stormm::modeling::AtomGraph Member List

This is the complete list of members for stormm::modeling::AtomGraph, including all inherited members.

AtomGraph()	stormm::modeling::AtomGraph
AtomGraph(const std::string &file_name, ExceptionResponse policy=ExceptionResponse::WARN, TopologyKind engine_format=TopologyKind::AMBER)	stormm::modeling::AtomGraph
AtomGraph(const std::string &file_name, ExceptionResponse policy, TopologyKind engine_format, double coulomb_constant_in, double default_elec14_screening, double default_vdw14_screening, double charge_rounding_tol, double charge_discretization, ApplyConstraints use_bond_constraints_in=ApplyConstraints::NO, ApplyConstraints use_settle_in=ApplyConstraints::NO) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
AtomGraph(const std::vector< AtomGraph * > &agv, const std::vector< int > &counts, MoleculeOrdering arrangement=MoleculeOrdering::REORDER_ALL, ExceptionResponse policy=ExceptionResponse::DIE) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
AtomGraph(const AtomGraph &ag_a, int n_a, const AtomGraph &ag_b, int n_b, MoleculeOrdering arrangement=MoleculeOrdering::REORDER_ALL, ExceptionResponse policy=ExceptionResponse::DIE) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
AtomGraph(const AtomGraph &ag_a, const AtomGraph &ag_b, int n_b, MoleculeOrdering arrangement=MoleculeOrdering::REORDER_ALL, ExceptionResponse policy=ExceptionResponse::DIE) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
AtomGraph(const AtomGraph &ag_a, const AtomGraph &ag_b, MoleculeOrdering arrangement=MoleculeOrdering::REORDER_ALL, ExceptionResponse policy=ExceptionResponse::DIE) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
AtomGraph(const AtomGraph &original, const std::vector< int > &atom_subset, ExceptionResponse policy=ExceptionResponse::DIE, double charge_rounding_tol=default_charge_rounding_tol, double charge_discretization=default_charge_precision_inc, ApplyConstraints use_bond_constraints_in=ApplyConstraints::NO, ApplyConstraints use_settle_in=ApplyConstraints::NO) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
AtomGraph(const AtomGraph &original, const std::vector< bool > &mask, ExceptionResponse policy=ExceptionResponse::DIE, double charge_rounding_tol=default_charge_rounding_tol, double charge_discretization=default_charge_precision_inc, ApplyConstraints use_bond_constraints_in=ApplyConstraints::NO, ApplyConstraints use_settle_in=ApplyConstraints::NO) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
AtomGraph(const AtomGraph &original)	stormm::modeling::AtomGraph
AtomGraph(AtomGraph &&original)	stormm::modeling::AtomGraph
AtomGraphStage class	stormm::modeling::AtomGraph	friend
buildFromPrmtop(const std::string &file_name, const ExceptionResponse policy=ExceptionResponse::WARN, double coulomb_constant_in=amber_ancient_bioq, double default_elec14_screening=amber_default_elec14_screen, double default_vdw14_screening=amber_default_vdw14_screen, double charge_rounding_tol=default_charge_rounding_tol, double charge_discretization=default_charge_precision_inc)	stormm::modeling::AtomGraph
findVirtualSites() const	stormm::modeling::AtomGraph
findVirtualSites(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
findVirtualSites(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAngleParameterCount() const	stormm::modeling::AtomGraph
getAngleTerm(int index) const	stormm::modeling::AtomGraph
getAngleTermCount() const	stormm::modeling::AtomGraph
getAtomCount() const	stormm::modeling::AtomGraph
getAtomExclusions(int index) const	stormm::modeling::AtomGraph
getAtomicMass(MassForm rep=MassForm::ORDINARY) const	stormm::modeling::AtomGraph
getAtomicMass(int low_index, int high_index, MassForm rep=MassForm::ORDINARY) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomicMass(int index, MassForm rep=MassForm::ORDINARY) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomicNumber() const	stormm::modeling::AtomGraph
getAtomicNumber(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomicNumber(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomMobility() const	stormm::modeling::AtomGraph
getAtomMobility(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomMobility(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomMobilityMask() const	stormm::modeling::AtomGraph
getAtomMobilityMask(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomName() const	stormm::modeling::AtomGraph
getAtomName(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomName(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomPBRadius() const	stormm::modeling::AtomGraph
getAtomPBRadius(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomPBRadius(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomType() const	stormm::modeling::AtomGraph
getAtomType(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomType(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getAtomTypeNameTable() const	stormm::modeling::AtomGraph
getBondConstraintCount() const	stormm::modeling::AtomGraph
getBondParameterCount() const	stormm::modeling::AtomGraph
getBondTerm(int index) const	stormm::modeling::AtomGraph
getBondTermCount() const	stormm::modeling::AtomGraph
getChargeIndex() const	stormm::modeling::AtomGraph
getChargeIndex(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getChargeIndex(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getChargeParameter(int index) const	stormm::modeling::AtomGraph
getChargeTypeCount() const	stormm::modeling::AtomGraph
getCharmmImprParameterCount() const	stormm::modeling::AtomGraph
getCharmmImprTerm(int index) const	stormm::modeling::AtomGraph
getCharmmImprTermCount() const	stormm::modeling::AtomGraph
getChemicalDetailsKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getCmapDimension(int index) const	stormm::modeling::AtomGraph
getCmapSurfaceCount() const	stormm::modeling::AtomGraph
getCmapTerm(int index) const	stormm::modeling::AtomGraph
getCmapTermCount() const	stormm::modeling::AtomGraph
getConstrainedDegreesOfFreedom() const	stormm::modeling::AtomGraph
getConstraintGroupAtoms(int index) const	stormm::modeling::AtomGraph
getConstraintGroupCount() const	stormm::modeling::AtomGraph
getConstraintGroupTotalSize() const	stormm::modeling::AtomGraph
getCoulombConstant() const	stormm::modeling::AtomGraph
getDegreesOfFreedom() const	stormm::modeling::AtomGraph
getDescriptor(TopologyDescriptor choice) const	stormm::modeling::AtomGraph
getDescriptor(SanderDescriptor choice) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getDielectricConstant() const	stormm::modeling::AtomGraph
getDihedralParameterCount() const	stormm::modeling::AtomGraph
getDihedralTerm(int index) const	stormm::modeling::AtomGraph
getDihedralTermCount() const	stormm::modeling::AtomGraph
getDoublePrecisionConstraintKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getDoublePrecisionImplicitSolventKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getDoublePrecisionNonbondedKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getDoublePrecisionValenceKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getDoublePrecisionVirtualSiteKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getElectrostatic14Screening() const	stormm::modeling::AtomGraph
getFileName() const	stormm::modeling::AtomGraph
getFirstSolventAtom() const	stormm::modeling::AtomGraph
getFirstSolventMolecule() const	stormm::modeling::AtomGraph
getFullAtomName(int index) const	stormm::modeling::AtomGraph
getGBScreeningFactor() const	stormm::modeling::AtomGraph
getGBScreeningFactor(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getGBScreeningFactor(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getImplicitSolventModel() const	stormm::modeling::AtomGraph
getLargestMoleculeSize() const	stormm::modeling::AtomGraph
getLargestResidueSize() const	stormm::modeling::AtomGraph
getLastSoluteAtom() const	stormm::modeling::AtomGraph
getLastSoluteResidue() const	stormm::modeling::AtomGraph
getLennardJonesEpsilon(int index_a, int index_b) const	stormm::modeling::AtomGraph
getLennardJonesEpsilon(int index_a) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getLennardJonesEpsilon() const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getLennardJonesIndex() const	stormm::modeling::AtomGraph
getLennardJonesIndex(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getLennardJonesIndex(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getLennardJonesSigma(int index_a, int index_b) const	stormm::modeling::AtomGraph
getLennardJonesSigma(int index_a) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getLennardJonesSigma() const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getLJTypeCount() const	stormm::modeling::AtomGraph
getMoleculeContents() const	stormm::modeling::AtomGraph
getMoleculeContents(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getMoleculeCount() const	stormm::modeling::AtomGraph
getMoleculeKind(int mol_index) const	stormm::modeling::AtomGraph
getMoleculeLimits() const	stormm::modeling::AtomGraph
getMoleculeLimits(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getMoleculeMembership() const	stormm::modeling::AtomGraph
getMoleculeMembership(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getMoleculeMembership(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getNonbonded11Exclusions(int index) const	stormm::modeling::AtomGraph
getNonbonded12Exclusions(int index) const	stormm::modeling::AtomGraph
getNonbonded13Exclusions(int index) const	stormm::modeling::AtomGraph
getNonbonded14Exclusions(int index) const	stormm::modeling::AtomGraph
getNonrigidParticleCount() const	stormm::modeling::AtomGraph
getOrganicAtomCount() const	stormm::modeling::AtomGraph
getOrganicMoleculeCount() const	stormm::modeling::AtomGraph
getPartialCharge() const	stormm::modeling::AtomGraph
getPartialCharge(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getPartialCharge(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getParticlesPerMolecule() const	stormm::modeling::AtomGraph
getParticlesPerMolecule(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getPBRadiiSet() const	stormm::modeling::AtomGraph
getResidueCount() const	stormm::modeling::AtomGraph
getResidueIndex() const	stormm::modeling::AtomGraph
getResidueIndex(int atom_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getResidueLimits() const	stormm::modeling::AtomGraph
getResidueLimits(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getResidueName() const	stormm::modeling::AtomGraph
getResidueName(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getResidueNumber() const	stormm::modeling::AtomGraph
getResidueNumber(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getResidueNumber(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getRigidWaterAtomCount() const	stormm::modeling::AtomGraph
getRigidWaterCount() const	stormm::modeling::AtomGraph
getSaltConcentration() const	stormm::modeling::AtomGraph
getSelfPointer() const	stormm::modeling::AtomGraph
getSelfPointer() (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getSettleGroupCount() const	stormm::modeling::AtomGraph
getSinglePrecisionConstraintKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getSinglePrecisionImplicitSolventKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getSinglePrecisionNonbondedKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getSinglePrecisionValenceKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getSinglePrecisionVirtualSiteKit(HybridTargetLevel tier=HybridTargetLevel::HOST) const	stormm::modeling::AtomGraph
getStructuralAtomNumber() const	stormm::modeling::AtomGraph
getStructuralAtomNumber(int low_index, int high_index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getStructuralAtomNumber(int index) const (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
getTitle() const	stormm::modeling::AtomGraph
getTotalExclusions() const	stormm::modeling::AtomGraph
getTotalMass() const	stormm::modeling::AtomGraph
getUnitCellType() const	stormm::modeling::AtomGraph
getUreyBradleyParameterCount() const	stormm::modeling::AtomGraph
getUreyBradleyTerm(int index) const	stormm::modeling::AtomGraph
getUreyBradleyTermCount() const	stormm::modeling::AtomGraph
getVanDerWaals14Screening() const	stormm::modeling::AtomGraph
getVirtualSiteCount() const	stormm::modeling::AtomGraph
getVirtualSiteFrameAtom(int index, int nfrm) const	stormm::modeling::AtomGraph
getVirtualSiteFrameDimension(int index, int ndim)	stormm::modeling::AtomGraph
getVirtualSiteFrameType(int index) const	stormm::modeling::AtomGraph
getVirtualSiteIndex(int atom_index, ExceptionResponse policy=ExceptionResponse::DIE) const	stormm::modeling::AtomGraph
getVirtualSiteParameterSetCount() const	stormm::modeling::AtomGraph
getWaterResidueCount() const	stormm::modeling::AtomGraph
getWaterResidueName() const	stormm::modeling::AtomGraph
getWaterResidueSize() const	stormm::modeling::AtomGraph
matchOverflowAtomName(const std::string &query) const	stormm::modeling::AtomGraph
matchOverflowAtomType(const std::string &query) const	stormm::modeling::AtomGraph
matchOverflowResidueName(const std::string &query) const	stormm::modeling::AtomGraph
modifyAtomMobility(MobilitySetting movement)	stormm::modeling::AtomGraph
modifyAtomMobility(int low_index, int high_index, MobilitySetting movement) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
modifyAtomMobility(int index, MobilitySetting movement) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
modifyAtomMobility(const std::vector< int > &mask, MobilitySetting movement) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
operator=(const AtomGraph &other)	stormm::modeling::AtomGraph
operator=(AtomGraph &&other)	stormm::modeling::AtomGraph
printAmberFormat(const std::string &output_file={}, PrintSituation expectation=PrintSituation::OPEN_NEW, ExceptionResponse pr_policy=ExceptionResponse::DIE) const	stormm::modeling::AtomGraph
printToFile(const std::string &output_file={}, TopologyKind output_style=TopologyKind::AMBER, PrintSituation expectation=PrintSituation::OPEN_NEW, ExceptionResponse pr_policy=ExceptionResponse::DIE) const	stormm::modeling::AtomGraph
setAngleParameters(double new_keq, double new_teq, bool set_keq, bool set_teq, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)	stormm::modeling::AtomGraph
setAngleParameters(double new_keq, double new_teq, bool set_keq, bool set_teq, char4 type_a, char4 type_b, char4 type_c, ExceptionResponse policy=ExceptionResponse::SILENT) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
setBondParameters(double new_keq, double new_leq, bool set_keq, bool set_leq, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)	stormm::modeling::AtomGraph
setBondParameters(double new_keq, double new_leq, bool set_keq, bool set_leq, char4 type_a, char4 type_b, ExceptionResponse policy=ExceptionResponse::SILENT) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
setCharmmImprParameters(double new_stiffness, double new_phase_angle, bool set_stiffness, bool set_phase_angle, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)	stormm::modeling::AtomGraph
setCharmmImprParameters(double new_stiffness, double new_phase_angle, bool set_stiffness, bool set_phase_angle, char4 type_a, char4 type_b, char4 type_c, char4 type_d, ExceptionResponse policy=ExceptionResponse::SILENT) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
setDihedralParameters(double new_amplitude, double new_phase_angle, bool set_amplitude, bool set_phase_angle, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)	stormm::modeling::AtomGraph
setDihedralParameters(double new_amplitude, double new_phase_angle, bool set_amplitude, bool set_phase_angle, char4 type_a, char4 type_b, char4 type_c, char4 type_d, double periodicity, ExceptionResponse policy=ExceptionResponse::SILENT) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
setImplicitSolventModel(ImplicitSolventModel igb_in, double dielectric_in=80.0, double saltcon_in=0.0, AtomicRadiusSet radii_set=AtomicRadiusSet::NONE, ExceptionResponse policy=ExceptionResponse::WARN)	stormm::modeling::AtomGraph
setSource(const std::string &new_source)	stormm::modeling::AtomGraph
setUreyBradleyParameters(double new_keq, double new_leq, bool set_keq, bool set_leq, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)	stormm::modeling::AtomGraph
setUreyBradleyParameters(double new_keq, double new_leq, bool set_keq, bool set_leq, char4 type_a, char4 type_b, char4 type_c, ExceptionResponse policy=ExceptionResponse::SILENT) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
setWaterResidueName(const char4 new_name)	stormm::modeling::AtomGraph
setWaterResidueName(const std::string &new_name) (defined in stormm::modeling::AtomGraph)	stormm::modeling::AtomGraph
usesSettle() const	stormm::modeling::AtomGraph
usesShake() const	stormm::modeling::AtomGraph
~AtomGraph()=default	stormm::modeling::AtomGraph