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#include "molmodel/internal/Compound.h"
#include "SimTKmolmodel.h"
#include "molmodel/internal/Pdb.h"
#include <iostream>
#include <fstream>
#include <string>
#include <ctime>
using namespace SimTK;
using namespace std;
void testExactMatch(const std::string& pdbFileName)
{
time_t startTime = time(NULL);
// In order for Biotypes to work correctly,
// amber99 parameters must be loaded first?
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem forces(system);
forces.loadAmber99Parameters();
cout << "Loading Structure from File..." << endl;
std::ifstream pdbInputStream(pdbFileName.c_str());
assert(pdbInputStream.is_open());
// Check speed of various pdb file matching operations
PdbStructure inputPdbStructure(pdbInputStream, PdbStructure::InputType::PDB);
pdbInputStream.close();
time_t endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Creating internal coordinate model..." << endl;
RNA rna(inputPdbStructure);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Noting target atom locations..." << endl;
Compound::AtomTargetLocations atomTargets =
rna.createAtomTargets(inputPdbStructure);
cout << atomTargets.size() << " matches found" << endl;
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Matching chirality..." << endl;
double myMaxObservedSinePlaneDeviation;
rna.matchDefaultAtomChirality(atomTargets,myMaxObservedSinePlaneDeviation, 0.01);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Matching bond angles..." << endl;
rna.matchDefaultBondAngles(atomTargets);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Matching bond lengths..." << endl;
rna.matchDefaultBondLengths(atomTargets);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Matching dihedral angles..." << endl;
rna.matchDefaultDihedralAngles(atomTargets, Compound::DistortPlanarBonds);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Matching top level transform..." << endl;
rna.matchDefaultTopLevelTransform(atomTargets);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Creating simbody system..." << endl;
system.adoptCompound(rna);
rna.assignBiotypes();
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Creating multibody model..." << endl;
system.modelCompounds();
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Writing PDB file" << endl;
PdbStructure outputPdbStructure(rna);
std::ofstream pdbOutputStream("test1.pdb");
outputPdbStructure.write(pdbOutputStream);
pdbOutputStream.close();
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Done." << endl;
}
void testIdealizedMatch(const std::string& pdbFileName)
{
time_t startTime = time(NULL);
// In order for Biotypes to work correctly,
// amber99 parameters must be loaded first?
CompoundSystem system;
SimbodyMatterSubsystem matter(system);
DuMMForceFieldSubsystem forces(system);
forces.loadAmber99Parameters();
cout << "Loading Structure from File..." << endl;
std::ifstream pdbInputStream(pdbFileName.c_str());
assert(pdbInputStream.is_open());
// Check speed of various pdb file matching operations
PdbStructure inputPdbStructure(pdbInputStream, PdbStructure::InputType::PDB);
pdbInputStream.close();
time_t endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Creating internal coordinate model..." << endl;
RNA rna(inputPdbStructure);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Noting target atom locations..." << endl;
Compound::AtomTargetLocations atomTargets =
rna.createAtomTargets(inputPdbStructure);
cout << atomTargets.size() << " matches found" << endl;
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Matching chirality..." << endl;
double myMaxObservedSinePlaneDeviation;
rna.matchDefaultAtomChirality(atomTargets,myMaxObservedSinePlaneDeviation, 90*Deg2Rad);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Matching dihedral angles..." << endl;
rna.matchDefaultDihedralAngles(atomTargets, Compound::KeepPlanarBonds);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Matching top level transform..." << endl;
rna.matchDefaultTopLevelTransform(atomTargets);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Final fitting..." << endl;
rna.fitDefaultConfiguration(atomTargets, 0.005);
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Creating simbody system..." << endl;
system.adoptCompound(rna);
rna.assignBiotypes();
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Creating multibody model..." << endl;
system.modelCompounds();
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Writing PDB file" << endl;
PdbStructure outputPdbStructure(rna);
std::ofstream pdbOutputStream("test2.pdb");
outputPdbStructure.write(pdbOutputStream);
pdbOutputStream.close();
endTime = time(NULL);
cout << endTime - startTime << " s elapsed time" << endl;
startTime = endTime;
cout << "Done." << endl;
}
int main(int argc, char *argv[])
{
// PDB file name is required as argument
assert(argc > 1);
const std::string pdbFileName(argv[1]);
testExactMatch(pdbFileName);
testIdealizedMatch(pdbFileName);
}
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