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/* -------------------------------------------------------------------------- *
* SimTK Core: SimTK Simbody(tm) *
* -------------------------------------------------------------------------- *
* 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 "molmodel/internal/Pdb.h"
#include <sstream>
using namespace SimTK;
using namespace std;
int main() {
try
{
// TODO - this should be a very small protein
// Use slight modifications of default configuration to test the import of state
String inputPdb = ""
"ATOM 1 N HIS A 19 28.165 29.227 23.618 1.00 91.78 N\n"
"ATOM 2 CA HIS A 19 27.004 29.173 22.731 1.00 91.74 C\n"
"ATOM 3 C HIS A 19 26.321 27.818 22.666 1.00 81.05 C\n"
"ATOM 4 O HIS A 19 25.105 27.739 22.805 1.00 89.56 O\n"
"ATOM 5 CB HIS A 19 27.248 29.629 21.270 1.00 98.21 C\n"
"ATOM 6 CG HIS A 19 27.954 30.936 21.082 1.00100.00 C\n"
"ATOM 7 ND1 HIS A 19 28.852 31.112 20.015 1.00100.00 N\n"
"ATOM 8 CD2 HIS A 19 27.882 32.111 21.798 1.00100.00 C\n"
"ATOM 9 CE1 HIS A 19 29.310 32.368 20.116 1.00100.00 C\n"
"ATOM 10 NE2 HIS A 19 28.753 32.997 21.176 1.00100.00 N\n"
"ATOM 11 N SER A 20 27.057 26.778 22.303 1.00 58.48 N\n"
"ATOM 12 CA SER A 20 26.412 25.501 22.190 1.00 45.35 C\n"
"ATOM 13 C SER A 20 26.089 24.909 23.558 1.00 30.40 C\n"
"ATOM 14 O SER A 20 26.808 25.067 24.542 1.00 29.60 O\n"
"ATOM 15 CB SER A 20 27.206 24.513 21.344 1.00 49.69 C\n"
"ATOM 16 OG SER A 20 26.466 23.310 21.049 1.00 22.13 O\n"
"END\n";
std::istringstream inStream(inputPdb);
PdbStructure pdbStructure(inStream, PdbStructure::InputType::PDB);
Protein protein("HS");
protein.setPdbChainId("A");
protein.updResidue(ResidueInfo::Index(1)).setPdbResidueNumber(19);
protein.updResidue(ResidueInfo::Index(2)).setPdbResidueNumber(20);
Compound::AtomTargetLocations atomTargets = protein.createAtomTargets(pdbStructure);
SimTK_ASSERT_ALWAYS(atomTargets.size() == 16, "Wrong number of atoms used for matching");
protein.writeDefaultPdb(cout);
// Four steps to a perfect match
protein.matchDefaultBondLengths(atomTargets);
protein.matchDefaultBondAngles(atomTargets);
protein.matchDefaultDihedralAngles(atomTargets);
protein.matchDefaultTopLevelTransform(atomTargets);
Real residual = protein.getTransformAndResidual(atomTargets).residual;
cout << "residual = " << residual << " nanometers" << endl;
SimTK_ASSERT_ALWAYS(residual < 0.02, "Structure matching was too inaccurate");
protein.writeDefaultPdb(cout, protein.getTopLevelTransform());
cout << "PASSED" << endl;
return 0;
}
catch (const std::exception& e)
{
printf("EXCEPTION THROWN: %s\n", e.what());
}
catch (...)
{
printf("UNKNOWN EXCEPTION THROWN\n");
} return 0;
}
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