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/* -------------------------------------------------------------------------- *
* SimTK Core: SimTK Molmodel *
* -------------------------------------------------------------------------- *
* This is part of the SimTK Core biosimulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2006-7 Stanford University and the Authors. *
* Authors: Christopher Bruns *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "SimTKmolmodel.h"
#include <iostream>
#include <vector>
using std::cout;
using std::endl;
using namespace SimTK;
using namespace std;
#define ASSERT(x) SimTK_ASSERT_ALWAYS(x, "Assertion failed")
// define CREATE_VIZ_WINDOW to see animated window of simulation
// undefine for automated nightly builds
// #define CREATE_VIZ_WINDOW
class Oxygen2 : public Compound {
public:
Oxygen2() {
if (! Biotype::exists("Oxygen2", "O") )
Biotype::defineBiotype(Element::getBySymbol("O"), 1, "Oxygen2", "O");
BiotypeIndex biotypeIx = Biotype::get("Oxygen2", "O").getIndex();
setBaseAtom( UnivalentAtom("O1", Element::getBySymbol("O")) );
bondAtom( UnivalentAtom("O2", Element::getBySymbol("O")), "O1/bond", 0.13);
setBiotypeIndex("O1", biotypeIx);
setBiotypeIndex("O2", biotypeIx);
}
};
void testWater() {
Compound water;
Real angle = 105 * SimTK::Deg2Rad;
Real length = 0.09;
water.setBaseAtom(BivalentAtom("O", Element::getBySymbol("O"), angle));
water.bondAtom(UnivalentAtom("H1", Element::getBySymbol("H")), "O/bond1", length);
water.bondAtom(UnivalentAtom("H2", Element::getBySymbol("H")), "O/bond2", length);
ASSERT((water.calcDefaultAtomLocationInGroundFrame("O") - Vec3(0,0,0)).norm() < 0.01);
ASSERT((water.calcDefaultAtomLocationInGroundFrame("H1") - Vec3(length,0,0)).norm() < 0.01);
ASSERT((water.calcDefaultAtomLocationInGroundFrame("H2") - Vec3(std::cos(angle)*length,std::sin(angle)*length,0)).norm() < 0.01);
water.writeDefaultPdb(std::cout);
}
int main() {
testWater();
Oxygen2 oxygen1;
oxygen1.writeDefaultPdb(std::cout);
Oxygen2 oxygen2;
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem dumm(system);
// ifstream tinkerStream("C:/cygwin/home/cmbruns/svn/molmodel/resources/tinker_amber99_clean.prm");
// dumm.populateFromTinkerParameterFile(tinkerStream);
// tinkerStream.close();
dumm.loadAmber99Parameters();
DuMM::ChargedAtomTypeIndex atomTypeId(4000);
DuMM::AtomClassIndex atomClassId(24); // carbonyl oxygen
dumm.defineChargedAtomType(atomTypeId, "Oxygen2 O", atomClassId, 0.00);
BiotypeIndex biotypeIx = Biotype::get("Oxygen2", "O").getIndex();
dumm.setBiotypeChargedAtomType(atomTypeId, biotypeIx);
dumm.defineBondStretch_KA(atomClassId, atomClassId, 570, 1.3);
system.adoptCompound(oxygen1);
system.adoptCompound(oxygen2, Vec3(0.5, 0, 0));
Methane methane;
dumm.defineChargedAtomType(DuMM::ChargedAtomTypeIndex(5000), "Methane C", DuMM::AtomClassIndex(1), 0.04);
dumm.defineChargedAtomType(DuMM::ChargedAtomTypeIndex(5001), "Methane H", DuMM::AtomClassIndex(34), -0.01);
dumm.defineChargedAtomType(DuMM::ChargedAtomTypeIndex(5002), "Ethane C", DuMM::AtomClassIndex(1), 0.03);
dumm.defineChargedAtomType(DuMM::ChargedAtomTypeIndex(5003), "Ethane H", DuMM::AtomClassIndex(34), -0.01);
dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(5000), Biotype::MethaneC().getIndex());
dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(5001), Biotype::MethaneH().getIndex());
dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(5002), Biotype::EthaneC().getIndex());
dumm.setBiotypeChargedAtomType(DuMM::ChargedAtomTypeIndex(5003), Biotype::EthaneH().getIndex());
system.adoptCompound(methane, Vec3(0, 0.5, 0));
system.modelCompounds();
State state = system.realizeTopology();
system.realize(state, Stage::Position);
oxygen1.writePdb(state, std::cout);
#ifdef CREATE_VIZ_WINDOW
Visualizer display(system, 0.1);
#endif
RungeKuttaMersonIntegrator study(system);
study.initialize(state);
#ifdef CREATE_VIZ_WINDOW
display.report(study.getState());
#endif
Real timeInterval = 0.05;
for (Real time=0.0; time < (10 * timeInterval); time += timeInterval) // picoseconds
{
study.stepTo(time);
#ifdef CREATE_VIZ_WINDOW
display.report(study.getState());
#endif
}
}
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