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stormm::trajectory::AtomGraph Member List

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

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