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#include "SimTKmolmodel.h"
#include "molmodel/internal/VanderWallSphere.h"
#include "molmodel/internal/PeriodicVmdReporter.h"
#include <iostream>
#include <exception>
#include <fstream>
using namespace SimTK;
using namespace std;
class PeriodicTorsionMeasurer : public PeriodicEventReporter {
public:
PeriodicTorsionMeasurer(
std::vector<Angle>& torsions,
const Compound& compound,
const char* atom1Name,
const char* atom2Name,
const char* atom3Name,
const char* atom4Name,
Real interval)
: PeriodicEventReporter(interval),
torsions(torsions),
compound(compound),
atom1Index( compound.getAtomIndex(atom1Name) ),
atom2Index( compound.getAtomIndex(atom2Name) ),
atom3Index( compound.getAtomIndex(atom3Name) ),
atom4Index( compound.getAtomIndex(atom4Name) )
{
}
void handleEvent(const State& state) const
{
Vec3 p1 = compound.calcAtomLocationInGroundFrame(state, atom1Index);
Vec3 p2 = compound.calcAtomLocationInGroundFrame(state, atom2Index);
Vec3 p3 = compound.calcAtomLocationInGroundFrame(state, atom3Index);
Vec3 p4 = compound.calcAtomLocationInGroundFrame(state, atom4Index);
torsions.push_back( calcDihedralAngle(p1, p2, p3, p4) );
}
private:
const Compound& compound;
Compound::AtomIndex atom1Index;
Compound::AtomIndex atom2Index;
Compound::AtomIndex atom3Index;
Compound::AtomIndex atom4Index;
std::vector<Angle>& torsions;
};
std::ostream& printHistogram(const std::vector<Angle>& torsions, std::ostream& os)
{
int nBins = 30;
std::vector<int> bin(nBins);
// initialize counts to zero
for (int b = 0; b < nBins; ++b) bin[b] = 0;
// accumulate counts
Angle binWidth = 360.0 / nBins;
int maxBinSize = 0;
for (size_t t = 0; t < torsions.size(); ++t)
{
Angle torsion = torsions[t] * Rad2Deg;
while (torsion < 0) torsion += 360.0;
while (torsion >= 360.0) torsion -= 360.0;
int binNumber = static_cast<int>((torsion / 360.0) * nBins);
++bin[binNumber];
if (bin[binNumber] > maxBinSize) maxBinSize = bin[binNumber];
}
// print histogram
// counts per hash mark
float poundSize = maxBinSize / 40.0f;
for (int b = 0; b < nBins; ++b)
{
os << setw(6) << fixed << setprecision(1) << b * binWidth;
os << " -- ";
os << setw(6) << fixed << setprecision(1) << (b + 1) * binWidth;
os << " ";
os << setw(5) << bin[b];
os << " ";
for (int h = 0; h < (int)(bin[b] / poundSize); ++h )
os << "#";
os << std::endl;
}
return os;
}
int main() { try
{
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem dumm(system);
// Atom classes are available, but not charged atom types for ethane
// in standard Amber force field
dumm.loadAmber99Parameters();
GeneralForceSubsystem forces(system);
// Sulfur vdw params are 0.2 nm, 1.046
VanderWallSphere boundary(forces, dumm, Vec3(0,0,0), 1.00, 0.2, 1.046);
if (! Biotype::exists("ethane", "C"))
Biotype::defineBiotype(Element::getBySymbol("C"), 4, "ethane", "C");
if (! Biotype::exists("ethane", "H"))
Biotype::defineBiotype(Element::getBySymbol("H"), 1, "ethane", "H");
dumm.defineChargedAtomType(
DuMM::ChargedAtomTypeIndex(5000),
"ethane C",
DuMM::AtomClassIndex(1), // "CT" type in amber
-0.060 // made up
);
dumm.setBiotypeChargedAtomType( DuMM::ChargedAtomTypeIndex(5000), Biotype::get("ethane", "C").getIndex() );
dumm.defineChargedAtomType(
DuMM::ChargedAtomTypeIndex(5001),
"ethane H",
DuMM::AtomClassIndex(34), // "HC" type in amber
0.020 // made up, use net neutral charge
);
dumm.setBiotypeChargedAtomType( DuMM::ChargedAtomTypeIndex(5001), Biotype::get("ethane", "H").getIndex() );
Ethane ethane1, ethane2;
ethane2.setPdbResidueNumber(2);
// place first ethane, units are nanometers
// skew it a little to break strict symmetry
system.adoptCompound(ethane1, Transform(Vec3(-0.5, 0, 0)) * Transform(Rotation(0.1, YAxis)) );
// place second ethane, units are nanometers
system.adoptCompound(ethane2, Vec3( 0.5, 0, 0));
// Write PDB coordinates to the screen
/*
system.addEventReporter(new PeriodicPdbWriter(system, std::cout, 0.050));
/* */
system.addEventHandler(
new VelocityRescalingThermostat(system, 5000.0, 0.100));
std::vector<Angle> torsions;
system.addEventReporter(
new PeriodicTorsionMeasurer(torsions, ethane1, "H1", "C1", "C2", "H4", 0.030) );
// Send coordinates to VMD visualization program
/*
system.addEventReporter(
new PeriodicVmdReporter(system, 0.008, 3001, true) );
/* */
system.modelCompounds(); // finalize multibody system
State state = system.realizeTopology();
// Simulate it.
VerletIntegrator integ(system);
TimeStepper ts(system, integ);
ts.initialize(state);
ts.stepTo(0.200);
printHistogram(torsions, cerr);
return 0;
}
catch(const std::exception& e) {
std::cerr << "ERROR: " << e.what() << std::endl;
return 1;
}
catch(...) {
std::cerr << "ERROR: An unknown exception was raised" << std::endl;
return 1;
}
}
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