| 117 |
|
GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info); |
| 118 |
|
compositeVisitor->addVisitor(gbLipidVisitor, 740); |
| 119 |
|
|
| 120 |
+ |
Ring5gbAtomVisitor* ring5Visitor = new Ring5gbAtomVisitor(info); |
| 121 |
+ |
compositeVisitor->addVisitor(ring5Visitor, 730); |
| 122 |
+ |
|
| 123 |
+ |
HeadAtomVisitor* headVisitor = new HeadAtomVisitor(info); |
| 124 |
+ |
compositeVisitor->addVisitor(headVisitor, 720); |
| 125 |
+ |
|
| 126 |
|
//create default atom visitor |
| 127 |
|
DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info); |
| 128 |
|
compositeVisitor->addVisitor(defaultAtomVisitor, 700); |
| 129 |
|
|
| 130 |
< |
//create waterType visitor |
| 131 |
< |
if(args_info.watertype_flag){ |
| 132 |
< |
WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor; |
| 133 |
< |
compositeVisitor->addVisitor(waterTypeVisitor, 600); |
| 130 |
> |
// if we gave the -w option, we want to skip the waters: |
| 131 |
> |
std::cerr << "-w flag was set to:" << args_info.water_given << "\n"; |
| 132 |
> |
if (!args_info.water_given) { |
| 133 |
> |
//create waterType visitor |
| 134 |
> |
if(args_info.watertype_flag){ |
| 135 |
> |
WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor; |
| 136 |
> |
compositeVisitor->addVisitor(waterTypeVisitor, 600); |
| 137 |
> |
} |
| 138 |
|
} |
| 139 |
|
|
| 140 |
|
if (args_info.basetype_flag) { |
| 180 |
|
|
| 181 |
|
//create xyzVisitor |
| 182 |
|
XYZVisitor* xyzVisitor; |
| 183 |
+ |
|
| 184 |
|
if (args_info.selection_given) { |
| 185 |
|
xyzVisitor = new XYZVisitor(info, args_info.selection_arg); |
| 186 |
|
} else { |
| 187 |
|
xyzVisitor = new XYZVisitor(info); |
| 188 |
|
} |
| 189 |
+ |
|
| 190 |
+ |
if(args_info.printPosOnly_flag){ |
| 191 |
+ |
bool posOnly = true; |
| 192 |
+ |
xyzVisitor->setPosOnly(posOnly); |
| 193 |
+ |
} |
| 194 |
+ |
|
| 195 |
|
compositeVisitor->addVisitor(xyzVisitor, 200); |
| 196 |
|
|
| 197 |
|
std::cout << compositeVisitor->toString(); |
| 204 |
|
int nframes = dumpReader->getNFrames(); |
| 205 |
|
|
| 206 |
|
|
| 207 |
< |
std::ofstream xyzStream; |
| 191 |
< |
xyzStream .open(xyzFileName.c_str()); |
| 207 |
> |
std::ofstream xyzStream(xyzFileName.c_str()); |
| 208 |
|
|
| 193 |
– |
|
| 209 |
|
SimInfo::MoleculeIterator miter; |
| 210 |
|
Molecule::IntegrableObjectIterator iiter; |
| 211 |
|
Molecule::RigidBodyIterator rbIter; |
| 268 |
|
xyzVisitor->clear(); |
| 269 |
|
|
| 270 |
|
}//end for (int i = 0; i < nframes; i += args_info.frame_arg) |
| 271 |
< |
|
| 271 |
> |
|
| 272 |
|
xyzStream.close(); |
| 258 |
– |
|
| 273 |
|
delete prepareVisitor; |
| 274 |
|
delete compositeVisitor; |
| 275 |
|
delete info; |
| 262 |
– |
|
| 276 |
|
} |
