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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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//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass |
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//of the water with a dipole moment |
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//we need to convert SSD into 4 different atoms |
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//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of |
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//the mass of the water with a dipole moment |
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Vector3d h1(0.0, -0.75695, 0.5206); |
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Vector3d h2(0.0, 0.75695, 0.5206); |
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Vector3d ox(0.0, 0.0, -0.0654); |
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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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|
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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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|
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bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
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|
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bool TREDAtomVisitor::isTREDAtom(const std::string&atomType) { |
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std::set<std::string>::iterator strIter; |
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strIter = tredAtomType.find(atomType); |
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return strIter != tredAtomType.end() ? true : false; |
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} |
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|
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void TREDAtomVisitor::visit(DirectionalAtom *datom) { |
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std::vector<AtomInfo*>atoms; |
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|
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// we need to convert a TRED into 4 different atoms: |
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// one oxygen atom, two hydrogen atoms, and one atom which is the center of |
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// the mass of the water with a dipole moment |
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Vector3d h1(0.0, -0.75695, 0.5206); |
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Vector3d h2(0.0, 0.75695, 0.5206); |
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Vector3d ox(0.0, 0.0, -0.0654); |
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Vector3d u(0, 0, 1); |
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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 the atom is not a TRED atom, skip it |
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if (!isTREDAtom(datom->getType())) |
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return; |
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|
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data = datom->getPropertyByName("ATOMDATA"); |
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|
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if (data != NULL) { |
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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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} 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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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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// transposeMat3(rotMatrix, rotTrans); |
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rotTrans = rotMatrix.transpose(); |
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|
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// center of mass of the water molecule |
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// matVecMul3(rotTrans, u, newVec); |
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newVec = rotTrans * u; |
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|
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atomInfo = new AtomInfo; |
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atomInfo->atomTypeName = "TRED"; |
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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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atomInfo->dipole[0] = newVec[0]; |
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atomInfo->dipole[1] = newVec[1]; |
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atomInfo->dipole[2] = newVec[2]; |
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|
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atomData->addAtomInfo(atomInfo); |
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|
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// oxygen |
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// matVecMul3(rotTrans, ox, newVec); |
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newVec = rotTrans * ox; |
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|
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atomInfo = new AtomInfo; |
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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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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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// hydrogen1 |
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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->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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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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// hydrogen2 |
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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->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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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 |
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> |
|
| 329 |
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if (!haveAtomData) { |
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atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
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> |
} |
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> |
|
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> |
setVisited(datom); |
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} |
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> |
|
| 337 |
> |
const std::string TREDAtomVisitor::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, |
| 342 |
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"------------------------------------------------------------------\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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|
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sprintf(buffer, |
| 349 |
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"Visitor Description: Convert the TRED atom into 4 different atoms\n"); |
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result += buffer; |
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|
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sprintf(buffer, |
| 353 |
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"------------------------------------------------------------------\n"); |
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result += buffer; |
| 355 |
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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 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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|
| 364 |
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return strIter != linearAtomType.end() ? true : false; |
| 365 |
< |
} |
| 365 |
> |
} |
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|
| 367 |
< |
void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
| 367 |
> |
void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){ |
| 368 |
> |
linearAtomType.insert(atomType); |
| 369 |
> |
} |
| 370 |
> |
|
| 371 |
> |
void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
| 372 |
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std::vector<AtomInfo*> atoms; |
| 373 |
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//we need to convert linear into 4 different atoms |
| 374 |
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Vector3d c1(0.0, 0.0, -1.8); |
| 384 |
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AtomData* atomData; |
| 385 |
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GenericData* data; |
| 386 |
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bool haveAtomData; |
| 387 |
+ |
AtomType* atomType; |
| 388 |
+ |
//if atom is not linear atom, just skip it |
| 389 |
+ |
if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne()) |
| 390 |
+ |
return; |
| 391 |
|
|
| 392 |
< |
//if atom is not SSD atom, just skip it |
| 393 |
< |
if(!isLinearAtom(datom->getType())) |
| 394 |
< |
return; |
| 392 |
> |
//setup GayBerne type in fortran side |
| 393 |
> |
data = datom->getAtomType()->getPropertyByName("GayBerne"); |
| 394 |
> |
if (data != NULL) { |
| 395 |
> |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 396 |
|
|
| 397 |
+ |
if (gayBerneData != NULL) { |
| 398 |
+ |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
| 399 |
+ |
|
| 400 |
+ |
// double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0; |
| 401 |
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double halfLen = gayBerneParam.GB_l/2.0; |
| 402 |
+ |
c1[2] = -halfLen; |
| 403 |
+ |
c2[2] = -halfLen /2; |
| 404 |
+ |
c3[2] = halfLen/2; |
| 405 |
+ |
c4[2] = halfLen; |
| 406 |
+ |
|
| 407 |
+ |
} |
| 408 |
+ |
|
| 409 |
+ |
else { |
| 410 |
+ |
sprintf( painCave.errMsg, |
| 411 |
+ |
"Can not cast GenericData to GayBerneParam\n"); |
| 412 |
+ |
painCave.severity = OOPSE_ERROR; |
| 413 |
+ |
painCave.isFatal = 1; |
| 414 |
+ |
simError(); |
| 415 |
+ |
} |
| 416 |
+ |
} |
| 417 |
+ |
|
| 418 |
+ |
|
| 419 |
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data = datom->getPropertyByName("ATOMDATA"); |
| 420 |
|
if(data != NULL){ |
| 421 |
< |
atomData = dynamic_cast<AtomData*>(data); |
| 422 |
< |
if(atomData == NULL){ |
| 423 |
< |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 424 |
< |
atomData = new AtomData; |
| 425 |
< |
haveAtomData = false; |
| 426 |
< |
} else { |
| 427 |
< |
haveAtomData = true; |
| 428 |
< |
} |
| 421 |
> |
atomData = dynamic_cast<AtomData*>(data); |
| 422 |
> |
if(atomData == NULL){ |
| 423 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 424 |
> |
atomData = new AtomData; |
| 425 |
> |
haveAtomData = false; |
| 426 |
> |
} else { |
| 427 |
> |
haveAtomData = true; |
| 428 |
> |
} |
| 429 |
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} else { |
| 430 |
< |
atomData = new AtomData; |
| 431 |
< |
haveAtomData = false; |
| 430 |
> |
atomData = new AtomData; |
| 431 |
> |
haveAtomData = false; |
| 432 |
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} |
| 433 |
|
|
| 434 |
|
|
| 441 |
|
|
| 442 |
|
newVec = rotTrans * c1; |
| 443 |
|
atomInfo = new AtomInfo; |
| 444 |
< |
atomInfo->AtomType = "C"; |
| 444 |
> |
atomInfo->atomTypeName = "C"; |
| 445 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 446 |
|
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 447 |
|
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 452 |
|
|
| 453 |
|
newVec = rotTrans * c2; |
| 454 |
|
atomInfo = new AtomInfo; |
| 455 |
< |
atomInfo->AtomType = "C"; |
| 455 |
> |
atomInfo->atomTypeName = "C"; |
| 456 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 457 |
|
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 458 |
|
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 463 |
|
|
| 464 |
|
newVec = rotTrans * c3; |
| 465 |
|
atomInfo = new AtomInfo; |
| 466 |
< |
atomInfo->AtomType = "C"; |
| 466 |
> |
atomInfo->atomTypeName = "C"; |
| 467 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 468 |
|
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 469 |
|
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 474 |
|
|
| 475 |
|
newVec = rotTrans * c4; |
| 476 |
|
atomInfo = new AtomInfo; |
| 477 |
< |
atomInfo->AtomType = "C"; |
| 477 |
> |
atomInfo->atomTypeName = "C"; |
| 478 |
|
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 479 |
|
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 480 |
|
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 486 |
|
//add atom data into atom's property |
| 487 |
|
|
| 488 |
|
if(!haveAtomData){ |
| 489 |
< |
atomData->setID("ATOMDATA"); |
| 490 |
< |
datom->addProperty(atomData); |
| 489 |
> |
atomData->setID("ATOMDATA"); |
| 490 |
> |
datom->addProperty(atomData); |
| 491 |
|
} |
| 492 |
|
|
| 493 |
|
setVisited(datom); |
| 494 |
|
|
| 495 |
< |
} |
| 495 |
> |
} |
| 496 |
|
|
| 497 |
< |
const std::string LinearAtomVisitor::toString(){ |
| 498 |
< |
char buffer[65535]; |
| 499 |
< |
std::string result; |
| 497 |
> |
const std::string LinearAtomVisitor::toString(){ |
| 498 |
> |
char buffer[65535]; |
| 499 |
> |
std::string result; |
| 500 |
|
|
| 501 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 502 |
< |
result += buffer; |
| 501 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 502 |
> |
result += buffer; |
| 503 |
|
|
| 504 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 505 |
< |
result += buffer; |
| 504 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 505 |
> |
result += buffer; |
| 506 |
|
|
| 507 |
< |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
| 508 |
< |
result += buffer; |
| 507 |
> |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
| 508 |
> |
result += buffer; |
| 509 |
|
|
| 510 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 511 |
< |
result += buffer; |
| 510 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 511 |
> |
result += buffer; |
| 512 |
|
|
| 513 |
< |
return result; |
| 514 |
< |
} |
| 513 |
> |
return result; |
| 514 |
> |
} |
| 515 |
|
|
| 516 |
< |
//----------------------------------------------------------------------------// |
| 516 |
> |
bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){ |
| 517 |
> |
std::set<std::string>::iterator strIter; |
| 518 |
> |
strIter = GBLipidAtomType.find(atomType); |
| 519 |
|
|
| 520 |
< |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 520 |
> |
return strIter != GBLipidAtomType.end() ? true : false; |
| 521 |
> |
} |
| 522 |
> |
|
| 523 |
> |
void GBLipidAtomVisitor::visit(DirectionalAtom* datom){ |
| 524 |
> |
std::vector<AtomInfo*> atoms; |
| 525 |
> |
//we need to convert linear into 4 different atoms |
| 526 |
> |
//Vector3d c1(0.0, 0.0, -6.25); |
| 527 |
> |
//Vector3d c2(0.0, 0.0, -2.1); |
| 528 |
> |
//Vector3d c3(0.0, 0.0, 2.1); |
| 529 |
> |
//Vector3d c4(0.0, 0.0, 6.25); |
| 530 |
> |
Vector3d c1(0.0, 0.0, 0.0); |
| 531 |
> |
Vector3d c2(0.0, 0.0, 1.0); |
| 532 |
> |
RotMat3x3d rotMatrix; |
| 533 |
> |
RotMat3x3d rotTrans; |
| 534 |
> |
AtomInfo* atomInfo; |
| 535 |
> |
Vector3d pos; |
| 536 |
> |
Vector3d newVec; |
| 537 |
> |
Vector3d dVec; |
| 538 |
> |
Quat4d q; |
| 539 |
> |
AtomData* atomData; |
| 540 |
> |
GenericData* data; |
| 541 |
> |
bool haveAtomData; |
| 542 |
> |
|
| 543 |
> |
//if atom is not GBlipid atom, just skip it |
| 544 |
> |
if(!isGBLipidAtom(datom->getType())) |
| 545 |
> |
return; |
| 546 |
> |
|
| 547 |
> |
data = datom->getPropertyByName("ATOMDATA"); |
| 548 |
> |
if(data != NULL){ |
| 549 |
> |
atomData = dynamic_cast<AtomData*>(data); |
| 550 |
> |
if(atomData == NULL){ |
| 551 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 552 |
> |
atomData = new AtomData; |
| 553 |
> |
haveAtomData = false; |
| 554 |
> |
} else { |
| 555 |
> |
haveAtomData = true; |
| 556 |
> |
} |
| 557 |
> |
} else { |
| 558 |
> |
atomData = new AtomData; |
| 559 |
> |
haveAtomData = false; |
| 560 |
> |
} |
| 561 |
> |
|
| 562 |
> |
|
| 563 |
> |
pos = datom->getPos(); |
| 564 |
> |
q = datom->getQ(); |
| 565 |
> |
rotMatrix = datom->getA(); |
| 566 |
> |
|
| 567 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
| 568 |
> |
rotTrans = rotMatrix.transpose(); |
| 569 |
> |
|
| 570 |
> |
newVec = rotTrans * c1; |
| 571 |
> |
dVec = rotTrans * c2; |
| 572 |
> |
atomInfo = new AtomInfo; |
| 573 |
> |
atomInfo->atomTypeName = "GB"; |
| 574 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 575 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 576 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 577 |
> |
atomInfo->dipole[0] = dVec[0]; |
| 578 |
> |
atomInfo->dipole[1] = dVec[1]; |
| 579 |
> |
atomInfo->dipole[2] = dVec[2]; |
| 580 |
> |
atomInfo->hasVector = true; |
| 581 |
> |
atomInfo->charge = 3.0; |
| 582 |
> |
atomInfo->hasCharge = true; |
| 583 |
> |
atomData->addAtomInfo(atomInfo); |
| 584 |
> |
|
| 585 |
> |
//newVec = rotTrans * c2; |
| 586 |
> |
//atomInfo = new AtomInfo; |
| 587 |
> |
//atomInfo->atomTypeName = "K"; |
| 588 |
> |
//atomInfo->pos[0] = pos[0] + newVec[0]; |
| 589 |
> |
//atomInfo->pos[1] = pos[1] + newVec[1]; |
| 590 |
> |
//atomInfo->pos[2] = pos[2] + newVec[2]; |
| 591 |
> |
//atomInfo->dipole[0] = 0.0; |
| 592 |
> |
//atomInfo->dipole[1] = 0.0; |
| 593 |
> |
//atomInfo->dipole[2] = 0.0; |
| 594 |
> |
//atomData->addAtomInfo(atomInfo); |
| 595 |
> |
|
| 596 |
> |
//newVec = rotTrans * c3; |
| 597 |
> |
//atomInfo = new AtomInfo; |
| 598 |
> |
//atomInfo->atomTypeName = "K"; |
| 599 |
> |
//atomInfo->pos[0] = pos[0] + newVec[0]; |
| 600 |
> |
//atomInfo->pos[1] = pos[1] + newVec[1]; |
| 601 |
> |
//atomInfo->pos[2] = pos[2] + newVec[2]; |
| 602 |
> |
//atomInfo->dipole[0] = 0.0; |
| 603 |
> |
//atomInfo->dipole[1] = 0.0; |
| 604 |
> |
//atomInfo->dipole[2] = 0.0; |
| 605 |
> |
//atomData->addAtomInfo(atomInfo); |
| 606 |
> |
|
| 607 |
> |
//newVec = rotTrans * c4; |
| 608 |
> |
//atomInfo = new AtomInfo; |
| 609 |
> |
//atomInfo->atomTypeName = "K"; |
| 610 |
> |
//atomInfo->pos[0] = pos[0] + newVec[0]; |
| 611 |
> |
//atomInfo->pos[1] = pos[1] + newVec[1]; |
| 612 |
> |
//atomInfo->pos[2] = pos[2] + newVec[2]; |
| 613 |
> |
//atomInfo->dipole[0] = 0.0; |
| 614 |
> |
//atomInfo->dipole[1] = 0.0; |
| 615 |
> |
//atomInfo->dipole[2] = 0.0; |
| 616 |
> |
//atomData->addAtomInfo(atomInfo); |
| 617 |
> |
|
| 618 |
> |
//add atom data into atom's property |
| 619 |
> |
|
| 620 |
> |
if(!haveAtomData){ |
| 621 |
> |
atomData->setID("ATOMDATA"); |
| 622 |
> |
datom->addProperty(atomData); |
| 623 |
> |
} |
| 624 |
> |
|
| 625 |
> |
setVisited(datom); |
| 626 |
> |
|
| 627 |
> |
} |
| 628 |
> |
|
| 629 |
> |
const std::string GBLipidAtomVisitor::toString(){ |
| 630 |
> |
char buffer[65535]; |
| 631 |
> |
std::string result; |
| 632 |
> |
|
| 633 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 634 |
> |
result += buffer; |
| 635 |
> |
|
| 636 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 637 |
> |
result += buffer; |
| 638 |
> |
|
| 639 |
> |
sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n"); |
| 640 |
> |
result += buffer; |
| 641 |
> |
|
| 642 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 643 |
> |
result += buffer; |
| 644 |
> |
|
| 645 |
> |
return result; |
| 646 |
> |
} |
| 647 |
> |
|
| 648 |
> |
bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){ |
| 649 |
> |
std::set<std::string>::iterator strIter; |
| 650 |
> |
strIter = Ring5gbAtomType.find(atomType); |
| 651 |
> |
|
| 652 |
> |
return strIter != Ring5gbAtomType.end() ? true : false; |
| 653 |
> |
} |
| 654 |
> |
|
| 655 |
> |
void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){ |
| 656 |
> |
std::vector<AtomInfo*> atoms; |
| 657 |
> |
//we need to convert linear into 4 different atoms |
| 658 |
> |
Vector3d c1(0.0, 0.0, -5.5); |
| 659 |
> |
Vector3d c2(0.0, 0.0, -1.8); |
| 660 |
> |
Vector3d c3(0.0, 0.0, 1.8); |
| 661 |
> |
Vector3d c4(0.0, 0.0, 5.5); |
| 662 |
> |
RotMat3x3d rotMatrix; |
| 663 |
> |
RotMat3x3d rotTrans; |
| 664 |
> |
AtomInfo* atomInfo; |
| 665 |
> |
Vector3d pos; |
| 666 |
> |
Vector3d newVec; |
| 667 |
> |
Vector3d dVec; |
| 668 |
> |
Quat4d q; |
| 669 |
> |
AtomData* atomData; |
| 670 |
> |
GenericData* data; |
| 671 |
> |
bool haveAtomData; |
| 672 |
> |
|
| 673 |
> |
//if atom is not Ring5GB atom, just skip it |
| 674 |
> |
if(!isRing5gbAtom(datom->getType())) |
| 675 |
> |
return; |
| 676 |
> |
|
| 677 |
> |
data = datom->getPropertyByName("ATOMDATA"); |
| 678 |
> |
if(data != NULL){ |
| 679 |
> |
atomData = dynamic_cast<AtomData*>(data); |
| 680 |
> |
if(atomData == NULL){ |
| 681 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 682 |
> |
atomData = new AtomData; |
| 683 |
> |
haveAtomData = false; |
| 684 |
> |
} else { |
| 685 |
> |
haveAtomData = true; |
| 686 |
> |
} |
| 687 |
> |
} else { |
| 688 |
> |
atomData = new AtomData; |
| 689 |
> |
haveAtomData = false; |
| 690 |
> |
} |
| 691 |
> |
|
| 692 |
> |
|
| 693 |
> |
pos = datom->getPos(); |
| 694 |
> |
q = datom->getQ(); |
| 695 |
> |
rotMatrix = datom->getA(); |
| 696 |
> |
|
| 697 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
| 698 |
> |
rotTrans = rotMatrix.transpose(); |
| 699 |
> |
|
| 700 |
> |
newVec = rotTrans * c1; |
| 701 |
> |
atomInfo = new AtomInfo; |
| 702 |
> |
atomInfo->atomTypeName = "K"; |
| 703 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 704 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 705 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 706 |
> |
atomInfo->dipole[0] = 0.0; |
| 707 |
> |
atomInfo->dipole[1] = 0.0; |
| 708 |
> |
atomInfo->dipole[2] = 0.0; |
| 709 |
> |
atomData->addAtomInfo(atomInfo); |
| 710 |
> |
|
| 711 |
> |
newVec = rotTrans * c2; |
| 712 |
> |
atomInfo = new AtomInfo; |
| 713 |
> |
atomInfo->atomTypeName = "K"; |
| 714 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 715 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 716 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 717 |
> |
atomInfo->dipole[0] = 0.0; |
| 718 |
> |
atomInfo->dipole[1] = 0.0; |
| 719 |
> |
atomInfo->dipole[2] = 0.0; |
| 720 |
> |
atomData->addAtomInfo(atomInfo); |
| 721 |
> |
|
| 722 |
> |
newVec = rotTrans * c3; |
| 723 |
> |
atomInfo = new AtomInfo; |
| 724 |
> |
atomInfo->atomTypeName = "K"; |
| 725 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 726 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 727 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 728 |
> |
atomInfo->dipole[0] = 0.0; |
| 729 |
> |
atomInfo->dipole[1] = 0.0; |
| 730 |
> |
atomInfo->dipole[2] = 0.0; |
| 731 |
> |
atomData->addAtomInfo(atomInfo); |
| 732 |
> |
|
| 733 |
> |
newVec = rotTrans * c4; |
| 734 |
> |
atomInfo = new AtomInfo; |
| 735 |
> |
atomInfo->atomTypeName = "K"; |
| 736 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 737 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 738 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 739 |
> |
atomInfo->dipole[0] = 0.0; |
| 740 |
> |
atomInfo->dipole[1] = 0.0; |
| 741 |
> |
atomInfo->dipole[2] = 0.0; |
| 742 |
> |
atomData->addAtomInfo(atomInfo); |
| 743 |
> |
|
| 744 |
> |
//add atom data into atom's property |
| 745 |
> |
|
| 746 |
> |
if(!haveAtomData){ |
| 747 |
> |
atomData->setID("ATOMDATA"); |
| 748 |
> |
datom->addProperty(atomData); |
| 749 |
> |
} |
| 750 |
> |
|
| 751 |
> |
setVisited(datom); |
| 752 |
> |
|
| 753 |
> |
} |
| 754 |
> |
|
| 755 |
> |
const std::string Ring5gbAtomVisitor::toString(){ |
| 756 |
> |
char buffer[65535]; |
| 757 |
> |
std::string result; |
| 758 |
> |
|
| 759 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 760 |
> |
result += buffer; |
| 761 |
> |
|
| 762 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 763 |
> |
result += buffer; |
| 764 |
> |
|
| 765 |
> |
sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n"); |
| 766 |
> |
result += buffer; |
| 767 |
> |
|
| 768 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 769 |
> |
result += buffer; |
| 770 |
> |
|
| 771 |
> |
return result; |
| 772 |
> |
} |
| 773 |
> |
|
| 774 |
> |
bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){ |
| 775 |
> |
std::set<std::string>::iterator strIter; |
| 776 |
> |
strIter = HeadAtomType.find(atomType); |
| 777 |
> |
|
| 778 |
> |
return strIter != HeadAtomType.end() ? true : false; |
| 779 |
> |
} |
| 780 |
> |
|
| 781 |
> |
void HeadAtomVisitor::visit(DirectionalAtom* datom){ |
| 782 |
> |
std::vector<AtomInfo*> atoms; |
| 783 |
> |
//we need to convert linear into 2 different atoms |
| 784 |
> |
Vector3d c1(0.0, 0.0, -1.5); |
| 785 |
> |
Vector3d c2(0.0, 0.0, 1.5); |
| 786 |
> |
RotMat3x3d rotMatrix; |
| 787 |
> |
RotMat3x3d rotTrans; |
| 788 |
> |
AtomInfo* atomInfo; |
| 789 |
> |
Vector3d pos; |
| 790 |
> |
Vector3d newVec; |
| 791 |
> |
Vector3d dVec; |
| 792 |
> |
Quat4d q; |
| 793 |
> |
AtomData* atomData; |
| 794 |
> |
GenericData* data; |
| 795 |
> |
bool haveAtomData; |
| 796 |
> |
|
| 797 |
> |
//if atom is not Head atom, just skip it |
| 798 |
> |
if(!isHeadAtom(datom->getType())) |
| 799 |
> |
return; |
| 800 |
> |
|
| 801 |
> |
data = datom->getPropertyByName("ATOMDATA"); |
| 802 |
> |
if(data != NULL){ |
| 803 |
> |
atomData = dynamic_cast<AtomData*>(data); |
| 804 |
> |
if(atomData == NULL){ |
| 805 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 806 |
> |
atomData = new AtomData; |
| 807 |
> |
haveAtomData = false; |
| 808 |
> |
} else { |
| 809 |
> |
haveAtomData = true; |
| 810 |
> |
} |
| 811 |
> |
} else { |
| 812 |
> |
atomData = new AtomData; |
| 813 |
> |
haveAtomData = false; |
| 814 |
> |
} |
| 815 |
> |
|
| 816 |
> |
|
| 817 |
> |
pos = datom->getPos(); |
| 818 |
> |
q = datom->getQ(); |
| 819 |
> |
rotMatrix = datom->getA(); |
| 820 |
> |
|
| 821 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
| 822 |
> |
rotTrans = rotMatrix.transpose(); |
| 823 |
> |
|
| 824 |
> |
newVec = rotTrans * c1; |
| 825 |
> |
atomInfo = new AtomInfo; |
| 826 |
> |
atomInfo->atomTypeName = "C"; |
| 827 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 828 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 829 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 830 |
> |
atomInfo->dipole[0] = 0.0; |
| 831 |
> |
atomInfo->dipole[1] = 0.0; |
| 832 |
> |
atomInfo->dipole[2] = 0.0; |
| 833 |
> |
atomData->addAtomInfo(atomInfo); |
| 834 |
> |
|
| 835 |
> |
newVec = rotTrans * c2; |
| 836 |
> |
atomInfo = new AtomInfo; |
| 837 |
> |
atomInfo->atomTypeName = "O"; |
| 838 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 839 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 840 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 841 |
> |
atomInfo->dipole[0] = 0.0; |
| 842 |
> |
atomInfo->dipole[1] = 0.0; |
| 843 |
> |
atomInfo->dipole[2] = 0.0; |
| 844 |
> |
atomData->addAtomInfo(atomInfo); |
| 845 |
> |
|
| 846 |
> |
//add atom data into atom's property |
| 847 |
> |
|
| 848 |
> |
if(!haveAtomData){ |
| 849 |
> |
atomData->setID("ATOMDATA"); |
| 850 |
> |
datom->addProperty(atomData); |
| 851 |
> |
} |
| 852 |
> |
|
| 853 |
> |
setVisited(datom); |
| 854 |
> |
|
| 855 |
> |
} |
| 856 |
> |
|
| 857 |
> |
const std::string HeadAtomVisitor::toString(){ |
| 858 |
> |
char buffer[65535]; |
| 859 |
> |
std::string result; |
| 860 |
> |
|
| 861 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 862 |
> |
result += buffer; |
| 863 |
> |
|
| 864 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 865 |
> |
result += buffer; |
| 866 |
> |
|
| 867 |
> |
sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n"); |
| 868 |
> |
result += buffer; |
| 869 |
> |
|
| 870 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 871 |
> |
result += buffer; |
| 872 |
> |
|
| 873 |
> |
return result; |
| 874 |
> |
} |
| 875 |
> |
|
| 876 |
> |
|
| 877 |
> |
//----------------------------------------------------------------------------// |
| 878 |
> |
|
| 879 |
> |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 880 |
|
AtomData *atomData; |
| 881 |
|
AtomInfo *atomInfo; |
| 882 |
|
Vector3d pos; |
| 883 |
|
|
| 884 |
|
if (isVisited(atom)) |
| 885 |
< |
return; |
| 885 |
> |
return; |
| 886 |
|
|
| 887 |
|
atomInfo = new AtomInfo; |
| 888 |
|
|
| 890 |
|
atomData->setID("ATOMDATA"); |
| 891 |
|
|
| 892 |
|
pos = atom->getPos(); |
| 893 |
< |
atomInfo->AtomType = atom->getType(); |
| 893 |
> |
atomInfo->atomTypeName = atom->getType(); |
| 894 |
|
atomInfo->pos[0] = pos[0]; |
| 895 |
|
atomInfo->pos[1] = pos[1]; |
| 896 |
|
atomInfo->pos[2] = pos[2]; |
| 903 |
|
atom->addProperty(atomData); |
| 904 |
|
|
| 905 |
|
setVisited(atom); |
| 906 |
< |
} |
| 906 |
> |
} |
| 907 |
|
|
| 908 |
< |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 908 |
> |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 909 |
|
AtomData *atomData; |
| 910 |
|
AtomInfo *atomInfo; |
| 911 |
|
Vector3d pos; |
| 912 |
|
Vector3d u; |
| 913 |
|
|
| 914 |
|
if (isVisited(datom)) |
| 915 |
< |
return; |
| 915 |
> |
return; |
| 916 |
|
|
| 917 |
|
pos = datom->getPos(); |
| 918 |
< |
u = datom->getElectroFrame().getColumn(3); |
| 919 |
< |
|
| 918 |
> |
if (datom->getAtomType()->isGayBerne()) { |
| 919 |
> |
u = datom->getA().transpose()*V3Z; |
| 920 |
> |
} else if (datom->getAtomType()->isMultipole()) { |
| 921 |
> |
u = datom->getElectroFrame().getColumn(2); |
| 922 |
> |
} |
| 923 |
|
atomData = new AtomData; |
| 924 |
|
atomData->setID("ATOMDATA"); |
| 925 |
|
atomInfo = new AtomInfo; |
| 926 |
|
|
| 927 |
< |
atomInfo->AtomType = datom->getType(); |
| 927 |
> |
atomInfo->atomTypeName = datom->getType(); |
| 928 |
|
atomInfo->pos[0] = pos[0]; |
| 929 |
|
atomInfo->pos[1] = pos[1]; |
| 930 |
|
atomInfo->pos[2] = pos[2]; |
| 937 |
|
datom->addProperty(atomData); |
| 938 |
|
|
| 939 |
|
setVisited(datom); |
| 940 |
< |
} |
| 940 |
> |
} |
| 941 |
|
|
| 942 |
< |
const std::string DefaultAtomVisitor::toString() { |
| 942 |
> |
const std::string DefaultAtomVisitor::toString() { |
| 943 |
|
char buffer[65535]; |
| 944 |
|
std::string result; |
| 945 |
|
|
| 959 |
|
result += buffer; |
| 960 |
|
|
| 961 |
|
return result; |
| 962 |
< |
} |
| 962 |
> |
} |
| 963 |
|
} //namespace oopse |
