1 |
< |
/* |
1 |
> |
/* |
2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
|
* |
4 |
|
* The University of Notre Dame grants you ("Licensee") a |
42 |
|
#include <cstring> |
43 |
|
#include "visitors/AtomVisitor.hpp" |
44 |
|
#include "primitives/DirectionalAtom.hpp" |
45 |
– |
#include "math/MatVec3.h" |
45 |
|
#include "primitives/RigidBody.hpp" |
46 |
|
|
47 |
|
namespace oopse { |
48 |
< |
void BaseAtomVisitor::visit(RigidBody *rb) { |
49 |
< |
//vector<Atom*> myAtoms; |
50 |
< |
//vector<Atom*>::iterator atomIter; |
48 |
> |
void BaseAtomVisitor::visit(RigidBody *rb) { |
49 |
> |
//vector<Atom*> myAtoms; |
50 |
> |
//vector<Atom*>::iterator atomIter; |
51 |
|
|
52 |
< |
//myAtoms = rb->getAtoms(); |
52 |
> |
//myAtoms = rb->getAtoms(); |
53 |
|
|
54 |
< |
//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
55 |
< |
// (*atomIter)->accept(this); |
56 |
< |
} |
54 |
> |
//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
55 |
> |
// (*atomIter)->accept(this); |
56 |
> |
} |
57 |
|
|
58 |
< |
void BaseAtomVisitor::setVisited(Atom *atom) { |
58 |
> |
void BaseAtomVisitor::setVisited(Atom *atom) { |
59 |
|
GenericData *data; |
60 |
|
data = atom->getPropertyByName("VISITED"); |
61 |
|
|
62 |
|
//if visited property is not existed, add it as new property |
63 |
|
if (data == NULL) { |
64 |
< |
data = new GenericData(); |
65 |
< |
data->setID("VISITED"); |
66 |
< |
atom->addProperty(data); |
64 |
> |
data = new GenericData(); |
65 |
> |
data->setID("VISITED"); |
66 |
> |
atom->addProperty(data); |
67 |
|
} |
68 |
< |
} |
68 |
> |
} |
69 |
|
|
70 |
< |
bool BaseAtomVisitor::isVisited(Atom *atom) { |
70 |
> |
bool BaseAtomVisitor::isVisited(Atom *atom) { |
71 |
|
GenericData *data; |
72 |
|
data = atom->getPropertyByName("VISITED"); |
73 |
|
return data == NULL ? false : true; |
74 |
< |
} |
74 |
> |
} |
75 |
|
|
76 |
< |
bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
77 |
< |
std::vector<std::string>::iterator strIter; |
76 |
> |
bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
77 |
> |
std::set<std::string>::iterator strIter; |
78 |
> |
strIter = ssdAtomType.find(atomType); |
79 |
> |
return strIter != ssdAtomType.end() ? true : false; |
80 |
> |
} |
81 |
|
|
82 |
< |
for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); |
83 |
< |
++strIter ) |
82 |
< |
if (*strIter == atomType) |
83 |
< |
return true; |
82 |
> |
void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
83 |
> |
std::vector<AtomInfo*>atoms; |
84 |
|
|
85 |
– |
return false; |
86 |
– |
} |
87 |
– |
|
88 |
– |
void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
89 |
– |
std::vector<AtomInfo *>atoms; |
90 |
– |
|
85 |
|
//we need to convert SSD into 4 differnet atoms |
86 |
|
//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass |
87 |
|
//of the water with a dipole moment |
101 |
|
|
102 |
|
//if atom is not SSD atom, just skip it |
103 |
|
if (!isSSDAtom(datom->getType())) |
104 |
< |
return; |
104 |
> |
return; |
105 |
|
|
106 |
|
data = datom->getPropertyByName("ATOMDATA"); |
107 |
|
|
108 |
|
if (data != NULL) { |
109 |
< |
atomData = dynamic_cast<AtomData *>(data); |
109 |
> |
atomData = dynamic_cast<AtomData *>(data); |
110 |
|
|
111 |
< |
if (atomData == NULL) { |
112 |
< |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
113 |
< |
atomData = new AtomData; |
114 |
< |
haveAtomData = false; |
115 |
< |
} else |
116 |
< |
haveAtomData = true; |
111 |
> |
if (atomData == NULL) { |
112 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
113 |
> |
atomData = new AtomData; |
114 |
> |
haveAtomData = false; |
115 |
> |
} else |
116 |
> |
haveAtomData = true; |
117 |
|
} else { |
118 |
< |
atomData = new AtomData; |
119 |
< |
haveAtomData = false; |
118 |
> |
atomData = new AtomData; |
119 |
> |
haveAtomData = false; |
120 |
|
} |
121 |
|
|
122 |
|
pos = datom->getPos(); |
132 |
|
newVec = rotTrans * u; |
133 |
|
|
134 |
|
atomInfo = new AtomInfo; |
135 |
< |
atomInfo->AtomType = "X"; |
135 |
> |
atomInfo->atomTypeName = "X"; |
136 |
|
atomInfo->pos[0] = pos[0]; |
137 |
|
atomInfo->pos[1] = pos[1]; |
138 |
|
atomInfo->pos[2] = pos[2]; |
147 |
|
newVec = rotTrans * ox; |
148 |
|
|
149 |
|
atomInfo = new AtomInfo; |
150 |
< |
atomInfo->AtomType = "O"; |
150 |
> |
atomInfo->atomTypeName = "O"; |
151 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
152 |
|
atomInfo->pos[1] = pos[1] + newVec[1]; |
153 |
|
atomInfo->pos[2] = pos[2] + newVec[2]; |
160 |
|
//matVecMul3(rotTrans, h1, newVec); |
161 |
|
newVec = rotTrans * h1; |
162 |
|
atomInfo = new AtomInfo; |
163 |
< |
atomInfo->AtomType = "H"; |
163 |
> |
atomInfo->atomTypeName = "H"; |
164 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
165 |
|
atomInfo->pos[1] = pos[1] + newVec[1]; |
166 |
|
atomInfo->pos[2] = pos[2] + newVec[2]; |
173 |
|
//matVecMul3(rotTrans, h2, newVec); |
174 |
|
newVec = rotTrans * h2; |
175 |
|
atomInfo = new AtomInfo; |
176 |
< |
atomInfo->AtomType = "H"; |
176 |
> |
atomInfo->atomTypeName = "H"; |
177 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
178 |
|
atomInfo->pos[1] = pos[1] + newVec[1]; |
179 |
|
atomInfo->pos[2] = pos[2] + newVec[2]; |
185 |
|
//add atom data into atom's property |
186 |
|
|
187 |
|
if (!haveAtomData) { |
188 |
< |
atomData->setID("ATOMDATA"); |
189 |
< |
datom->addProperty(atomData); |
188 |
> |
atomData->setID("ATOMDATA"); |
189 |
> |
datom->addProperty(atomData); |
190 |
|
} |
191 |
|
|
192 |
|
setVisited(datom); |
193 |
< |
} |
193 |
> |
} |
194 |
|
|
195 |
< |
const std::string SSDAtomVisitor::toString() { |
195 |
> |
const std::string SSDAtomVisitor::toString() { |
196 |
|
char buffer[65535]; |
197 |
|
std::string result; |
198 |
|
|
212 |
|
result += buffer; |
213 |
|
|
214 |
|
return result; |
215 |
< |
} |
215 |
> |
} |
216 |
|
|
217 |
< |
bool LinearAtomVisitor::isLinearAtom(const string& atomType){ |
218 |
< |
vector<string>::iterator strIter; |
219 |
< |
|
226 |
< |
for(strIter = linearAtomType.begin(); strIter != linearAtomType.end(); |
227 |
< |
++strIter) |
228 |
< |
if(*strIter == atomType) |
229 |
< |
return true; |
230 |
< |
|
231 |
< |
return false; |
232 |
< |
} |
217 |
> |
bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
218 |
> |
std::set<std::string>::iterator strIter; |
219 |
> |
strIter = linearAtomType.find(atomType); |
220 |
|
|
221 |
< |
void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
221 |
> |
return strIter != linearAtomType.end() ? true : false; |
222 |
> |
} |
223 |
|
|
224 |
< |
vector<AtomInfo*> atoms; |
224 |
> |
void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){ |
225 |
> |
linearAtomType.insert(atomType); |
226 |
> |
} |
227 |
|
|
228 |
< |
//we need to convert linear into 4 different atoms |
229 |
< |
double c1[3] = {0.0, 0.0, -1.8}; |
230 |
< |
double c2[3] = {0.0, 0.0, -0.6}; |
231 |
< |
double c3[3] = {0.0, 0.0, 0.6}; |
232 |
< |
double c4[3] = {0.0, 0.0, 1.8}; |
233 |
< |
double rotMatrix[3][3]; |
234 |
< |
double rotTrans[3][3]; |
235 |
< |
AtomInfo* atomInfo; |
236 |
< |
double pos[3]; |
237 |
< |
double newVec[3]; |
238 |
< |
double q[4]; |
239 |
< |
AtomData* atomData; |
240 |
< |
GenericData* data; |
241 |
< |
bool haveAtomData; |
242 |
< |
|
243 |
< |
//if atom is not SSD atom, just skip it |
254 |
< |
if(!isLinearAtom(datom->getType())) |
255 |
< |
return; |
256 |
< |
|
257 |
< |
data = datom->getProperty("ATOMDATA"); |
258 |
< |
if(data != NULL){ |
228 |
> |
void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
229 |
> |
std::vector<AtomInfo*> atoms; |
230 |
> |
//we need to convert linear into 4 different atoms |
231 |
> |
Vector3d c1(0.0, 0.0, -1.8); |
232 |
> |
Vector3d c2(0.0, 0.0, -0.6); |
233 |
> |
Vector3d c3(0.0, 0.0, 0.6); |
234 |
> |
Vector3d c4(0.0, 0.0, 1.8); |
235 |
> |
RotMat3x3d rotMatrix; |
236 |
> |
RotMat3x3d rotTrans; |
237 |
> |
AtomInfo* atomInfo; |
238 |
> |
Vector3d pos; |
239 |
> |
Vector3d newVec; |
240 |
> |
Quat4d q; |
241 |
> |
AtomData* atomData; |
242 |
> |
GenericData* data; |
243 |
> |
bool haveAtomData; |
244 |
|
|
245 |
< |
atomData = dynamic_cast<AtomData*>(data); |
246 |
< |
if(atomData == NULL){ |
247 |
< |
cerr << "can not get Atom Data from " << datom->getType() << endl; |
248 |
< |
atomData = new AtomData; |
249 |
< |
haveAtomData = false; |
245 |
> |
//if atom is not SSD atom, just skip it |
246 |
> |
if(!isLinearAtom(datom->getType())) |
247 |
> |
return; |
248 |
> |
|
249 |
> |
data = datom->getPropertyByName("ATOMDATA"); |
250 |
> |
if(data != NULL){ |
251 |
> |
atomData = dynamic_cast<AtomData*>(data); |
252 |
> |
if(atomData == NULL){ |
253 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
254 |
> |
atomData = new AtomData; |
255 |
> |
haveAtomData = false; |
256 |
> |
} else { |
257 |
> |
haveAtomData = true; |
258 |
> |
} |
259 |
> |
} else { |
260 |
> |
atomData = new AtomData; |
261 |
> |
haveAtomData = false; |
262 |
|
} |
266 |
– |
else |
267 |
– |
haveAtomData = true; |
268 |
– |
} |
269 |
– |
else{ |
270 |
– |
atomData = new AtomData; |
271 |
– |
haveAtomData = false; |
272 |
– |
} |
263 |
|
|
264 |
|
|
265 |
< |
datom->getPos(pos); |
266 |
< |
datom->getQ(q); |
267 |
< |
datom->getA(rotMatrix); |
265 |
> |
pos = datom->getPos(); |
266 |
> |
q = datom->getQ(); |
267 |
> |
rotMatrix = datom->getA(); |
268 |
|
|
269 |
< |
// We need A^T to convert from body-fixed to space-fixed: |
270 |
< |
transposeMat3(rotMatrix, rotTrans); |
281 |
< |
|
282 |
< |
matVecMul3(rotTrans, c1, newVec); |
283 |
< |
atomInfo = new AtomInfo; |
284 |
< |
atomInfo->AtomType = "C"; |
285 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
286 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
287 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
288 |
< |
atomInfo->dipole[0] = 0.0; |
289 |
< |
atomInfo->dipole[1] = 0.0; |
290 |
< |
atomInfo->dipole[2] = 0.0; |
291 |
< |
atomData->addAtomInfo(atomInfo); |
269 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
270 |
> |
rotTrans = rotMatrix.transpose(); |
271 |
|
|
272 |
< |
matVecMul3(rotTrans, c2, newVec); |
273 |
< |
atomInfo = new AtomInfo; |
274 |
< |
atomInfo->AtomType = "C"; |
275 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
276 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
277 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
278 |
< |
atomInfo->dipole[0] = 0.0; |
279 |
< |
atomInfo->dipole[1] = 0.0; |
280 |
< |
atomInfo->dipole[2] = 0.0; |
281 |
< |
atomData->addAtomInfo(atomInfo); |
272 |
> |
newVec = rotTrans * c1; |
273 |
> |
atomInfo = new AtomInfo; |
274 |
> |
atomInfo->atomTypeName = "C"; |
275 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
276 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
277 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
278 |
> |
atomInfo->dipole[0] = 0.0; |
279 |
> |
atomInfo->dipole[1] = 0.0; |
280 |
> |
atomInfo->dipole[2] = 0.0; |
281 |
> |
atomData->addAtomInfo(atomInfo); |
282 |
|
|
283 |
< |
matVecMul3(rotTrans, c3, newVec); |
284 |
< |
atomInfo = new AtomInfo; |
285 |
< |
atomInfo->AtomType = "C"; |
286 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
287 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
288 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
289 |
< |
atomInfo->dipole[0] = 0.0; |
290 |
< |
atomInfo->dipole[1] = 0.0; |
291 |
< |
atomInfo->dipole[2] = 0.0; |
292 |
< |
atomData->addAtomInfo(atomInfo); |
314 |
< |
|
315 |
< |
matVecMul3(rotTrans, c4, newVec); |
316 |
< |
atomInfo = new AtomInfo; |
317 |
< |
atomInfo->AtomType = "C"; |
318 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
319 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
320 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
321 |
< |
atomInfo->dipole[0] = 0.0; |
322 |
< |
atomInfo->dipole[1] = 0.0; |
323 |
< |
atomInfo->dipole[2] = 0.0; |
324 |
< |
atomData->addAtomInfo(atomInfo); |
325 |
< |
|
326 |
< |
//add atom data into atom's property |
283 |
> |
newVec = rotTrans * c2; |
284 |
> |
atomInfo = new AtomInfo; |
285 |
> |
atomInfo->atomTypeName = "C"; |
286 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
287 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
288 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
289 |
> |
atomInfo->dipole[0] = 0.0; |
290 |
> |
atomInfo->dipole[1] = 0.0; |
291 |
> |
atomInfo->dipole[2] = 0.0; |
292 |
> |
atomData->addAtomInfo(atomInfo); |
293 |
|
|
294 |
< |
if(!haveAtomData){ |
295 |
< |
atomData->setID("ATOMDATA"); |
296 |
< |
datom->addProperty(atomData); |
294 |
> |
newVec = rotTrans * c3; |
295 |
> |
atomInfo = new AtomInfo; |
296 |
> |
atomInfo->atomTypeName = "C"; |
297 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
298 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
299 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
300 |
> |
atomInfo->dipole[0] = 0.0; |
301 |
> |
atomInfo->dipole[1] = 0.0; |
302 |
> |
atomInfo->dipole[2] = 0.0; |
303 |
> |
atomData->addAtomInfo(atomInfo); |
304 |
> |
|
305 |
> |
newVec = rotTrans * c4; |
306 |
> |
atomInfo = new AtomInfo; |
307 |
> |
atomInfo->atomTypeName = "C"; |
308 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
309 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
310 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
311 |
> |
atomInfo->dipole[0] = 0.0; |
312 |
> |
atomInfo->dipole[1] = 0.0; |
313 |
> |
atomInfo->dipole[2] = 0.0; |
314 |
> |
atomData->addAtomInfo(atomInfo); |
315 |
> |
|
316 |
> |
//add atom data into atom's property |
317 |
> |
|
318 |
> |
if(!haveAtomData){ |
319 |
> |
atomData->setID("ATOMDATA"); |
320 |
> |
datom->addProperty(atomData); |
321 |
> |
} |
322 |
> |
|
323 |
> |
setVisited(datom); |
324 |
> |
|
325 |
|
} |
326 |
|
|
327 |
< |
setVisited(datom); |
327 |
> |
const std::string LinearAtomVisitor::toString(){ |
328 |
> |
char buffer[65535]; |
329 |
> |
std::string result; |
330 |
> |
|
331 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
332 |
> |
result += buffer; |
333 |
|
|
334 |
< |
} |
334 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
335 |
> |
result += buffer; |
336 |
|
|
337 |
< |
const string LinearAtomVisitor::toString(){ |
338 |
< |
char buffer[65535]; |
339 |
< |
string result; |
337 |
> |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
338 |
> |
result += buffer; |
339 |
> |
|
340 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
341 |
> |
result += buffer; |
342 |
> |
|
343 |
> |
return result; |
344 |
> |
} |
345 |
> |
|
346 |
> |
bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){ |
347 |
> |
std::set<std::string>::iterator strIter; |
348 |
> |
strIter = GBLipidAtomType.find(atomType); |
349 |
> |
|
350 |
> |
return strIter != GBLipidAtomType.end() ? true : false; |
351 |
> |
} |
352 |
> |
|
353 |
> |
void GBLipidAtomVisitor::visit(DirectionalAtom* datom){ |
354 |
> |
std::vector<AtomInfo*> atoms; |
355 |
> |
//we need to convert linear into 4 different atoms |
356 |
> |
Vector3d c1(0.0, 0.0, -6.25); |
357 |
> |
Vector3d c2(0.0, 0.0, -2.1); |
358 |
> |
Vector3d c3(0.0, 0.0, 2.1); |
359 |
> |
Vector3d c4(0.0, 0.0, 6.25); |
360 |
> |
RotMat3x3d rotMatrix; |
361 |
> |
RotMat3x3d rotTrans; |
362 |
> |
AtomInfo* atomInfo; |
363 |
> |
Vector3d pos; |
364 |
> |
Vector3d newVec; |
365 |
> |
Quat4d q; |
366 |
> |
AtomData* atomData; |
367 |
> |
GenericData* data; |
368 |
> |
bool haveAtomData; |
369 |
> |
|
370 |
> |
//if atom is not GBlipid atom, just skip it |
371 |
> |
if(!isGBLipidAtom(datom->getType())) |
372 |
> |
return; |
373 |
> |
|
374 |
> |
data = datom->getPropertyByName("ATOMDATA"); |
375 |
> |
if(data != NULL){ |
376 |
> |
atomData = dynamic_cast<AtomData*>(data); |
377 |
> |
if(atomData == NULL){ |
378 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
379 |
> |
atomData = new AtomData; |
380 |
> |
haveAtomData = false; |
381 |
> |
} else { |
382 |
> |
haveAtomData = true; |
383 |
> |
} |
384 |
> |
} else { |
385 |
> |
atomData = new AtomData; |
386 |
> |
haveAtomData = false; |
387 |
> |
} |
388 |
> |
|
389 |
|
|
390 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
391 |
< |
result += buffer; |
390 |
> |
pos = datom->getPos(); |
391 |
> |
q = datom->getQ(); |
392 |
> |
rotMatrix = datom->getA(); |
393 |
|
|
394 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
395 |
< |
result += buffer; |
394 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
395 |
> |
rotTrans = rotMatrix.transpose(); |
396 |
|
|
397 |
< |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
398 |
< |
result += buffer; |
397 |
> |
newVec = rotTrans * c1; |
398 |
> |
atomInfo = new AtomInfo; |
399 |
> |
atomInfo->atomTypeName = "K"; |
400 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
401 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
402 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
403 |
> |
atomInfo->dipole[0] = 0.0; |
404 |
> |
atomInfo->dipole[1] = 0.0; |
405 |
> |
atomInfo->dipole[2] = 0.0; |
406 |
> |
atomData->addAtomInfo(atomInfo); |
407 |
|
|
408 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
409 |
< |
result += buffer; |
408 |
> |
newVec = rotTrans * c2; |
409 |
> |
atomInfo = new AtomInfo; |
410 |
> |
atomInfo->atomTypeName = "K"; |
411 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
412 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
413 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
414 |
> |
atomInfo->dipole[0] = 0.0; |
415 |
> |
atomInfo->dipole[1] = 0.0; |
416 |
> |
atomInfo->dipole[2] = 0.0; |
417 |
> |
atomData->addAtomInfo(atomInfo); |
418 |
|
|
419 |
< |
return result; |
420 |
< |
} |
419 |
> |
newVec = rotTrans * c3; |
420 |
> |
atomInfo = new AtomInfo; |
421 |
> |
atomInfo->atomTypeName = "K"; |
422 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
423 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
424 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
425 |
> |
atomInfo->dipole[0] = 0.0; |
426 |
> |
atomInfo->dipole[1] = 0.0; |
427 |
> |
atomInfo->dipole[2] = 0.0; |
428 |
> |
atomData->addAtomInfo(atomInfo); |
429 |
|
|
430 |
< |
//----------------------------------------------------------------------------// |
430 |
> |
newVec = rotTrans * c4; |
431 |
> |
atomInfo = new AtomInfo; |
432 |
> |
atomInfo->atomTypeName = "K"; |
433 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
434 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
435 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
436 |
> |
atomInfo->dipole[0] = 0.0; |
437 |
> |
atomInfo->dipole[1] = 0.0; |
438 |
> |
atomInfo->dipole[2] = 0.0; |
439 |
> |
atomData->addAtomInfo(atomInfo); |
440 |
|
|
441 |
< |
void DefaultAtomVisitor::visit(Atom *atom) { |
441 |
> |
//add atom data into atom's property |
442 |
> |
|
443 |
> |
if(!haveAtomData){ |
444 |
> |
atomData->setID("ATOMDATA"); |
445 |
> |
datom->addProperty(atomData); |
446 |
> |
} |
447 |
> |
|
448 |
> |
setVisited(datom); |
449 |
> |
|
450 |
> |
} |
451 |
> |
|
452 |
> |
const std::string GBLipidAtomVisitor::toString(){ |
453 |
> |
char buffer[65535]; |
454 |
> |
std::string result; |
455 |
> |
|
456 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
457 |
> |
result += buffer; |
458 |
> |
|
459 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
460 |
> |
result += buffer; |
461 |
> |
|
462 |
> |
sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n"); |
463 |
> |
result += buffer; |
464 |
> |
|
465 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
466 |
> |
result += buffer; |
467 |
> |
|
468 |
> |
return result; |
469 |
> |
} |
470 |
> |
|
471 |
> |
//----------------------------------------------------------------------------// |
472 |
> |
|
473 |
> |
void DefaultAtomVisitor::visit(Atom *atom) { |
474 |
|
AtomData *atomData; |
475 |
|
AtomInfo *atomInfo; |
476 |
|
Vector3d pos; |
477 |
|
|
478 |
|
if (isVisited(atom)) |
479 |
< |
return; |
479 |
> |
return; |
480 |
|
|
481 |
|
atomInfo = new AtomInfo; |
482 |
|
|
484 |
|
atomData->setID("ATOMDATA"); |
485 |
|
|
486 |
|
pos = atom->getPos(); |
487 |
< |
atomInfo->AtomType = atom->getType(); |
487 |
> |
atomInfo->atomTypeName = atom->getType(); |
488 |
|
atomInfo->pos[0] = pos[0]; |
489 |
|
atomInfo->pos[1] = pos[1]; |
490 |
|
atomInfo->pos[2] = pos[2]; |
497 |
|
atom->addProperty(atomData); |
498 |
|
|
499 |
|
setVisited(atom); |
500 |
< |
} |
500 |
> |
} |
501 |
|
|
502 |
< |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
502 |
> |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
503 |
|
AtomData *atomData; |
504 |
|
AtomInfo *atomInfo; |
505 |
|
Vector3d pos; |
506 |
|
Vector3d u; |
507 |
|
|
508 |
|
if (isVisited(datom)) |
509 |
< |
return; |
509 |
> |
return; |
510 |
|
|
511 |
|
pos = datom->getPos(); |
512 |
< |
u = datom->getElectroFrame().getColumn(3); |
512 |
> |
u = datom->getElectroFrame().getColumn(2); |
513 |
|
|
514 |
|
atomData = new AtomData; |
515 |
|
atomData->setID("ATOMDATA"); |
516 |
|
atomInfo = new AtomInfo; |
517 |
|
|
518 |
< |
atomInfo->AtomType = datom->getType(); |
518 |
> |
atomInfo->atomTypeName = datom->getType(); |
519 |
|
atomInfo->pos[0] = pos[0]; |
520 |
|
atomInfo->pos[1] = pos[1]; |
521 |
|
atomInfo->pos[2] = pos[2]; |
528 |
|
datom->addProperty(atomData); |
529 |
|
|
530 |
|
setVisited(datom); |
531 |
< |
} |
531 |
> |
} |
532 |
|
|
533 |
< |
const std::string DefaultAtomVisitor::toString() { |
533 |
> |
const std::string DefaultAtomVisitor::toString() { |
534 |
|
char buffer[65535]; |
535 |
|
std::string result; |
536 |
|
|
550 |
|
result += buffer; |
551 |
|
|
552 |
|
return result; |
553 |
< |
} |
553 |
> |
} |
554 |
|
} //namespace oopse |