Index

_

__init__() (BioSimSpace._Config.Amber method) (BioSimSpace._Config.Gromacs method) (BioSimSpace._Config.Somd method) (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.SearchResult method) (BioSimSpace._SireWrappers.System method) (BioSimSpace._Utils.WorkDir method) (BioSimSpace.FreeEnergy.ATM method) (BioSimSpace.FreeEnergy.ATMSetup method) (BioSimSpace.FreeEnergy.Relative method) (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Node method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) (BioSimSpace.Metadynamics.Bound method) (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) (BioSimSpace.Metadynamics.Grid method) (BioSimSpace.Metadynamics.Restraint method) (BioSimSpace.Notebook.View method) (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Plumed method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Custom method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Minimisation method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) (BioSimSpace.Trajectory.Trajectory method) (BioSimSpace.Types.Angle method) (BioSimSpace.Types.Area method) (BioSimSpace.Types.Charge method) (BioSimSpace.Types.Coordinate method) (BioSimSpace.Types.Energy method) (BioSimSpace.Types.Length method) (BioSimSpace.Types.Pressure method) (BioSimSpace.Types.Temperature method) (BioSimSpace.Types.Time method) (BioSimSpace.Types.Vector method) (BioSimSpace.Types.Volume method)

_assert_imported() (in module BioSimSpace._Utils) _have_imported() (in module BioSimSpace._Utils) _module_stub() (in module BioSimSpace._Utils) _try_import() (in module BioSimSpace._Utils)

A

add_note() (BioSimSpace._Exceptions.AlignmentError method) (BioSimSpace._Exceptions.AnalysisError method) (BioSimSpace._Exceptions.ConversionError method) (BioSimSpace._Exceptions.IncompatibleError method) (BioSimSpace._Exceptions.MissingSoftwareError method) (BioSimSpace._Exceptions.ParameterisationError method) (BioSimSpace._Exceptions.StreamError method) (BioSimSpace._Exceptions.ThirdPartyError method) addArgs() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) addAuthor() (BioSimSpace.Gateway.Node method) addError() (BioSimSpace.Gateway.Node method) addInput() (BioSimSpace.Gateway.Node method) addMolecules() (BioSimSpace._SireWrappers.System method) addOutput() (BioSimSpace.Gateway.Node method) addProcess() (BioSimSpace.Process.ProcessRunner method) addToConfig() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) AlignmentError Amber (class in BioSimSpace._Config) (class in BioSimSpace.Process) amberForceFields() (in module BioSimSpace.Parameters) amberProteinForceFields() (in module BioSimSpace.Parameters) analyse() (BioSimSpace.FreeEnergy.ATM static method) (BioSimSpace.FreeEnergy.Relative static method)

AnalysisError Angle (class in BioSimSpace.Types) angle() (BioSimSpace.Types.Angle class method) (BioSimSpace.Types.Area class method) (BioSimSpace.Types.Charge class method) (BioSimSpace.Types.Energy class method) (BioSimSpace.Types.Length class method) (BioSimSpace.Types.Pressure class method) (BioSimSpace.Types.Temperature class method) (BioSimSpace.Types.Time class method) (BioSimSpace.Types.Vector method) (BioSimSpace.Types.Volume class method) angstrom (in module BioSimSpace.Units.Length) angstrom2 (in module BioSimSpace.Units.Area) angstrom3 (in module BioSimSpace.Units.Volume) angstroms() (BioSimSpace.Types.Length method) angstroms2() (BioSimSpace.Types.Area method) angstroms3() (BioSimSpace.Types.Volume method) Area (class in BioSimSpace.Gateway) (class in BioSimSpace.Types) ATM (class in BioSimSpace.FreeEnergy) atm (in module BioSimSpace.Units.Pressure) atm() (BioSimSpace.Types.Pressure method) ATMAnnealing (class in BioSimSpace.Protocol) ATMEquilibration (class in BioSimSpace.Protocol) ATMMinimisation (class in BioSimSpace.Protocol) ATMProduction (class in BioSimSpace.Protocol) ATMSetup (class in BioSimSpace.FreeEnergy) Atom (class in BioSimSpace._SireWrappers) atom0() (BioSimSpace._SireWrappers.Bond method) atom1() (BioSimSpace._SireWrappers.Bond method) atoms() (BioSimSpace._SireWrappers.SearchResult method)

B

bar (in module BioSimSpace.Units.Pressure) bar() (BioSimSpace.Types.Pressure method) BioSimSpace._Config module BioSimSpace._Exceptions module BioSimSpace._SireWrappers module BioSimSpace._Utils module BioSimSpace.Align module BioSimSpace.Box module BioSimSpace.Convert module BioSimSpace.FreeEnergy module BioSimSpace.Gateway module BioSimSpace.IO module BioSimSpace.MD module BioSimSpace.Metadynamics module

BioSimSpace.Metadynamics.CollectiveVariable module BioSimSpace.Node module BioSimSpace.Notebook module BioSimSpace.Parameters module BioSimSpace.Process module BioSimSpace.Protocol module BioSimSpace.Solvent module BioSimSpace.Stream module BioSimSpace.Trajectory module BioSimSpace.Types module BioSimSpace.Units module Bond (class in BioSimSpace._SireWrappers) bonds() (BioSimSpace._SireWrappers.SearchResult method) Boolean (class in BioSimSpace.Gateway) Bound (class in BioSimSpace.Metadynamics) boxTypes() (in module BioSimSpace.Box)

C

cd() (in module BioSimSpace._Utils) celsius (in module BioSimSpace.Units.Temperature) celsius() (BioSimSpace.Types.Temperature method) centimeters() (BioSimSpace.Types.Length method) chains() (BioSimSpace._SireWrappers.SearchResult method) Charge (class in BioSimSpace.Gateway) (class in BioSimSpace.Types) charge() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.System method) (BioSimSpace.Types.Angle class method) (BioSimSpace.Types.Area class method) (BioSimSpace.Types.Charge class method) (BioSimSpace.Types.Energy class method) (BioSimSpace.Types.Length class method) (BioSimSpace.Types.Pressure class method) (BioSimSpace.Types.Temperature class method) (BioSimSpace.Types.Time class method) (BioSimSpace.Types.Volume class method) checkOverlap() (BioSimSpace.FreeEnergy.Relative static method) clearArgs() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) clearCache() (in module BioSimSpace.IO)

command() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) command_split() (in module BioSimSpace._Utils) ConversionError Coordinate (class in BioSimSpace.Types) coordinates() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Residue method) copy() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.SearchResult method) (BioSimSpace._SireWrappers.System method) coulomb (in module BioSimSpace.Units.Charge) coulomb() (BioSimSpace.Types.Charge method) createConfig() (BioSimSpace._Config.Amber method) (BioSimSpace._Config.Gromacs method) (BioSimSpace._Config.Somd method) (BioSimSpace.Process.Plumed method) createProcess() (in module BioSimSpace.Process) createProtocol() (in module BioSimSpace.Protocol) cross() (BioSimSpace.Types.Vector method) cubic() (in module BioSimSpace.Box) Custom (class in BioSimSpace.Protocol)

D

day (in module BioSimSpace.Units.Time) days() (BioSimSpace.Types.Time method) degree (in module BioSimSpace.Units.Angle) degrees() (BioSimSpace.Types.Angle method) deleteArg() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) difference() (BioSimSpace.FreeEnergy.Relative static method) dimensions() (BioSimSpace.Types.Angle class method) (BioSimSpace.Types.Area class method) (BioSimSpace.Types.Charge class method) (BioSimSpace.Types.Energy class method) (BioSimSpace.Types.Length class method) (BioSimSpace.Types.Pressure class method) (BioSimSpace.Types.Temperature class method) (BioSimSpace.Types.Time class method) (BioSimSpace.Types.Volume class method)

disableCache() (in module BioSimSpace.IO) Distance (class in BioSimSpace.Metadynamics.CollectiveVariable) dot() (BioSimSpace.Types.Vector method)

E

electron_charge (in module BioSimSpace.Units.Charge) electron_charge() (BioSimSpace.Types.Charge method) element() (BioSimSpace._SireWrappers.Atom method) enableCache() (in module BioSimSpace.IO) Energy (class in BioSimSpace.Gateway) (class in BioSimSpace.Types) energy() (BioSimSpace._SireWrappers.Bond method) engines() (in module BioSimSpace.FreeEnergy) (in module BioSimSpace.MD) (in module BioSimSpace.Metadynamics) (in module BioSimSpace.Process)

Equilibration (class in BioSimSpace.Protocol) errored() (BioSimSpace.Process.ProcessRunner method) eta() (BioSimSpace.Process.Namd method) exe() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) extract() (BioSimSpace._SireWrappers.Molecule method)

F

fahrenheit (in module BioSimSpace.Units.Temperature) fahrenheit() (BioSimSpace.Types.Temperature method) femtosecond (in module BioSimSpace.Units.Time) femtoseconds() (BioSimSpace.Types.Time method) ff03() (in module BioSimSpace.Parameters) ff14SB() (in module BioSimSpace.Parameters) ff99() (in module BioSimSpace.Parameters) ff99SB() (in module BioSimSpace.Parameters) ff99SBildn() (in module BioSimSpace.Parameters) File (class in BioSimSpace.Gateway) fileFormat() (BioSimSpace._SireWrappers.System method) fileFormats() (in module BioSimSpace.IO)

FileSet (class in BioSimSpace.Gateway) flexAlign() (in module BioSimSpace.Align) Float (class in BioSimSpace.Gateway) forceFields() (in module BioSimSpace.Parameters) formalCharge() (in module BioSimSpace.Parameters) formatInfo() (in module BioSimSpace.IO) FreeEnergy (in module BioSimSpace.Protocol) FreeEnergyEquilibration (class in BioSimSpace.Protocol) FreeEnergyMinimisation (class in BioSimSpace.Protocol) FreeEnergyProduction (class in BioSimSpace.Protocol) fromVector() (BioSimSpace.Types.Coordinate static method) Funnel (class in BioSimSpace.Metadynamics.CollectiveVariable)

G

gaff() (in module BioSimSpace.Parameters) gaff2() (in module BioSimSpace.Parameters) generateBoxParameters() (in module BioSimSpace.Box) generateNetwork() (in module BioSimSpace.Align) get_window_index() (BioSimSpace.Protocol.ATMProduction method) getAlignKDistance() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getAlignKPsi() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getAlignKTheta() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getAlignmentType() (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) getAllowedValues() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) getAlpha() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) getAminoAcids() (BioSimSpace._SireWrappers.System method) getAngleEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getAnnealNumCycles() (BioSimSpace.Protocol.ATMAnnealing method) getAnnealValues() (BioSimSpace.Protocol.ATMAnnealing method) getArgs() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getArgString() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getArgStringList() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getArgType() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) getAtom() (BioSimSpace._SireWrappers.System method) getAtom0() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) getAtom1() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) getAtoms() (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.System method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) getAtoms0() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) getAtoms1() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) getAuthors() (BioSimSpace.Gateway.Node method) getAxisAlignedBoundingBox() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.System method) getBiasFactor() (BioSimSpace.Protocol.Metadynamics method) getBins() (BioSimSpace.Metadynamics.Grid method) getBondEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getBoundaryEnergy() (BioSimSpace.Process.Namd method) getBox() (BioSimSpace._SireWrappers.System method) getBuffer() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) getCentreOfMassKineticEnergy() (BioSimSpace.Process.Amber method) getCollectiveVariable() (BioSimSpace.Process.Plumed method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Steering method) getColvarFile() (BioSimSpace.Protocol.Steering method) getCoM0() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) getCoM1() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) getCOMDistanceRestraint() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getCOMk() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getComponent() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) getCOMWidth() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getConfig() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) (BioSimSpace.Protocol.Custom method) getConservedEnergy() (BioSimSpace.Process.Gromacs method) getConstraintRMSD() (BioSimSpace.Process.Gromacs method) getCoreAlignment() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getCorrection() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) getCoulomb14() (BioSimSpace.Process.Gromacs method) getCoulombReciprocal() (BioSimSpace.Process.Gromacs method) getCoulombSR() (BioSimSpace.Process.Gromacs method) getCurrentAngleEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getCurrentBondEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getCurrentBoundaryEnergy() (BioSimSpace.Process.Namd method) getCurrentCentreOfMassKineticEnergy() (BioSimSpace.Process.Amber method) getCurrentConservedEnergy() (BioSimSpace.Process.Gromacs method) getCurrentConstraintRMSD() (BioSimSpace.Process.Gromacs method) getCurrentCoulomb14() (BioSimSpace.Process.Gromacs method) getCurrentCoulombReciprocal() (BioSimSpace.Process.Gromacs method) getCurrentCoulombSR() (BioSimSpace.Process.Gromacs method) getCurrentDensity() (BioSimSpace.Process.Amber method) getCurrentDihedralEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getCurrentDispersionCorrection() (BioSimSpace.Process.Gromacs method) getCurrentDVDL() (BioSimSpace.Process.Amber method) getCurrentElectrostaticEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Namd method) getCurrentElectrostaticEnergy14() (BioSimSpace.Process.Amber method) getCurrentGPressure() (BioSimSpace.Process.Namd method) getCurrentGPressureAverage() (BioSimSpace.Process.Namd method) getCurrentGradient() (BioSimSpace.Process.Somd method) getCurrentHydrogenBondEnergy() (BioSimSpace.Process.Amber method) getCurrentImproperEnergy() (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getCurrentKineticEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getCurrentLennardJones14() (BioSimSpace.Process.Gromacs method) getCurrentLennardJonesSR() (BioSimSpace.Process.Gromacs method) getCurrentMiscEnergy() (BioSimSpace.Process.Namd method) getCurrentNonBondedEnergy14() (BioSimSpace.Process.Amber method) getCurrentPotentialEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getCurrentPressure() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getCurrentPressureAverage() (BioSimSpace.Process.Namd method) getCurrentPressureDC() (BioSimSpace.Process.Gromacs method) getCurrentProperEnergy() (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getCurrentRecord() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getCurrentRecords() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getCurrentRestraintEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) getCurrentStep() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getCurrentSystem() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getCurrentTemperature() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getCurrentTemperatureAverage() (BioSimSpace.Process.Namd method) getCurrentTime() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getCurrentTotal2Energy() (BioSimSpace.Process.Namd method) getCurrentTotal3Energy() (BioSimSpace.Process.Namd method) getCurrentTotalEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getCurrentVanDerWaalsEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Namd method) getCurrentVanDerWaalsEnergy14() (BioSimSpace.Process.Amber method) getCurrentVirial() (BioSimSpace.Process.Amber method) getCurrentVolume() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getData() (BioSimSpace.FreeEnergy.ATM method) (BioSimSpace.FreeEnergy.Relative method) (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) (in module BioSimSpace.FreeEnergy) getDefault() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) getDensity() (BioSimSpace.Process.Amber method) getDihedralEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getDirection() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) getDispersionCorrection() (BioSimSpace.Process.Gromacs method) getDVDL() (BioSimSpace.Process.Amber method) getElectrostaticEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Namd method) getElectrostaticEnergy14() (BioSimSpace.Process.Amber method) getEndTemperature() (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) getEpsilon() (BioSimSpace.Metadynamics.Bound method) getExponent() (BioSimSpace.Metadynamics.Bound method) getExtent() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) getForceConstant() (BioSimSpace.Metadynamics.Bound method) (BioSimSpace.Metadynamics.Restraint method) (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Minimisation method) (BioSimSpace.Protocol.Production method) getFrame() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getFrames() (BioSimSpace.Trajectory.Trajectory method) getFreeEnergy() (BioSimSpace.Process.Plumed method) getGPressure() (BioSimSpace.Process.Namd method) getGPressureAverage() (BioSimSpace.Process.Namd method) getGradient() (BioSimSpace.Process.Somd method) getGrid() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) getHelp() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) getHillFrequency() (BioSimSpace.Protocol.Metadynamics method) getHillHeight() (BioSimSpace.Protocol.Metadynamics method) getHillWidth() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) getHydrogenBondEnergy() (BioSimSpace.Process.Amber method) getImproperEnergy() (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getIndex() (BioSimSpace._SireWrappers.System method) getInflection() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) getInitialValue() (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) getInput() (BioSimSpace.Gateway.Node method) (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method)

getInputs() (BioSimSpace.Gateway.Node method) getKineticEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getLambda() (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) getLambda1() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) getLambda2() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) getLambdaIndex() (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) getLambdaValues() (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) getLennardJones14() (BioSimSpace.Process.Gromacs method) getLennardJonesSR() (BioSimSpace.Process.Gromacs method) getLicense() (BioSimSpace.Gateway.Node method) getLowerBound() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) getMax() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) getMaximum() (BioSimSpace.Metadynamics.Grid method) getMin() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) getMinimum() (BioSimSpace.Metadynamics.Grid method) getMiscEnergy() (BioSimSpace.Process.Namd method) getMolecule() (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.System method) getMolecules() (BioSimSpace._SireWrappers.System method) getName() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) getNonBondedEnergy14() (BioSimSpace.Process.Amber method) getNucleotides() (BioSimSpace._SireWrappers.System method) getNumLambda() (BioSimSpace.Protocol.ATMProduction method) getOutput() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getPackageName() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getPeriodicBoundaries() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) getPerturbableMolecules() (BioSimSpace._SireWrappers.System method) getPerturbationType() (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) getPosRestWidth() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getPotentialEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getPressure() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) getPressureAverage() (BioSimSpace.Process.Namd method) getPressureDC() (BioSimSpace.Process.Gromacs method) getProperEnergy() (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) getRecord() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getRecordKey() (BioSimSpace.Process.Amber method) getRecords() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getReferenceIndex() (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) getReferencePDB() (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) getReportInterval() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) getResidue() (BioSimSpace._SireWrappers.System method) getResidues() (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.System method) getRestartInterval() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) getRestraint() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Custom method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Minimisation method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) getRestraintAtoms() (BioSimSpace._SireWrappers.System method) getRestraintEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) getRestraints() (BioSimSpace.Protocol.Steering method) getResult() (BioSimSpace._SireWrappers.SearchResult method) getRunTime() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) getSchedule() (BioSimSpace.Protocol.Steering method) getSeed() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getSlope() (BioSimSpace.Metadynamics.Restraint method) getSoftCoreA() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getSoftCoreU0() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getSoftCoreUmax() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) getStartTemperature() (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) getStderr() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getStdout() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getSteepness() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) getStep() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getSteps() (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.Minimisation method) getSystem() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) getTemperature() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) getTemperatureAverage() (BioSimSpace.Process.Namd method) getThermostatTimeConstant() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) getTime() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Plumed method) (BioSimSpace.Process.Somd method) getTimeStep() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) getTotal2Energy() (BioSimSpace.Process.Namd method) getTotal3Energy() (BioSimSpace.Process.Namd method) getTotalEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getTrajectory() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) (BioSimSpace.Trajectory.Trajectory method) getUh() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) getUnit() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) getUpperBound() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) getUseATMForce() (BioSimSpace.Protocol.ATMEquilibration method) getValue() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) (BioSimSpace.Metadynamics.Bound method) (BioSimSpace.Metadynamics.Restraint method) getVanDerWaalsEnergy() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Namd method) getVanDerWaalsEnergy14() (BioSimSpace.Process.Amber method) getVerse() (BioSimSpace.Protocol.Steering method) getVirial() (BioSimSpace.Process.Amber method) getVolume() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) getW0() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) getWaterMolecules() (BioSimSpace._SireWrappers.System method) getWeights0() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) getWeights1() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) getWidth() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) Grid (class in BioSimSpace.Metadynamics) Gromacs (class in BioSimSpace._Config) (class in BioSimSpace.Process)

H

hasBox() (BioSimSpace._Config.Amber static method) (BioSimSpace._Config.Gromacs static method) (BioSimSpace._Config.Somd static method) hasWater() (BioSimSpace._Config.Amber static method) (BioSimSpace._Config.Gromacs static method) (BioSimSpace._Config.Somd static method)

help() (in module BioSimSpace.Node) hour (in module BioSimSpace.Units.Time) hours() (BioSimSpace.Types.Time method)

I

IncompatibleError index() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Residue method) inputFiles() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) insertArg() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) Integer (class in BioSimSpace.Gateway) is_temp_dir() (BioSimSpace._Utils.WorkDir method) isAmberWater() (BioSimSpace._SireWrappers.Molecule method) isConstantTemp() (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) isError() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) isGromacsWater() (BioSimSpace._SireWrappers.Molecule method) isMulti() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method)

isOptional() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) isPerturbable() (BioSimSpace._SireWrappers.Molecule method) isQueued() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) isRestart() (BioSimSpace._Config.Amber method) (BioSimSpace._Config.Gromacs method) (BioSimSpace._Config.Somd method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Production method) isRunning() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) isSame() (BioSimSpace._SireWrappers.System method) isWater() (BioSimSpace._SireWrappers.Molecule method)

K

kcal_per_mol (in module BioSimSpace.Units.Energy) kcal_per_mol() (BioSimSpace.Types.Energy method) kelvin (in module BioSimSpace.Units.Temperature) kelvin() (BioSimSpace.Types.Temperature method) kill() (BioSimSpace.FreeEnergy.ATM method) (BioSimSpace.FreeEnergy.Relative method) (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method)

killAll() (BioSimSpace.FreeEnergy.ATM method) (BioSimSpace.FreeEnergy.Relative method) (BioSimSpace.Process.ProcessRunner method) kj_per_mol (in module BioSimSpace.Units.Energy) kj_per_mol() (BioSimSpace.Types.Energy method) kt (in module BioSimSpace.Units.Energy) kt() (BioSimSpace.Types.Energy method)

L

Length (class in BioSimSpace.Gateway) (class in BioSimSpace.Types) length() (BioSimSpace._SireWrappers.Bond method) (BioSimSpace.Types.Angle class method) (BioSimSpace.Types.Area class method) (BioSimSpace.Types.Charge class method) (BioSimSpace.Types.Energy class method) (BioSimSpace.Types.Length class method) (BioSimSpace.Types.Pressure class method) (BioSimSpace.Types.Temperature class method) (BioSimSpace.Types.Time class method) (BioSimSpace.Types.Volume class method)

list() (in module BioSimSpace.Metadynamics.CollectiveVariable) (in module BioSimSpace.Node) load() (in module BioSimSpace.Stream)

M

magnitude() (BioSimSpace.Types.Vector method) makeCompatibleWith() (BioSimSpace._SireWrappers.Molecule method) makeFunnel() (in module BioSimSpace.Metadynamics.CollectiveVariable) makeWhole() (BioSimSpace._SireWrappers.System method) mass() (BioSimSpace.Types.Angle class method) (BioSimSpace.Types.Area class method) (BioSimSpace.Types.Charge class method) (BioSimSpace.Types.Energy class method) (BioSimSpace.Types.Length class method) (BioSimSpace.Types.Pressure class method) (BioSimSpace.Types.Temperature class method) (BioSimSpace.Types.Time class method) (BioSimSpace.Types.Volume class method) matchAtoms() (in module BioSimSpace.Align) merge() (in module BioSimSpace.Align) Metadynamics (class in BioSimSpace.Protocol) meter (in module BioSimSpace.Units.Length) meter2 (in module BioSimSpace.Units.Area) meter3 (in module BioSimSpace.Units.Volume) meters() (BioSimSpace.Types.Length method) meters2() (BioSimSpace.Types.Area method) meters3() (BioSimSpace.Types.Volume method) millimeters() (BioSimSpace.Types.Length method) millisecond (in module BioSimSpace.Units.Time) milliseconds() (BioSimSpace.Types.Time method) Minimisation (class in BioSimSpace.Protocol) minute (in module BioSimSpace.Units.Time) minutes() (BioSimSpace.Types.Time method) MissingSoftwareError module BioSimSpace._Config BioSimSpace._Exceptions BioSimSpace._SireWrappers BioSimSpace._Utils BioSimSpace.Align BioSimSpace.Box BioSimSpace.Convert BioSimSpace.FreeEnergy BioSimSpace.Gateway BioSimSpace.IO BioSimSpace.MD BioSimSpace.Metadynamics BioSimSpace.Metadynamics.CollectiveVariable BioSimSpace.Node BioSimSpace.Notebook BioSimSpace.Parameters BioSimSpace.Process BioSimSpace.Protocol BioSimSpace.Solvent BioSimSpace.Stream BioSimSpace.Trajectory BioSimSpace.Types BioSimSpace.Units

Molecule (class in BioSimSpace._SireWrappers) molecule() (BioSimSpace.Notebook.View method) molecule0() (BioSimSpace._SireWrappers.Molecule method) molecule1() (BioSimSpace._SireWrappers.Molecule method) moleculeNumber() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Residue method) Molecules (class in BioSimSpace._SireWrappers) molecules() (BioSimSpace._SireWrappers.SearchResult method) (BioSimSpace.Notebook.View method)

N

Namd (class in BioSimSpace.Process) name() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Residue method) nAminoAcids() (BioSimSpace._SireWrappers.System method) nanometer (in module BioSimSpace.Units.Length) nanometer2 (in module BioSimSpace.Units.Area) nanometer3 (in module BioSimSpace.Units.Volume) nanometers() (BioSimSpace.Types.Length method) nanometers2() (BioSimSpace.Types.Area method) nanometers3() (BioSimSpace.Types.Volume method) nanosecond (in module BioSimSpace.Units.Time) nanoseconds() (BioSimSpace.Types.Time method) nAtoms() (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.System method) nChains() (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.System method) nComponents() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method)

nError() (BioSimSpace.Process.ProcessRunner method) nFrames() (BioSimSpace.Trajectory.Trajectory method) nMolecules() (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.System method) nNucleotides() (BioSimSpace._SireWrappers.System method) Node (class in BioSimSpace.Gateway) normalise() (BioSimSpace.Types.Vector method) nPerturbableMolecules() (BioSimSpace._SireWrappers.System method) nProcesses() (BioSimSpace.Process.ProcessRunner method) nQueued() (BioSimSpace.Process.ProcessRunner method) nResidues() (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.System method) nResults() (BioSimSpace._SireWrappers.SearchResult method) nRunning() (BioSimSpace.Process.ProcessRunner method) number() (BioSimSpace._SireWrappers.Molecule method) nViews() (BioSimSpace.Notebook.View method) nWaterMolecules() (BioSimSpace._SireWrappers.System method)

O

openff_unconstrained_1_0_0() (in module BioSimSpace.Parameters) openff_unconstrained_1_0_0_RC1() (in module BioSimSpace.Parameters) openff_unconstrained_1_0_0_RC2() (in module BioSimSpace.Parameters) openff_unconstrained_1_0_1() (in module BioSimSpace.Parameters) openff_unconstrained_1_1_0() (in module BioSimSpace.Parameters) openff_unconstrained_1_1_1() (in module BioSimSpace.Parameters) openff_unconstrained_1_2_0() (in module BioSimSpace.Parameters) openff_unconstrained_1_2_1() (in module BioSimSpace.Parameters) openff_unconstrained_1_3_0() (in module BioSimSpace.Parameters) openff_unconstrained_1_3_1() (in module BioSimSpace.Parameters) openff_unconstrained_1_3_1_alpha_1() (in module BioSimSpace.Parameters)

openff_unconstrained_2_0_0() (in module BioSimSpace.Parameters) openff_unconstrained_2_0_0_rc_1() (in module BioSimSpace.Parameters) openff_unconstrained_2_0_0_rc_2() (in module BioSimSpace.Parameters) openff_unconstrained_2_1_0() (in module BioSimSpace.Parameters) openff_unconstrained_2_1_0_rc_1() (in module BioSimSpace.Parameters) openff_unconstrained_2_1_1() (in module BioSimSpace.Parameters) openff_unconstrained_2_2_0() (in module BioSimSpace.Parameters) openff_unconstrained_2_2_0_rc1() (in module BioSimSpace.Parameters) openff_unconstrained_2_2_1() (in module BioSimSpace.Parameters) openff_unconstrained_2_2_1_rc1() (in module BioSimSpace.Parameters) openForceFields() (in module BioSimSpace.Parameters) OpenMM (class in BioSimSpace.Process)

P

ParameterisationError parameterise() (in module BioSimSpace.Parameters) picometer (in module BioSimSpace.Units.Length) picometer2 (in module BioSimSpace.Units.Area) picometer3 (in module BioSimSpace.Units.Volume) picometers() (BioSimSpace.Types.Length method) picometers2() (BioSimSpace.Types.Area method) picometers3() (BioSimSpace.Types.Volume method) picosecond (in module BioSimSpace.Units.Time) picoseconds() (BioSimSpace.Types.Time method)

plot() (in module BioSimSpace.Notebook) plotContour() (in module BioSimSpace.Notebook) plotOverlapMatrix() (in module BioSimSpace.Notebook) Plumed (class in BioSimSpace.Process) prepare() (BioSimSpace.FreeEnergy.ATMSetup method) Pressure (class in BioSimSpace.Gateway) (class in BioSimSpace.Types) processes() (BioSimSpace.Process.ProcessRunner method) ProcessRunner (class in BioSimSpace.Process) Production (class in BioSimSpace.Protocol) protocols() (in module BioSimSpace.Protocol)

Q

quantity() (BioSimSpace.Types.Angle class method) (BioSimSpace.Types.Area class method) (BioSimSpace.Types.Charge class method) (BioSimSpace.Types.Energy class method) (BioSimSpace.Types.Length class method) (BioSimSpace.Types.Pressure class method) (BioSimSpace.Types.Temperature class method) (BioSimSpace.Types.Time class method) (BioSimSpace.Types.Volume class method)

queued() (BioSimSpace.Process.ProcessRunner method)

R

radian (in module BioSimSpace.Units.Angle) radians() (BioSimSpace.Types.Angle method) readMolecules() (in module BioSimSpace.IO) readPDB() (in module BioSimSpace.IO) readPerturbableSystem() (in module BioSimSpace.IO) reduceBoxVectors() (BioSimSpace._SireWrappers.System method) Relative (class in BioSimSpace.FreeEnergy) reload() (BioSimSpace.Notebook.View method) removeBox() (BioSimSpace._SireWrappers.System method) removeMolecules() (BioSimSpace._SireWrappers.System method) removeProcess() (BioSimSpace.Process.ProcessRunner method) removeWaterMolecules() (BioSimSpace._SireWrappers.System method) repartitionHydrogenMass() (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.System method) reportInterval() (BioSimSpace._Config.Amber method) (BioSimSpace._Config.Gromacs method) (BioSimSpace._Config.Somd method) reset() (BioSimSpace.Notebook.View method) resetArgs() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) resetConfig() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) Residue (class in BioSimSpace._SireWrappers) residues() (BioSimSpace._SireWrappers.SearchResult method) restartFailed() (BioSimSpace.Process.ProcessRunner method) restartInterval() (BioSimSpace._Config.Amber method) (BioSimSpace._Config.Gromacs method) (BioSimSpace._Config.Somd method)

Restraint (class in BioSimSpace.Metadynamics) restraints() (BioSimSpace.Protocol.ATMAnnealing class method) (BioSimSpace.Protocol.ATMEquilibration class method) (BioSimSpace.Protocol.ATMMinimisation class method) (BioSimSpace.Protocol.ATMProduction class method) (BioSimSpace.Protocol.Equilibration class method) (BioSimSpace.Protocol.FreeEnergyEquilibration class method) (BioSimSpace.Protocol.FreeEnergyMinimisation class method) (BioSimSpace.Protocol.FreeEnergyProduction class method) (BioSimSpace.Protocol.Minimisation class method) (BioSimSpace.Protocol.Production class method) rhombicDodecahedronHexagon() (in module BioSimSpace.Box) rhombicDodecahedronSquare() (in module BioSimSpace.Box) RMSD (class in BioSimSpace.Metadynamics.CollectiveVariable) rmsd() (BioSimSpace.Trajectory.Trajectory method) rmsdAlign() (in module BioSimSpace.Align) rotateBoxVectors() (BioSimSpace._SireWrappers.System method) run() (BioSimSpace.FreeEnergy.ATM method) (BioSimSpace.FreeEnergy.Relative method) (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) (in module BioSimSpace.MD) (in module BioSimSpace.Metadynamics) (in module BioSimSpace.Node) running() (BioSimSpace.Process.ProcessRunner method) runTime() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method)

S

save() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.System method) (in module BioSimSpace.Stream) saveMolecules() (in module BioSimSpace.IO) savePDB() (BioSimSpace.Notebook.View method) savePerturbableSystem() (in module BioSimSpace.IO) search() (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.System method) SearchResult (class in BioSimSpace._SireWrappers) second (in module BioSimSpace.Units.Time) seconds() (BioSimSpace.Types.Time method) segments() (BioSimSpace._SireWrappers.SearchResult method) set_current_index() (BioSimSpace.Protocol.ATMProduction method) setAlignKDistance() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setAlignKPsi() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setAlignKTheta() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setAlignmentType() (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) setAlpha() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) setAnalysisMethod() (BioSimSpace.Protocol.ATMProduction method) setAnnealNumCycles() (BioSimSpace.Protocol.ATMAnnealing method) setAnnealValues() (BioSimSpace.Protocol.ATMAnnealing method) setArg() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) setArgs() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) setAtom0() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) setAtom1() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) setAtoms() (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) setAtoms0() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) setAtoms1() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) setBiasFactor() (BioSimSpace.Protocol.Metadynamics method) setBins() (BioSimSpace.Metadynamics.Grid method) setBox() (BioSimSpace._SireWrappers.System method) setBuffer() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) setCollectiveVariable() (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Steering method) setColvarFile() (BioSimSpace.Protocol.Steering method) setCoM0() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) setCoM1() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) setCOMDistanceRestraint() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setCOMk() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setComponent() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) setCOMWidth() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setConfig() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) (BioSimSpace.Protocol.Custom method) setCoreAlignment() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setDirection() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) setEndTemperature() (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) setEpsilon() (BioSimSpace.Metadynamics.Bound method) setExponent() (BioSimSpace.Metadynamics.Bound method) setForceConstant() (BioSimSpace.Metadynamics.Bound method) (BioSimSpace.Metadynamics.Restraint method) (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Minimisation method) (BioSimSpace.Protocol.Production method) setGrid() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) setHillFrequency() (BioSimSpace.Protocol.Metadynamics method) setHillHeight() (BioSimSpace.Protocol.Metadynamics method) setHillWidth() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) setInflection() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) setLambda1() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) setLambda2() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) setLambdaValues() (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) setLicense() (BioSimSpace.Gateway.Node method) setLowerBound() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) setMaximum() (BioSimSpace.Metadynamics.Grid method) setMinimum() (BioSimSpace.Metadynamics.Grid method) setName() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) setNodeDirectory() (in module BioSimSpace.Node) setNumLambda() (BioSimSpace.Protocol.ATMProduction method) setOutput() (BioSimSpace.Gateway.Node method) setPeriodicBoundaries() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) setPerturbationType() (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) setPosRestWidth() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setPressure() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method)

setReportInterval() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) setRestart() (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Production method) setRestartInterval() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) setRestraint() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Minimisation method) (BioSimSpace.Protocol.Production method) setRestraints() (BioSimSpace.Protocol.Steering method) setRuntime() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) setRunTime() (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) setSchedule() (BioSimSpace.Protocol.Steering method) setSeed() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) setSlope() (BioSimSpace.Metadynamics.Restraint method) setSoftCoreA() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setSoftCoreU0() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setSoftCoreUmax() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.ATMProduction method) setStartTemperature() (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) setSteepness() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) setSteps() (BioSimSpace.Protocol.ATMMinimisation method) (BioSimSpace.Protocol.FreeEnergyMinimisation method) (BioSimSpace.Protocol.Minimisation method) setTemperature() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) setThermostatTimeConstant() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) setTimestep() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) setTimeStep() (BioSimSpace.Protocol.Equilibration method) (BioSimSpace.Protocol.FreeEnergyEquilibration method) (BioSimSpace.Protocol.FreeEnergyProduction method) (BioSimSpace.Protocol.Metadynamics method) (BioSimSpace.Protocol.Production method) (BioSimSpace.Protocol.Steering method) setUh() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) setUpperBound() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) (BioSimSpace.Metadynamics.CollectiveVariable.RMSD method) (BioSimSpace.Metadynamics.CollectiveVariable.Torsion method) setUseATMForce() (BioSimSpace.Protocol.ATMEquilibration method) setValue() (BioSimSpace.Gateway.Area method) (BioSimSpace.Gateway.Boolean method) (BioSimSpace.Gateway.Charge method) (BioSimSpace.Gateway.Energy method) (BioSimSpace.Gateway.File method) (BioSimSpace.Gateway.FileSet method) (BioSimSpace.Gateway.Float method) (BioSimSpace.Gateway.Integer method) (BioSimSpace.Gateway.Length method) (BioSimSpace.Gateway.Pressure method) (BioSimSpace.Gateway.String method) (BioSimSpace.Gateway.Temperature method) (BioSimSpace.Gateway.Time method) (BioSimSpace.Gateway.Volume method) (BioSimSpace.Metadynamics.Bound method) (BioSimSpace.Metadynamics.Restraint method) setVerse() (BioSimSpace.Protocol.Steering method) setW0() (BioSimSpace.Protocol.ATMAnnealing method) (BioSimSpace.Protocol.ATMEquilibration method) (BioSimSpace.Protocol.ATMProduction method) setWeights0() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) setWeights1() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method) setWidth() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method) showControls() (BioSimSpace.Gateway.Node method) smiles() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.System method) (in module BioSimSpace.Convert) solvate() (in module BioSimSpace.Solvent) Somd (class in BioSimSpace._Config) (class in BioSimSpace.Process) spc() (in module BioSimSpace.Solvent) spce() (in module BioSimSpace.Solvent) start() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) startAll() (BioSimSpace.Process.ProcessRunner method) stderr() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) stdout() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method) Steering (class in BioSimSpace.Protocol) steps() (BioSimSpace._Config.Amber method) (BioSimSpace._Config.Gromacs method) (BioSimSpace._Config.Somd method) StreamError String (class in BioSimSpace.Gateway) supportedFormats() (in module BioSimSpace.Convert) System (class in BioSimSpace._SireWrappers) system() (BioSimSpace.Notebook.View method)

T

Temperature (class in BioSimSpace.Gateway) (class in BioSimSpace.Types) temperature() (BioSimSpace.Types.Angle class method) (BioSimSpace.Types.Area class method) (BioSimSpace.Types.Charge class method) (BioSimSpace.Types.Energy class method) (BioSimSpace.Types.Length class method) (BioSimSpace.Types.Pressure class method) (BioSimSpace.Types.Temperature class method) (BioSimSpace.Types.Time class method) (BioSimSpace.Types.Volume class method) ThirdPartyError Time (class in BioSimSpace.Gateway) (class in BioSimSpace.Types) time() (BioSimSpace.Types.Angle class method) (BioSimSpace.Types.Area class method) (BioSimSpace.Types.Charge class method) (BioSimSpace.Types.Energy class method) (BioSimSpace.Types.Length class method) (BioSimSpace.Types.Pressure class method) (BioSimSpace.Types.Temperature class method) (BioSimSpace.Types.Time class method) (BioSimSpace.Types.Volume class method) tip3p() (in module BioSimSpace.Solvent) tip4p() (in module BioSimSpace.Solvent) tip5p() (in module BioSimSpace.Solvent) to() (BioSimSpace.Types.Angle method) (BioSimSpace.Types.Area method) (BioSimSpace.Types.Charge method) (BioSimSpace.Types.Energy method) (BioSimSpace.Types.Length method) (BioSimSpace.Types.Pressure method) (BioSimSpace.Types.Temperature method) (BioSimSpace.Types.Time method) (BioSimSpace.Types.Volume method) (in module BioSimSpace.Convert)

toBioSimSpace() (in module BioSimSpace.Convert) toMolecule() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Residue method) toOpenMM() (in module BioSimSpace.Convert) toRDKit() (in module BioSimSpace.Convert) Torsion (class in BioSimSpace.Metadynamics.CollectiveVariable) toSire() (in module BioSimSpace.Convert) toSystem() (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) toVector() (BioSimSpace.Types.Coordinate method) Trajectory (class in BioSimSpace.Trajectory) translate() (BioSimSpace._SireWrappers.Atom method) (BioSimSpace._SireWrappers.Bond method) (BioSimSpace._SireWrappers.Molecule method) (BioSimSpace._SireWrappers.Molecules method) (BioSimSpace._SireWrappers.Residue method) (BioSimSpace._SireWrappers.System method) truncatedOctahedron() (in module BioSimSpace.Box)

U

unit() (BioSimSpace.Types.Angle method) (BioSimSpace.Types.Area method) (BioSimSpace.Types.Charge method) (BioSimSpace.Types.Energy method) (BioSimSpace.Types.Length method) (BioSimSpace.Types.Pressure method) (BioSimSpace.Types.Temperature method) (BioSimSpace.Types.Time method) (BioSimSpace.Types.Volume method)

updateMolecule() (BioSimSpace._SireWrappers.System method) updateMolecules() (BioSimSpace._SireWrappers.System method)

V

validate() (BioSimSpace.Gateway.Node method) value() (BioSimSpace.Types.Angle method) (BioSimSpace.Types.Area method) (BioSimSpace.Types.Charge method) (BioSimSpace.Types.Energy method) (BioSimSpace.Types.Length method) (BioSimSpace.Types.Pressure method) (BioSimSpace.Types.Temperature method) (BioSimSpace.Types.Time method) (BioSimSpace.Types.Volume method)

Vector (class in BioSimSpace.Types) View (class in BioSimSpace.Notebook) viewFunnel() (in module BioSimSpace.Metadynamics.CollectiveVariable) viewMapping() (in module BioSimSpace.Align) viewRigidCores() (BioSimSpace.FreeEnergy.ATMSetup static method) Volume (class in BioSimSpace.Gateway) (class in BioSimSpace.Types)

W

wait() (BioSimSpace.FreeEnergy.ATM method) (BioSimSpace.FreeEnergy.Relative method) (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) waterModels() (in module BioSimSpace.Solvent) with_traceback() (BioSimSpace._Exceptions.AlignmentError method) (BioSimSpace._Exceptions.AnalysisError method) (BioSimSpace._Exceptions.ConversionError method) (BioSimSpace._Exceptions.IncompatibleError method) (BioSimSpace._Exceptions.MissingSoftwareError method) (BioSimSpace._Exceptions.ParameterisationError method) (BioSimSpace._Exceptions.StreamError method) (BioSimSpace._Exceptions.ThirdPartyError method)

WorkDir (class in BioSimSpace._Utils) workDir() (BioSimSpace.FreeEnergy.ATM method) (BioSimSpace.FreeEnergy.Relative method) (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.ProcessRunner method) (BioSimSpace.Process.Somd method) writeConfig() (BioSimSpace.Process.Amber method) (BioSimSpace.Process.Gromacs method) (BioSimSpace.Process.Namd method) (BioSimSpace.Process.OpenMM method) (BioSimSpace.Process.Somd method)

X

x() (BioSimSpace.Types.Coordinate method) (BioSimSpace.Types.Vector method)

Y

y() (BioSimSpace.Types.Coordinate method) (BioSimSpace.Types.Vector method)

Z

z() (BioSimSpace.Types.Coordinate method) (BioSimSpace.Types.Vector method)