atoms[0]]*site.originWeights[0] + templateAtomPositions[site.atoms[1]]*site.originWeights[1] + templateAtomPositions[site.atoms[2]]*site.originWeights[2];
+                                        xdir = templateAtomPositions[site.atoms[0]]*site.xWeights[0] + templateAtomPositions[site.atoms[1]]*site.xWeights[1] + templateAtomPositions[site.atoms[2]]*site.xWeights[2];
+                                        ydir = templateAtomPositions[site.atoms[0]]*site.yWeights[0] + templateAtomPositions[site.atoms[1]]*site.yWeights[1] + templateAtomPositions[site.atoms[2]]*site.yWeights[2];
+                                        zdir = Vec3(xdir[1]*ydir[2]-xdir[2]*ydir[1], xdir[2]*ydir[0]-xdir[0]*ydir[2], xdir[0]*ydir[1]-xdir[1]*ydir[0])
+                                        xdir /= norm(xdir);
+                                        zdir /= norm(zdir);
+                                        ydir = Vec3(zdir[1]*xdir[2]-zdir[2]*xdir[1], zdir[2]*xdir[0]-zdir[0]*xdir[2], zdir[0]*xdir[1]-zdir[1]*xdir[0])
+                                        position = origin + xdir*site.localPos[0] + ydir*site.localPos[1] + zdir*site.localPos[2];
                             if position is None and atom.type in drudeTypeMap:
                                 # This is a Drude particle.  Put it on top of its parent atom.
 

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -279,7 +279,7 @@ class SwigInputBuilder:
             self.fOut.write(",\n         OpenMM::%s" % name)
         self.fOut.write(");\n\n")
 
-        self.fOut.write("%factory(OpenMM::VirtualSite& OpenMM::System::getVirtualSite, OpenMM::TwoParticleAverageSite, OpenMM::ThreeParticleAverageSite, OpenMM::OutOfPlaneSite);\n\n")
+        self.fOut.write("%factory(OpenMM::VirtualSite& OpenMM::System::getVirtualSite, OpenMM::TwoParticleAverageSite, OpenMM::ThreeParticleAverageSite, OpenMM::OutOfPlaneSite, OpenMM::LocalCoordinatesSite);\n\n")
         self.fOut.write("\n")
 
     def writeGlobalConstants(self):

wrappers/python/tests/TestModeller.py

@@ -923,10 +923,73 @@ class TestModeller(unittest.TestCase):
             self.assertEqual(1, len(ep))
 
 
+    def test_addVirtualSites(self):
+        """Test adding extra particles defined by virtual sites."""
+        xml = """
+            <ForceField>
+             <AtomTypes>
+              <Type name="C" class="C" element="C" mass="10"/>
+              <Type name="N" class="N" element="N" mass="10"/>
+              <Type name="O" class="O" element="O" mass="10"/>
+              <Type name="V" class="V" mass="0.0"/>
+             </AtomTypes>
+             <Residues>
+              <Residue name="Test">
+               <Atom name="C" type="C"/>
+               <Atom name="N" type="N"/>
+               <Atom name="O" type="O"/>
+               <Atom name="V1" type="V"/>
+               <Atom name="V2" type="V"/>
+               <Atom name="V3" type="V"/>
+               <Atom name="V4" type="V"/>
+               <VirtualSite type="average2" index="3" atom1="0" atom2="1" weight1="0.7" weight2="0.3"/>
+               <VirtualSite type="average3" index="4" atom1="0" atom2="1" atom3="2" weight1="0.2" weight2="0.3" weight3="0.5"/>
+               <VirtualSite type="outOfPlane" index="5" atom1="0" atom2="1" atom3="2" weight12="0.1" weight13="-0.2" weightCross="0.8"/>
+               <VirtualSite type="localCoords" index="6" atom1="0" atom2="1" atom3="2" wo1="0.1" wo2="0.5" wo3="0.4" wx1="1" wx2="-0.6" wx3="-0.4" wy1="0.1" wy2="0.9" wy3="-1" p1="-0.5" p2="0.4" p3="1.1"/>
+              </Residue>
+             </Residues>
+            </ForceField>"""
+        ff = ForceField(StringIO(xml))
+
+        # Create the three real atoms.
+
+        topology = Topology()
+        chain = topology.addChain()
+        residue = topology.addResidue('Test', chain)
+        topology.addAtom('C', element.carbon, residue)
+        topology.addAtom('N', element.nitrogen, residue)
+        topology.addAtom('V', element.oxygen, residue)
+        
+
+        # Add the virtual sites.
+
+        modeller = Modeller(topology, [Vec3(0.1, 0.2, 0.3), Vec3(1.0, 0.9, 0.8), Vec3(1.5, 1.1, 0.7)]*nanometers)
+        modeller.addExtraParticles(ff)
+        top = modeller.topology
+        pos = modeller.positions
+
+        # Check that the correct particles were added.
+
+        self.assertEqual(len(pos), 7)
+        for atom, elem in zip(top.atoms(), [element.carbon, element.nitrogen, element.oxygen, None, None, None, None]):
+            self.assertEqual(elem, atom.element)
+
+        # Check that the positions were calculated correctly.
+
+        system = ff.createSystem(top)
+        integ = VerletIntegrator(1.0)
+        context = Context(system, integ)
+        context.setPositions(pos)
+        context.computeVirtualSites()
+        state = context.getState(getPositions=True)
+        for p1, p2 in zip (pos, state.getPositions()):
+            self.assertVecAlmostEqual(p1.value_in_unit(nanometers), p2.value_in_unit(nanometers), 1e-6)
+
+
     def test_multiSiteIon(self):
         """Test adding extra particles whose positions are determined based on bonds."""
         xml = """
-<ForceField>
+            <ForceField>
              <AtomTypes>
               <Type name="Zn" class="Zn" element="Zn" mass="53.380"/>
               <Type name="DA" class="DA" mass="3.0"/>
@@ -954,7 +1017,7 @@ class TestModeller(unittest.TestCase):
               <Bond class1="DA" class2="Zn" length="0.09" k="535552.0"/>
               <Bond class1="DA" class2="DA" length="0.147" k="535552.0"/>
              </HarmonicBondForce>
-</ForceField>"""
+            </ForceField>"""
         ff = ForceField(StringIO(xml))
 
         # Create two zinc atoms.