本文整理汇总了C++中Transforms::rmsdAlignment方法的典型用法代码示例。如果您正苦于以下问题:C++ Transforms::rmsdAlignment方法的具体用法?C++ Transforms::rmsdAlignment怎么用?C++ Transforms::rmsdAlignment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。
在下文中一共展示了Transforms::rmsdAlignment方法的2个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: printResults
//.........这里部分代码省略.........
// Get AtomVectors of matching windows
AtomPointerVector ca1 = minWindow1.getSmallAVec();
AtomPointerVector ca2 = minWindow2.getSmallAVec();
//for(int i=0; i<ca2.size();i++) cout<<*ca2[i]<<endl;
// Read PDB1 in
PDBReader r1;
r1.open(dm1.getPDBid());
r1.read();
r1.close();
AtomPointerVector &ref = r1.getAtomPointers();
if (ref.size() == 0){
cerr << "ERRROR 3453 in ManageDistanceMatrixResults::printResults while aligning pdbs, ref pdb not found?: "<<dm1.getPDBid()<<endl;
exit(3453);
}
PDBReader r2;
r2.open(dm2.getPDBid());
r2.read();
r2.close();
AtomPointerVector &vec = r2.getAtomPointers();
Transforms t;
//for(int i=0; i<vec.size();i++) cout<<*vec[i]<<endl;
//cout<<endl;
// cout << ca2.size() << "\t" << ca1.size() << "\t" << vec.size() << endl;
bool result = t.rmsdAlignment(ca2,ca1, vec);
// This align is to a get vec (full pdb coordinates)
//ca2,ca1 did not changed; vec changed
if (!result){
cerr << "Alignment has failed!"<<endl;
exit(1211);
}
ca2.saveCoor("pre");
// here record old ca2 coordinates
result = t.rmsdAlignment(ca2,ca1);
// this align is to get a new ca2 to calculate rmsd
if (!result){
cerr << "Alignment has failed!"<<endl;
exit(1212);
}
double rmsd=ca1.rmsd(ca2);
cout << "RMSD: "<<rmsd<<endl;
if (rmsd <= rmsdTol){
// a smaller rmsd is to get optimized structures
numberAligned++;
/*
// Write out aligned PDB for dm2
char a[80];
sprintf(a, "%s.aligned.%5.3f.pdb",MslTools::getFileName(dm2.getPDBid()).c_str(),rmsd);
PDBWriter w;
w.open(a);
w.write(vec);
示例2: main
//.........这里部分代码省略.........
if (opt.setModel2) {
// set the current NMR model
sys2.setActiveModel(opt.model2);
}
AtomPointerVector av1 = sys1.getAtomPointers();
AtomPointerVector av2 = sys2.getAtomPointers();
AtomPointerVector alignAtoms1;
if (opt.sele1.size() == 0) {
// select all atoms
alignAtoms1.insert(alignAtoms1.end(), av1.begin(), av1.end());
} else {
AtomSelection sel1(av1);
for (unsigned int i=0; i<opt.sele1.size(); i++) {
char c [1000];
sprintf(c, "keyatoms, %s", opt.sele1[i].c_str());
AtomPointerVector selAtom = sel1.select(c);
alignAtoms1.insert(alignAtoms1.end(), selAtom.begin(), selAtom.end());
}
}
cout << "Selected " << alignAtoms1.size() << " reference atoms for pdb " << opt.pdb1 << endl;
AtomPointerVector alignAtoms2;
if (opt.sele2.size() == 0) {
// select all atoms
alignAtoms2.insert(alignAtoms2.end(), av2.begin(), av2.end());
} else {
AtomSelection sel2(av2);
for (unsigned int i=0; i<opt.sele2.size(); i++) {
char c [1000];
sprintf(c, "keyatoms, %s", opt.sele2[i].c_str());
AtomPointerVector selAtom = sel2.select(c);
alignAtoms2.insert(alignAtoms2.end(), selAtom.begin(), selAtom.end());
}
}
cout << "Selected " << alignAtoms2.size() << " reference atoms for pdb " << opt.pdb2 << endl;
if (alignAtoms1.size() != alignAtoms2.size()) {
cerr << "The number of atoms selected for pdb 1 (" << alignAtoms1.size() << ") does not match the number of atoms selected for pdb 2 (" << alignAtoms2.size() << ")" << endl;
exit(1);
}
cout << endl;
cout << "Set 1 ================================" << endl;
cout << endl;
cout << alignAtoms1;
cout << endl;
cout << "Set 2 ================================" << endl;
cout << endl;
cout << alignAtoms2;
cout << endl;
cout << " ================================" << endl;
if (opt.noAlign) {
// only calc the rmsd
double rmsd = alignAtoms2.rmsd(alignAtoms1);
cout << endl;
cout << opt.pdb2 << " was NOT aligned to " << opt.pdb1 << "." << endl;
cout << "RMSD " << rmsd << endl;
} else {
Transforms tm;
if (!tm.rmsdAlignment(alignAtoms2,alignAtoms1,av2)) {
cerr << "Alignment failed!" << endl;
exit(1);
}
//double rmsd = tm.getRMSD();
double rmsd = alignAtoms2.rmsd(alignAtoms1);
Matrix rotMatrix = tm.getLastRotationMatrix();
CartesianPoint translation = tm.getLastTranslation();
cout << rotMatrix << endl;
cout << translation << endl;
cout << endl;
cout << "Aligned " << opt.pdb2;
if (opt.setModel2) {
cout << " (model " << opt.model2 << ")";
}
cout << " to " << opt.pdb1;
if (opt.setModel1) {
cout << " (model " << opt.model1 << ")";
}
cout << "." << endl;
cout << "RMSD " << rmsd << endl;
if (!opt.noOutputPdb) {
if (!sys2.writePdb(opt.outputPdb2, opt.writeAllModels)) {
cerr << "Cannot open " << opt.outputPdb2 << " for writing" << endl;
exit(1);
}
cout << "Written to " << opt.outputPdb2 << endl;
} else {
cout << "Aligned PDB not written" << endl;
}
}
return 0;
}