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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. *
* -------------------------------------------------------------------------- */
// define CREATE_VIZ_WINDOW to see animated window of simulation
// undefine for automated nightly builds
// #define CREATE_VIZ_WINDOW
#include "SimTKmolmodel.h"
#include <iostream>
#include <vector>
using std::cout;
using std::endl;
using namespace SimTK;
using namespace std;
int main() {
AminoAcidResidue::Serine serine;
serine.writeDefaultPdb(std::cout);
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DecorationSubsystem decorations(system);
DuMMForceFieldSubsystem dumm(system);
if (!serine.assignBiotypes())
throw std::runtime_error("Failed to assign biotypes");
system.adoptCompound(serine);
// ifstream tinkerStream("C:/cygwin/home/cmbruns/svn/molmodel/resources/tinker_amber99_clean.prm");
// dumm.populateFromTinkerParameterFile(tinkerStream);
// tinkerStream.close();
dumm.loadAmber99Parameters();
system.modelCompounds();
State state = system.realizeTopology();
system.realize(state, Stage::Position);
serine.writePdb(state, std::cout);
#ifdef CREATE_VIZ_WINDOW
Visualizer viz(system);
system.addEventReporter( new Visualizer::Reporter(viz, 0.01) );
#endif
RungeKuttaMersonIntegrator study(system);
Real timeInterval = 0.005;
TimeStepper ts(system, study);
ts.initialize(state);
ts.stepTo(10 * timeInterval);
}
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