| AddBondedInteraction(Interaction *ic) | votca::csg::Topology | |
| autoDetectBoxType(const Eigen::Matrix3d &box) const | votca::csg::Topology | protected |
| bc_ | votca::csg::Topology | protected |
| BCShortestConnection(const Eigen::Vector3d &r_i, const Eigen::Vector3d &r_j) const | votca::csg::Topology | |
| BeadCount() const | votca::csg::Topology | inline |
| Beads() | votca::csg::Topology | inline |
| beads_ | votca::csg::Topology | protected |
| BeadTypeExist(std::string type) const | votca::csg::Topology | |
| beadtypes_ | votca::csg::Topology | protected |
| BondedInteractions() | votca::csg::Topology | inline |
| BondedInteractions() const | votca::csg::Topology | inline |
| BoxVolume() const | votca::csg::Topology | |
| CheckMoleculeNaming(void) | votca::csg::Topology | |
| Cleanup() | votca::csg::Topology | |
| ClearMoleculeList() | votca::csg::Topology | inline |
| CopyTopologyData(Topology *top) | votca::csg::Topology | |
| CreateBead(Bead::Symmetry symmetry, std::string name, std::string type, Index resnr, double m, double q) | votca::csg::Topology | inline |
| CreateMolecule(std::string name) | votca::csg::Topology | inline |
| CreateMoleculesByRange(std::string name, Index first, Index nbeads, Index nmolecules) | votca::csg::Topology | |
| CreateResidue(std::string name) | votca::csg::Topology | inline |
| CreateResidue(std::string name, Index id) | votca::csg::Topology | inline |
| exclusions_ | votca::csg::Topology | protected |
| getBead(const Index i) | votca::csg::Topology | inline |
| getBead(const Index i) const | votca::csg::Topology | inline |
| getBeadTypeId(std::string type) const | votca::csg::Topology | |
| getBoundary() const | votca::csg::Topology | inline |
| getBox() const | votca::csg::Topology | inline |
| getBoxType() const | votca::csg::Topology | inline |
| getDist(Index bead1, Index bead2) const | votca::csg::Topology | |
| getExclusions() | votca::csg::Topology | inline |
| getExclusions() const | votca::csg::Topology | inline |
| getMolecule(const Index i) | votca::csg::Topology | inline |
| getMolecule(const Index i) const | votca::csg::Topology | inline |
| getParticleGroup() const | votca::csg::Topology | inline |
| getResidue(const Index i) | votca::csg::Topology | inline |
| getResidue(const Index i) const | votca::csg::Topology | inline |
| getStep() const | votca::csg::Topology | inline |
| getTime() const | votca::csg::Topology | inline |
| has_force_ | votca::csg::Topology | protected |
| has_vel_ | votca::csg::Topology | protected |
| HasForce() | votca::csg::Topology | inline |
| HasVel() | votca::csg::Topology | inline |
| InsertExclusion(Bead *bead1, iteratable &l) | votca::csg::Topology | inline |
| interaction_groups_ | votca::csg::Topology | protected |
| interactions_ | votca::csg::Topology | protected |
| interactions_by_group_ | votca::csg::Topology | protected |
| InteractionsInGroup(const std::string &group) | votca::csg::Topology | |
| MoleculeByIndex(Index index) | votca::csg::Topology | inline |
| MoleculeCount() const | votca::csg::Topology | inline |
| Molecules() | votca::csg::Topology | inline |
| Molecules() const | votca::csg::Topology | inline |
| molecules_ | votca::csg::Topology | protected |
| particle_group_ | votca::csg::Topology | protected |
| RebuildExclusions() | votca::csg::Topology | |
| RegisterBeadType(std::string type) | votca::csg::Topology | |
| RenameBeadType(std::string name, std::string newname) | votca::csg::Topology | |
| RenameMolecules(std::string range, std::string name) | votca::csg::Topology | |
| ResidueCount() const | votca::csg::Topology | inline |
| Residues() | votca::csg::Topology | inline |
| Residues() const | votca::csg::Topology | inline |
| residues_ | votca::csg::Topology | protected |
| SetBeadTypeMass(std::string name, double value) | votca::csg::Topology | |
| setBox(const Eigen::Matrix3d &box, BoundaryCondition::eBoxtype boxtype=BoundaryCondition::typeAuto) | votca::csg::Topology | inline |
| SetHasForce(const bool v) | votca::csg::Topology | inline |
| SetHasVel(const bool v) | votca::csg::Topology | inline |
| setParticleGroup(std::string particle_group) | votca::csg::Topology | inline |
| setStep(Index s) | votca::csg::Topology | inline |
| setTime(double t) | votca::csg::Topology | inline |
| ShortestBoxSize() const | votca::csg::Topology | |
| step_ | votca::csg::Topology | protected |
| time_ | votca::csg::Topology | protected |
| Topology() | votca::csg::Topology | inline |
| ~Topology() | votca::csg::Topology | |
