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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 19 28.165 29.227 23.618 1.00 91.78 N\n"
"ATOM 2 CA HIS 19 27.004 29.173 22.731 1.00 91.74 C\n"
"ATOM 3 C HIS 19 26.321 27.818 22.666 1.00 81.05 C\n"
"ATOM 4 O HIS 19 25.105 27.739 22.805 1.00 89.56 O\n"
"ATOM 5 CB HIS 19 27.248 29.629 21.270 1.00 98.21 C\n"
"ATOM 6 CG HIS 19 27.954 30.936 21.082 1.00100.00 C\n"
"ATOM 7 ND1 HIS 19 28.852 31.112 20.015 1.00100.00 N\n"
"ATOM 8 CD2 HIS 19 27.882 32.111 21.798 1.00100.00 C\n"
"ATOM 9 CE1 HIS 19 29.310 32.368 20.116 1.00100.00 C\n"
"ATOM 10 NE2 HIS 19 28.753 32.997 21.176 1.00100.00 N\n"
"ATOM 11 N SER 20 27.057 26.778 22.303 1.00 58.48 N\n"
"ATOM 12 CA SER 20 26.412 25.501 22.190 1.00 45.35 C\n"
"ATOM 13 C SER 20 26.089 24.909 23.558 1.00 30.40 C\n"
"ATOM 14 O SER 20 26.808 25.067 24.542 1.00 29.60 O\n"
"ATOM 15 CB SER 20 27.206 24.513 21.344 1.00 49.69 C\n"
"ATOM 16 OG SER 20 26.466 23.310 21.049 1.00 22.13 O\n"
"END\n";
std::istringstream inStream(inputPdb);
PdbStructure pdbStructure(inStream);
Protein protein("HS");
protein.writeDefaultPdb(cout); // OK
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);
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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