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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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#include <cstring> |
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#include "visitors/AtomVisitor.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "math/MatVec3.h" |
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#include "primitives/RigidBody.hpp" |
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namespace oopse { |
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void BaseAtomVisitor::visit(RigidBody *rb) { |
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//vector<Atom*> myAtoms; |
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//vector<Atom*>::iterator atomIter; |
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void BaseAtomVisitor::visit(RigidBody *rb) { |
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//vector<Atom*> myAtoms; |
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//vector<Atom*>::iterator atomIter; |
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|
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//myAtoms = rb->getAtoms(); |
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//myAtoms = rb->getAtoms(); |
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|
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//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
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// (*atomIter)->accept(this); |
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} |
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//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
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// (*atomIter)->accept(this); |
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} |
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|
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void BaseAtomVisitor::setVisited(Atom *atom) { |
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void BaseAtomVisitor::setVisited(Atom *atom) { |
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GenericData *data; |
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data = atom->getPropertyByName("VISITED"); |
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|
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//if visited property is not existed, add it as new property |
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if (data == NULL) { |
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data = new GenericData(); |
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data->setID("VISITED"); |
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atom->addProperty(data); |
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data = new GenericData(); |
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data->setID("VISITED"); |
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atom->addProperty(data); |
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} |
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} |
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} |
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|
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bool BaseAtomVisitor::isVisited(Atom *atom) { |
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bool BaseAtomVisitor::isVisited(Atom *atom) { |
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GenericData *data; |
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data = atom->getPropertyByName("VISITED"); |
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return data == NULL ? false : true; |
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} |
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} |
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|
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bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
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bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
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std::set<std::string>::iterator strIter; |
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strIter = ssdAtomType.find(atomType); |
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return strIter != ssdAtomType.end() ? true : false; |
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} |
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} |
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|
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void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
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void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
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std::vector<AtomInfo*>atoms; |
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|
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//we need to convert SSD into 4 differnet atoms |
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|
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//if atom is not SSD atom, just skip it |
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if (!isSSDAtom(datom->getType())) |
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return; |
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return; |
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data = datom->getPropertyByName("ATOMDATA"); |
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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atomData = dynamic_cast<AtomData *>(data); |
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|
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if (atomData == NULL) { |
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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else |
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haveAtomData = true; |
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if (atomData == NULL) { |
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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else |
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haveAtomData = true; |
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} else { |
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atomData = new AtomData; |
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haveAtomData = false; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} |
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pos = datom->getPos(); |
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newVec = rotTrans * u; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "X"; |
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atomInfo->atomTypeName = "X"; |
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atomInfo->pos[0] = pos[0]; |
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atomInfo->pos[1] = pos[1]; |
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atomInfo->pos[2] = pos[2]; |
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newVec = rotTrans * ox; |
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|
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "O"; |
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atomInfo->atomTypeName = "O"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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//matVecMul3(rotTrans, h1, newVec); |
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newVec = rotTrans * h1; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "H"; |
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atomInfo->atomTypeName = "H"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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//matVecMul3(rotTrans, h2, newVec); |
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newVec = rotTrans * h2; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "H"; |
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atomInfo->atomTypeName = "H"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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//add atom data into atom's property |
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if (!haveAtomData) { |
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atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
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atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
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} |
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setVisited(datom); |
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} |
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} |
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|
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const std::string SSDAtomVisitor::toString() { |
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const std::string SSDAtomVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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result += buffer; |
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return result; |
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} |
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} |
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bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
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bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
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std::set<std::string>::iterator strIter; |
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strIter = linearAtomType.find(atomType); |
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return strIter != linearAtomType.end() ? true : false; |
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} |
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} |
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|
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void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
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void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
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std::vector<AtomInfo*> atoms; |
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//we need to convert linear into 4 different atoms |
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Vector3d c1(0.0, 0.0, -1.8); |
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//if atom is not SSD atom, just skip it |
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if(!isLinearAtom(datom->getType())) |
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return; |
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return; |
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data = datom->getPropertyByName("ATOMDATA"); |
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if(data != NULL){ |
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atomData = dynamic_cast<AtomData*>(data); |
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if(atomData == NULL){ |
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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else { |
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haveAtomData = true; |
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} |
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atomData = dynamic_cast<AtomData*>(data); |
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if(atomData == NULL){ |
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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else { |
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haveAtomData = true; |
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} |
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} else { |
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atomData = new AtomData; |
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haveAtomData = false; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} |
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newVec = rotTrans * c1; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->atomTypeName = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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|
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newVec = rotTrans * c2; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->atomTypeName = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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|
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newVec = rotTrans * c3; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->atomTypeName = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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|
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newVec = rotTrans * c4; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->atomTypeName = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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//add atom data into atom's property |
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|
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if(!haveAtomData){ |
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atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
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atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
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} |
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setVisited(datom); |
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|
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} |
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} |
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|
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const std::string LinearAtomVisitor::toString(){ |
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char buffer[65535]; |
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std::string result; |
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const std::string LinearAtomVisitor::toString(){ |
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char buffer[65535]; |
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std::string result; |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
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result += buffer; |
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sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
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result += buffer; |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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return result; |
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} |
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return result; |
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} |
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|
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//----------------------------------------------------------------------------// |
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bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){ |
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std::set<std::string>::iterator strIter; |
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strIter = GBLipidAtomType.find(atomType); |
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|
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void DefaultAtomVisitor::visit(Atom *atom) { |
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return strIter != GBLipidAtomType.end() ? true : false; |
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} |
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|
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void GBLipidAtomVisitor::visit(DirectionalAtom* datom){ |
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std::vector<AtomInfo*> atoms; |
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//we need to convert linear into 4 different atoms |
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Vector3d c1(0.0, 0.0, -6.25); |
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Vector3d c2(0.0, 0.0, -2.1); |
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Vector3d c3(0.0, 0.0, 2.1); |
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Vector3d c4(0.0, 0.0, 6.25); |
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RotMat3x3d rotMatrix; |
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RotMat3x3d rotTrans; |
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AtomInfo* atomInfo; |
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Vector3d pos; |
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Vector3d newVec; |
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Quat4d q; |
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AtomData* atomData; |
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GenericData* data; |
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bool haveAtomData; |
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|
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//if atom is not GBlipid atom, just skip it |
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if(!isGBLipidAtom(datom->getType())) |
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return; |
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|
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data = datom->getPropertyByName("ATOMDATA"); |
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if(data != NULL){ |
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atomData = dynamic_cast<AtomData*>(data); |
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if(atomData == NULL){ |
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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else { |
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haveAtomData = true; |
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} |
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} else { |
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atomData = new AtomData; |
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haveAtomData = false; |
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} |
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|
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|
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pos = datom->getPos(); |
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q = datom->getQ(); |
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rotMatrix = datom->getA(); |
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|
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// We need A^T to convert from body-fixed to space-fixed: |
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rotTrans = rotMatrix.transpose(); |
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|
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newVec = rotTrans * c1; |
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atomInfo = new AtomInfo; |
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atomInfo->atomTypeName = "K"; |
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> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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newVec = rotTrans * c2; |
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atomInfo = new AtomInfo; |
| 406 |
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atomInfo->atomTypeName = "K"; |
| 407 |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
| 408 |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
| 409 |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
| 414 |
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|
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newVec = rotTrans * c3; |
| 416 |
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atomInfo = new AtomInfo; |
| 417 |
> |
atomInfo->atomTypeName = "K"; |
| 418 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 419 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 420 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
| 422 |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
| 425 |
> |
|
| 426 |
> |
newVec = rotTrans * c4; |
| 427 |
> |
atomInfo = new AtomInfo; |
| 428 |
> |
atomInfo->atomTypeName = "K"; |
| 429 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 430 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 431 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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> |
atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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> |
atomData->addAtomInfo(atomInfo); |
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> |
|
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> |
//add atom data into atom's property |
| 438 |
> |
|
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> |
if(!haveAtomData){ |
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> |
atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
| 442 |
> |
} |
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> |
|
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setVisited(datom); |
| 445 |
> |
|
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} |
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> |
|
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> |
const std::string GBLipidAtomVisitor::toString(){ |
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> |
char buffer[65535]; |
| 450 |
> |
std::string result; |
| 451 |
> |
|
| 452 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 453 |
> |
result += buffer; |
| 454 |
> |
|
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> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 456 |
> |
result += buffer; |
| 457 |
> |
|
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> |
sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n"); |
| 459 |
> |
result += buffer; |
| 460 |
> |
|
| 461 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 462 |
> |
result += buffer; |
| 463 |
> |
|
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> |
return result; |
| 465 |
> |
} |
| 466 |
> |
|
| 467 |
> |
//----------------------------------------------------------------------------// |
| 468 |
> |
|
| 469 |
> |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 470 |
|
AtomData *atomData; |
| 471 |
|
AtomInfo *atomInfo; |
| 472 |
|
Vector3d pos; |
| 473 |
|
|
| 474 |
|
if (isVisited(atom)) |
| 475 |
< |
return; |
| 475 |
> |
return; |
| 476 |
|
|
| 477 |
|
atomInfo = new AtomInfo; |
| 478 |
|
|
| 480 |
|
atomData->setID("ATOMDATA"); |
| 481 |
|
|
| 482 |
|
pos = atom->getPos(); |
| 483 |
< |
atomInfo->AtomType = atom->getType(); |
| 483 |
> |
atomInfo->atomTypeName = atom->getType(); |
| 484 |
|
atomInfo->pos[0] = pos[0]; |
| 485 |
|
atomInfo->pos[1] = pos[1]; |
| 486 |
|
atomInfo->pos[2] = pos[2]; |
| 493 |
|
atom->addProperty(atomData); |
| 494 |
|
|
| 495 |
|
setVisited(atom); |
| 496 |
< |
} |
| 496 |
> |
} |
| 497 |
|
|
| 498 |
< |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 498 |
> |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 499 |
|
AtomData *atomData; |
| 500 |
|
AtomInfo *atomInfo; |
| 501 |
|
Vector3d pos; |
| 502 |
|
Vector3d u; |
| 503 |
|
|
| 504 |
|
if (isVisited(datom)) |
| 505 |
< |
return; |
| 505 |
> |
return; |
| 506 |
|
|
| 507 |
|
pos = datom->getPos(); |
| 508 |
< |
u = datom->getElectroFrame().getColumn(3); |
| 508 |
> |
u = datom->getElectroFrame().getColumn(2); |
| 509 |
|
|
| 510 |
|
atomData = new AtomData; |
| 511 |
|
atomData->setID("ATOMDATA"); |
| 512 |
|
atomInfo = new AtomInfo; |
| 513 |
|
|
| 514 |
< |
atomInfo->AtomType = datom->getType(); |
| 514 |
> |
atomInfo->atomTypeName = datom->getType(); |
| 515 |
|
atomInfo->pos[0] = pos[0]; |
| 516 |
|
atomInfo->pos[1] = pos[1]; |
| 517 |
|
atomInfo->pos[2] = pos[2]; |
| 524 |
|
datom->addProperty(atomData); |
| 525 |
|
|
| 526 |
|
setVisited(datom); |
| 527 |
< |
} |
| 527 |
> |
} |
| 528 |
|
|
| 529 |
< |
const std::string DefaultAtomVisitor::toString() { |
| 529 |
> |
const std::string DefaultAtomVisitor::toString() { |
| 530 |
|
char buffer[65535]; |
| 531 |
|
std::string result; |
| 532 |
|
|
| 546 |
|
result += buffer; |
| 547 |
|
|
| 548 |
|
return result; |
| 549 |
< |
} |
| 549 |
> |
} |
| 550 |
|
} //namespace oopse |
