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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 CREATE_VIZ_WINDOW to see animated window of simulation
// undefine for automated nightly builds
// #define CREATE_VIZ_WINDOW
int main() {
//try
// {
Element e;
e = Element::Argon();
// cout << "Element=" << e << endl;
AliphaticCarbon ac;
// cout << "AliphaticCarbon " << ac << endl;
MethylGroup methyl;
// cout << "Methyl " << methyl << endl;
Methane methane1;
// cout << "Methane=" << methane1 << endl;
Methane methane2;
Ethane ethane1;
Ethane ethane2;
Ethane ethane3;
ethane1.setDefaultTorsionAngle(55*Deg2Rad);
// cout << "Ethane=" << ethane << endl;
// cout << " default torsion angle=" << ethane.getDefaultTorsionAngle() << endl;
AminoAcidResidue::Serine serine;
AminoAcidResidue::Alanine alanine1;
// AminoAcidResidue::Alanine alanine2;
// cout << "Alanine = " << alanine1 << endl;
//cout << "PROTEIN=" << protein << endl;
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem dumm(system);
DecorationSubsystem decorations(system);
// system.adoptCompound(methane1);
// system.adoptCompound(ethane1);
// system.adoptCompound(alanine1);
// system.adoptCompound(alanine1);
// system.adoptCompound(ethane2);
// system.adoptCompound(ethane3);
// system.adoptCompound(methane2);
// system.adoptCompound(protein);
// system.adoptCompound(alanine1);
// system.adoptCompound(alanine2);
dumm.loadAmber99Parameters();
//ifstream tinkerStream("../../resources/tinker_amber99_clean.prm");
//dumm.populateFromTinkerParameterFile(tinkerStream);
//tinkerStream.close();
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());
// Complete C-terminal group
// alanine1.bondAtom(UnivalentAtom("2OXT", Element::Oxygen()), "bondC", 0.1250);
// alanine1.nameAtom("1OXT", "O");
// Add one more hydrogen to nitrogen to create unnatural 3-body cluster
// alanine1.convertInboardBondCenterToOutboard();
// alanine1.bondAtom(UnivalentAtom("2HN", Element::Hydrogen()), "bondN", 0.1010);
// build acetyl alanine
//AminoAcidResidue::Alanine alanine1;
alanine1.assignBiotypes();
//AcetylResidue compound1;
//compound1.assignBiotypes(Ordinality::Initial);
//compound1.bondCompound("ala1", alanine1, "bondC", 0.13350);
//system.adoptCompound(compound1);
AcetylResidue acetyl1;
acetyl1.assignBiotypes(Ordinality::Initial);
acetyl1.bondCompound("ala1", alanine1, "bondC", 0.135);
acetyl1.setBondMobility(BondMobility::Rigid, "C", "ala1/N");
// Add some more alanines to make a peptide
AminoAcidResidue::Alanine alanine2;
AminoAcidResidue::Alanine alanine3;
AminoAcidResidue::Alanine alanine4;
alanine2.assignBiotypes();
alanine3.assignBiotypes();
alanine4.assignBiotypes(Ordinality::Final);
acetyl1.bondCompound("ala2", alanine2, "ala1/bondC", 0.135);
// system.adoptCompound(acetyl1);
// serine.assignBiotypes();
// system.adoptCompound();
AminoAcidResidue::Threonine thr;
thr.assignBiotypes();
// system.adoptCompound(thr);
// Protein protein("AAAAAAAAA");
Protein protein("GPRFS");
protein.writeDefaultPdb(cout);
protein.assignBiotypes();
system.adoptCompound(protein);
// bool biotypesComplete = alanine1.assignBiotypes();
// bool biotypesComplete = alanine1.assignBiotypes(Ordinality::ANY);
// assert(biotypesComplete);
// alanine2.assignBiotypes();
cout << "Methane = " << methane1 << endl;
cout << "Ethane = " << ethane1 << endl;
cout << "Alanine = " << alanine1 << endl;
// alanine1.writeDefaultPdb(cout);
system.modelCompounds();
State state = system.realizeTopology();
#ifdef CREATE_VIZ_WINDOW
Visualizer display(system);
#endif
RungeKuttaMersonIntegrator study(system);
//CPodesIntegrator study(system);
study.initialize(state);
#ifdef CREATE_VIZ_WINDOW
display.report(study.getState());
#endif
// getchar(); // for synchronizing movie capture
// ethane.setDihedralAngle(state, "torsion", 60*DuMM::Deg2Rad);
//cout << protein.getAtomLocation(state, "0/CA") << endl;
Real timeInterval = 0.005;
for (Real time=0.0; time < (10 * timeInterval); time += timeInterval) // picoseconds
{
// std::cout << "Ethane torsion angle = " << DuMM::Rad2Deg * ethane.getDihedralAngle(state, "torsion") << std::endl;
// study.stepTo(time, Infinity);
study.stepTo(time);
#ifdef CREATE_VIZ_WINDOW
display.report(study.getState());
#endif
//protein.writePdbCoordinates(state, fileName);
}
// }
//catch (const std::exception& e)
// {
// printf("EXCEPTION THROWN: %s\n", e.what());
// }
//catch (...)
// {
// printf("UNKNOWN EXCEPTION THROWN\n");
// } return 0;
}
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