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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;
/// Ensure that pdb coordinates of single atoms match those defined when the atom is placed
int main()
{
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem dumm(system);
dumm.loadAmber99Parameters();
MagnesiumIon m1;
MagnesiumIon::setAmberLikeParameters(dumm);
ChlorideIon c1;
ChlorideIon::setAmberLikeParameters(dumm);
Vec3 v1(0.73, -4.62, 0.001);
system.adoptCompound(m1, v1);
Vec3 v2(2, 0.00, -3.5);
system.adoptCompound(c1, Vec3(2, 0.00, -3.5));
system.modelCompounds();
State state = system.realizeTopology();
RungeKuttaMersonIntegrator study(system);
study.initialize(state);
double x, y, z;
ostringstream s4;
c1.writePdb(study.getState(), s4);
std::istringstream(s4.str().substr(30, 8)) >> x;
std::istringstream(s4.str().substr(38, 8)) >> y;
std::istringstream(s4.str().substr(46, 8)) >> z;
SimTK_ASSERT_ALWAYS( (Vec3(x, y, z) - 10*v2).scalarNormSqr() < 0.0001 ,
"Output PDB coordinates did not match input");
ostringstream s3;
c1.writeDefaultPdb(s3);
std::istringstream(s3.str().substr(30, 8)) >> x;
std::istringstream(s3.str().substr(38, 8)) >> y;
std::istringstream(s3.str().substr(46, 8)) >> z;
SimTK_ASSERT_ALWAYS( (Vec3(x, y, z) - 10*v2).scalarNormSqr() < 0.0001 ,
"Output PDB coordinates did not match input");
ostringstream s2;
m1.writePdb(study.getState(), s2);
std::istringstream(s2.str().substr(30, 8)) >> x;
std::istringstream(s2.str().substr(38, 8)) >> y;
std::istringstream(s2.str().substr(46, 8)) >> z;
SimTK_ASSERT_ALWAYS( (Vec3(x, y, z) - 10*v1).scalarNormSqr() < 0.0001 ,
"Output PDB coordinates did not match input");
ostringstream s1;
m1.writeDefaultPdb(s1);
std::istringstream(s1.str().substr(30, 8)) >> x;
std::istringstream(s1.str().substr(38, 8)) >> y;
std::istringstream(s1.str().substr(46, 8)) >> z;
SimTK_ASSERT_ALWAYS( (Vec3(x, y, z) - 10*v1).scalarNormSqr() < 0.0001 ,
"Output PDB coordinates did not match input");
}
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