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#include "SimTKmolmodel.h"
#include <iostream>
#include <string>
#include <stdexcept>
using namespace std;
using namespace SimTK;
void testBaseAtomTransform()
{
Compound compound;
Vec3 baseTransform(17, 0, 0);
compound.setBaseAtom( QuadrivalentAtom("A", Element::getBySymbol("C")), baseTransform );
// test initial default location
Vec3 atomLocation = compound.calcDefaultAtomLocationInGroundFrame("A");
Vec3 errorVec( baseTransform - atomLocation );
SimTK_ASSERT_ALWAYS(dot(errorVec, errorVec) < 0.1, "setBaseAtom() transform not applied correctly in default location");
SimTK_ASSERT_ALWAYS(dot(atomLocation, atomLocation) > 0.1, "setBaseAtom() transform not applied correctly in default location");
// test dynamic location
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
Amber99ForceSubsystem amber99(system);
compound.setAtomBiotype("A", "Alanine", " CA ");
system.adoptCompound(compound);
system.modelCompounds();
State state = system.realizeTopology();
system.realize(state, Stage::Position);
atomLocation = compound.calcAtomLocationInGroundFrame( state, Compound::AtomIndex(0) );
errorVec = baseTransform - atomLocation;
SimTK_ASSERT_ALWAYS(dot(errorVec, errorVec) < 0.1, "setBaseAtom() transform not applied correctly in dynamic location");
}
void testAdoptCompoundTransform()
{
Compound compound;
compound.setBaseAtom( QuadrivalentAtom("A", Element::getBySymbol("C")) );
Vec3 atomLocation = compound.calcDefaultAtomLocationInGroundFrame("A");
assert(dot(atomLocation, atomLocation) < 0.1);
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
Amber99ForceSubsystem amber99(system);
compound.setAtomBiotype("A", "Alanine", " CA ");
Vec3 adoptTransform(0, -6.8, 0);
assert(dot(adoptTransform, adoptTransform) > 0.1);
system.adoptCompound(compound, adoptTransform);
// adoptCompound(Transform) should affect default configuration too!!!
atomLocation = compound.calcDefaultAtomLocationInGroundFrame("A");
Vec3 errorVec = atomLocation - adoptTransform;
SimTK_ASSERT_ALWAYS(dot(atomLocation, atomLocation) > 0.1, "adoptCompound() transform not applied correctly in default location");
SimTK_ASSERT_ALWAYS(dot(errorVec, errorVec) < 0.1, "adoptCompound() transform not applied correctly in default location");
// test dynamic location
system.modelCompounds();
State state = system.realizeTopology();
system.realize(state, Stage::Position);
atomLocation = compound.calcAtomLocationInGroundFrame( state, Compound::AtomIndex(0) );
errorVec= adoptTransform - atomLocation;
SimTK_ASSERT_ALWAYS(dot(errorVec, errorVec) < 0.1, "adoptCompound() transform not applied correctly in dynamic location");
}
void testMatchTopLevelTransform()
{
Compound compound;
compound.setBaseAtom( QuadrivalentAtom("A", Element::getBySymbol("C")) );
Vec3 atomLocation = compound.calcDefaultAtomLocationInGroundFrame("A");
assert(dot(atomLocation, atomLocation) < 0.1);
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
Amber99ForceSubsystem amber99(system);
compound.setAtomBiotype("A", "Alanine", " CA ");
Vec3 adoptTransform(0, 0, 3.14159);
assert(dot(adoptTransform, adoptTransform) > 0.1);
system.adoptCompound(compound, adoptTransform);
Vec3 atomTarget(1.7, -3.6, 0.002);
Compound::AtomTargetLocations atomTargetLocations;
atomTargetLocations[Compound::AtomIndex(0)] = atomTarget;
// test getTransformAndResidual()
Transform transform1 = compound.getTransformAndResidual(atomTargetLocations).transform;
Vec3 errorVec = transform1 * adoptTransform - atomTarget;
SimTK_ASSERT_ALWAYS( dot(errorVec, errorVec) < 0.1, "getTransformAndResidual() got wrong answer");
// test matchDefaultTopLevelTransform()
compound.matchDefaultTopLevelTransform(atomTargetLocations);
errorVec = atomTarget - compound.calcDefaultAtomLocationInGroundFrame("A");
SimTK_ASSERT_ALWAYS( dot(errorVec, errorVec) < 0.1, "matchDefaultTopLevelTransform got wrong answer" );
}
int main()
{
try {
testBaseAtomTransform();
testAdoptCompoundTransform();
testMatchTopLevelTransform();
cout << "PASSED" << endl;
return 0;
}
catch (const std::exception& e)
{
cerr << "EXCEPTION THROWN: " << e.what() << endl;
cerr << "FAILED" << endl;
return 1;
}
catch (...)
{
cerr << "UNKNOWN EXCEPTION THROWN" << endl;
cerr << "FAILED" << endl;
return 1;
}
}
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