本文整理汇总了C++中Transforms::setTransformAllCoors方法的典型用法代码示例。如果您正苦于以下问题：C++ Transforms::setTransformAllCoors方法的具体用法？C++ Transforms::setTransformAllCoors怎么用？C++ Transforms::setTransformAllCoors使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Transforms的用法示例。
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示例1: main
int main(int argc, char *argv[]) {
time(&startTime);
Options defaults;
Options opt = parseOptions(argc, argv, defaults);
if (opt.errorFlag) {
cerr << endl;
cerr << "The program terminated with errors:" << endl;
cerr << endl;
cerr << opt.errorMessages << endl;
cerr << endl;
cerr << opt.OPerrors << endl;
usage();
exit(1);
}
/******************************************************************************
* === SYSTEM SETUP ===
******************************************************************************/
// Declare System
System sys;
// Set up Charmm System Builder
CharmmSystemBuilder CSB(sys, opt.topFile, opt.parFile, opt.solvFile);
//CharmmSystemBuilder CSB(sys, "/library/charmmTopPar/top_all22_prot.inp", "/library/charmmTopPar/par_all22_prot.inp", "/library/mslib/toppar/charmm/solvpar22.inp");
CSB.setSolvent("CHEX");
CSB.setVdwRescalingFactor(1.00);
// Read in PDB File
//if(!CSB.buildSystemFromPDB("/data00/bkmueller/gpaProject/createHelixAandB.pdb")) {
if(!CSB.buildSystemFromPDB(opt.pdbFile)) {
cerr << "Unable to build system" << endl;
exit(0);
}
// Build system
sys.buildAllAtoms();
// Add hydrogen bonds
HydrogenBondBuilder hb(sys, opt.hBondFile);
//HydrogenBondBuilder hb(sys, "/data00/bkmueller/dataFiles/hbondlist_nonCanon_adj.txt");
hb.buildInteractions(50);
// Redirect Output
string filename = opt.output;
freopen (filename.c_str(), "w", stdout);
// Set up APVs
AtomPointerVector &chainA = sys.getChain("A").getAtomPointers();
AtomPointerVector &chainB = sys.getChain("B").getAtomPointers();
/******************************************************************************
* === MONTE CARLO SET UP ===
******************************************************************************/
// Objects used for transformations
Transforms trans;
trans.setTransformAllCoors(true); // transform all coordinates (non-active rotamers)
trans.setNaturalMovements(true); // all atoms are rotated such as the total movement of the atoms is minimized
System helicalAxis;
helicalAxis.readPdb(opt.helicalAxisPdbFile);
//helicalAxis.readPdb("/data00/bkmueller/gpaProject/mutationRunWithPhiPsi/helicalAxis.pdb");
AtomPointerVector &axisA = helicalAxis.getChain("A").getAtomPointers();
AtomPointerVector &axisB = helicalAxis.getChain("B").getAtomPointers();
/******************************************************************************
* === INITIAL VARIABLE SET UP ===
******************************************************************************/
EnergySet* Eset = sys.getEnergySet();
AtomSelection sel(sys.getAtomPointers());
// Set all terms active, besides Charmm-Elec
Eset->setAllTermsInactive();
Eset->setTermActive("CHARMM_VDW", true);
Eset->setTermActive("SCWRL4_HBOND", true);
/******************************************************************************
* === INITIAL STARTING POSITION ===
******************************************************************************/
sys.saveCoor("initialState");
helicalAxis.saveCoor("initialState");
EnergySet* pESet = sys.getEnergySet();
vector<Interaction*> hbondInteractions = (*(pESet->getEnergyTerms()))["SCWRL4_HBOND"];
//cout << "Number of hbond interactions "<< hbondInteractions.size() << endl;
// Reference points to set up Helical starting postions
CartesianPoint origin(0.0,0.0,0.0);
CartesianPoint zAxis(0.0,0.0,1.0);
CartesianPoint xAxis(1.0,0.0,0.0);
//.........这里部分代码省略.........