本文整理汇总了C++中Molecule::AddAtom方法的典型用法代码示例。如果您正苦于以下问题：C++ Molecule::AddAtom方法的具体用法？C++ Molecule::AddAtom怎么用？C++ Molecule::AddAtom使用的例子？那么, 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Molecule的用法示例。
在下文中一共展示了Molecule::AddAtom方法的4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: main
int main () {
PDBFile pdb ("temp.pdb");
Molecule * mol = pdb.Molecules(0);
mol->Name("qtz");
std::vector<Atom *> atoms = mol->Atoms();
/* cycle through each atom in order of the pdb file */
RUN (atoms)
{
Atom * atom = atoms[i];
atom->Residue("qtz");
VecR pos = atom->Position();
/* find the surface Oxygens */
if (atom->Name().find("O") != string::npos && pos[z] > -7.9)
{
/* add H's to the surface */
Atom * h = new Atom ("H", pos + VecR (0.0, 0.0, 1.1));
mol->AddAtom(h);
}
}
std::vector<Molecule *> mols;
mols.push_back(mol);
PDBFile::WritePDB(mols);
}示例2: MakeSingleMolecule
/* Take a set of molecules and return a single molecule with all the atoms */
Molecule * MakeSingleMolecule (Mol_ptr_vec& mols) {
Molecule * mol = new Molecule();
for (Mol_it mols_i = mols.begin(); mols_i != mols.end(); mols_i++) {
for (Atom_it atom_i = (*mols_i)->begin(); atom_i != (*mols_i)->end(); atom_i++) {
mol->AddAtom((*atom_i));
}
}
return mol;
}示例3: UnitCellToSlab
// Makes a repeating slab out of a single unit cell by creating copies and shifting
Mol_ptr_vec UnitCellToSlab (GridParams& params) {
std::vector<Molecule *> mols;
Molecule * uc = params.unitCell;
VecR yshift, xshift, zshift;
yshift.Zero();
for (int i = 0; i < params.y; i++) {
zshift.Zero();
for (int j = 0; j < params.x; j++) {
xshift.Zero();
if (!(j % 2))
xshift += params.x_shift * 0.5;
for (int k = 0; k < params.z; k++) {
// make a copy of the unitcell
Molecule * copy = new Molecule();
copy->Name(params.name);
// make copies of all the atoms in the unitcell
for (Atom_it atom_i = uc->begin(); atom_i != uc->end(); atom_i++) {
//for (int atom = 0; atom < uc->size(); atom++) {
Atom * pa = new Atom (*(*atom_i));
copy->AddAtom(pa);
}
// shift the new copy to the next lattice point
copy->Shift(yshift + xshift + zshift);
mols.push_back(copy);
xshift += params.x_shift;
}
zshift += params.z_shift;
}
yshift += params.y_shift;
}
return mols;
}示例4: UnitCellToSlab
// Makes a repeating slab out of a single unit cell by creating copies and shifting
Mol_ptr_vec UnitCellToSlab (Molecule * uc, VecR& x_shift,VecR& y_shift, VecR& z_shift) {
std::vector<Molecule *> mols;
VecR yshift, xshift, zshift;
for (int i = 0; i < 1; i++) {
zshift.Zero();
yshift.Zero();
for (int j = 0; j < 6; j++) {
xshift.Zero();
for (int k = 0; k < 6; k++) {
// make a copy of the unitcell
Molecule * copy = new Molecule();
copy->Name("qtz");
// make copies of all the atoms in the unitcell
for (int atom = 0; atom < uc->size(); atom++) {
Atom * pa = new Atom (*uc->Atoms(atom));
copy->AddAtom(pa);
}
// shift the new copy to the next lattice point
copy->Shift(yshift + xshift + zshift);
mols.push_back(copy);
xshift += x_shift;
}
yshift += y_shift;
}
zshift += z_shift;
}
return mols;
}