BioSimSpace
2023.0.0
Installation
Compatibility
Documentation
Developer’s guide
Changelog
Nodes
Notebook server
Protocols
Media
Legal notices
BioSimSpace
Index
Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
_
__init__() (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.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.Custom method)
(BioSimSpace.Protocol.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy 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)
A
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.Process)
analyse() (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 (in module BioSimSpace.Units.Pressure)
atm() (BioSimSpace.Types.Pressure method)
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._Exceptions (module)
BioSimSpace._SireWrappers (module)
BioSimSpace._Utils (module)
BioSimSpace.Align (module)
BioSimSpace.Box (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.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)
clearArgs() (BioSimSpace.Process.Amber method)
(BioSimSpace.Process.Gromacs method)
(BioSimSpace.Process.Namd method)
(BioSimSpace.Process.OpenMM method)
(BioSimSpace.Process.Somd method)
command() (BioSimSpace.Process.Amber method)
(BioSimSpace.Process.Gromacs method)
(BioSimSpace.Process.Namd method)
(BioSimSpace.Process.OpenMM method)
(BioSimSpace.Process.Somd method)
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.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)
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)
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)
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)
formalCharge() (in module BioSimSpace.Parameters)
formatInfo() (in module BioSimSpace.IO)
FreeEnergy (class in BioSimSpace.Protocol)
fromVector() (BioSimSpace.Types.Coordinate static method)
Funnel (class in BioSimSpace.Metadynamics.CollectiveVariable)
G
generateBoxParameters() (in module BioSimSpace.Box)
generateNetwork() (in module BioSimSpace.Align)
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)
getAngleEnergy() (BioSimSpace.Process.Amber method)
(BioSimSpace.Process.Gromacs method)
(BioSimSpace.Process.Namd 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.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)
getComponent() (BioSimSpace.Metadynamics.CollectiveVariable.Distance 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)
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)
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)
getCurrentVirial() (BioSimSpace.Process.Amber method)
getCurrentVolume() (BioSimSpace.Process.Amber method)
(BioSimSpace.Process.Namd method)
(BioSimSpace.Process.OpenMM method)
getData() (BioSimSpace.FreeEnergy.Relative 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)
getDispersionCorrection() (BioSimSpace.Process.Gromacs method)
getElectrostaticEnergy() (BioSimSpace.Process.Amber method)
(BioSimSpace.Process.Namd method)
getElectrostaticEnergy14() (BioSimSpace.Process.Amber method)
getEndTemperature() (BioSimSpace.Protocol.Equilibration method)
getEpsilon() (BioSimSpace.Metadynamics.Bound method)
getExponent() (BioSimSpace.Metadynamics.Bound method)
getExtent() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method)
getFirstStep() (BioSimSpace.Protocol.Production method)
getForceConstant() (BioSimSpace.Metadynamics.Bound method)
(BioSimSpace.Metadynamics.Restraint method)
(BioSimSpace.Protocol.Equilibration 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.FreeEnergy method)
getLambdaIndex() (BioSimSpace.Protocol.FreeEnergy method)
getLambdaValues() (BioSimSpace.Protocol.FreeEnergy 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)
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.FreeEnergy 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.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy 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)
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.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy method)
(BioSimSpace.Protocol.Metadynamics method)
(BioSimSpace.Protocol.Production method)
(BioSimSpace.Protocol.Steering method)
getResidue() (BioSimSpace._SireWrappers.System method)
getResidues() (BioSimSpace._SireWrappers.Molecule method)
getRestartInterval() (BioSimSpace.Protocol.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy method)
(BioSimSpace.Protocol.Metadynamics method)
(BioSimSpace.Protocol.Production method)
(BioSimSpace.Protocol.Steering method)
getRestraint() (BioSimSpace.Protocol.Equilibration 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.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy 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)
getStartTemperature() (BioSimSpace.Protocol.Equilibration 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.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.FreeEnergy method)
(BioSimSpace.Protocol.Metadynamics method)
(BioSimSpace.Protocol.Production method)
(BioSimSpace.Protocol.Steering method)
getTemperatureAverage() (BioSimSpace.Process.Namd 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.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy 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)
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)
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)
getVerse() (BioSimSpace.Protocol.Steering method)
getVirial() (BioSimSpace.Process.Amber method)
getVolume() (BioSimSpace.Process.Amber method)
(BioSimSpace.Process.Namd method)
(BioSimSpace.Process.OpenMM 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.Process)
H
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)
isAmberWater() (BioSimSpace._SireWrappers.Molecule method)
isConstantTemp() (BioSimSpace.Protocol.Equilibration 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.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)
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.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.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)
M
magnitude() (BioSimSpace.Types.Vector method)
makeCompatibleWith() (BioSimSpace._SireWrappers.Molecule method)
makeFunnel() (in module BioSimSpace.Metadynamics.CollectiveVariable)
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
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)
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)
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
OpenMM (class in BioSimSpace.Process)
P
ParameterisationError
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)
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)
Relative (class in BioSimSpace.FreeEnergy)
reload() (BioSimSpace.Notebook.View 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)
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)
Restraint (class in BioSimSpace.Metadynamics)
restraints() (BioSimSpace.Protocol.Equilibration 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)
run() (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
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)
setAlignmentType() (BioSimSpace.Metadynamics.CollectiveVariable.RMSD 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)
setComponent() (BioSimSpace.Metadynamics.CollectiveVariable.Distance 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)
setEndTemperature() (BioSimSpace.Protocol.Equilibration method)
setEpsilon() (BioSimSpace.Metadynamics.Bound method)
setExponent() (BioSimSpace.Metadynamics.Bound method)
setFirstStep() (BioSimSpace.Protocol.Production method)
setForceConstant() (BioSimSpace.Metadynamics.Bound method)
(BioSimSpace.Metadynamics.Restraint method)
(BioSimSpace.Protocol.Equilibration 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)
setLambdaValues() (BioSimSpace.Protocol.FreeEnergy 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)
setOutput() (BioSimSpace.Gateway.Node method)
setPeriodicBoundaries() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method)
(BioSimSpace.Metadynamics.CollectiveVariable.RMSD method)
(BioSimSpace.Metadynamics.CollectiveVariable.Torsion method)
setPerturbationType() (BioSimSpace.Protocol.FreeEnergy method)
setPressure() (BioSimSpace.Protocol.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy method)
(BioSimSpace.Protocol.Metadynamics method)
(BioSimSpace.Protocol.Production method)
(BioSimSpace.Protocol.Steering method)
setReportInterval() (BioSimSpace.Protocol.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy method)
(BioSimSpace.Protocol.Metadynamics method)
(BioSimSpace.Protocol.Production method)
(BioSimSpace.Protocol.Steering method)
setRestart() (BioSimSpace.Protocol.Production method)
setRestartInterval() (BioSimSpace.Protocol.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy method)
(BioSimSpace.Protocol.Metadynamics method)
(BioSimSpace.Protocol.Production method)
(BioSimSpace.Protocol.Steering method)
setRestraint() (BioSimSpace.Protocol.Equilibration method)
setRestraints() (BioSimSpace.Protocol.Steering method)
setRunTime() (BioSimSpace.Protocol.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy 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)
setStartTemperature() (BioSimSpace.Protocol.Equilibration method)
setSteepness() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method)
setSteps() (BioSimSpace.Protocol.Minimisation method)
setTemperature() (BioSimSpace.Protocol.FreeEnergy method)
(BioSimSpace.Protocol.Metadynamics method)
(BioSimSpace.Protocol.Production method)
(BioSimSpace.Protocol.Steering method)
setTimeStep() (BioSimSpace.Protocol.Equilibration method)
(BioSimSpace.Protocol.FreeEnergy method)
(BioSimSpace.Protocol.Metadynamics method)
(BioSimSpace.Protocol.Production method)
(BioSimSpace.Protocol.Steering method)
setUpperBound() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method)
(BioSimSpace.Metadynamics.CollectiveVariable.Funnel method)
(BioSimSpace.Metadynamics.CollectiveVariable.RMSD method)
(BioSimSpace.Metadynamics.CollectiveVariable.Torsion 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)
setWeights0() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method)
setWeights1() (BioSimSpace.Metadynamics.CollectiveVariable.Distance method)
setWidth() (BioSimSpace.Metadynamics.CollectiveVariable.Funnel method)
showControls() (BioSimSpace.Gateway.Node method)
solvate() (in module BioSimSpace.Solvent)
Somd (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)
String (class in BioSimSpace.Gateway)
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)
toMolecule() (BioSimSpace._SireWrappers.Atom method)
(BioSimSpace._SireWrappers.Bond method)
(BioSimSpace._SireWrappers.Residue method)
Torsion (class in BioSimSpace.Metadynamics.CollectiveVariable)
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)
Volume (class in BioSimSpace.Gateway)
(class in BioSimSpace.Types)
W
wait() (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.IncompatibleError method)
(BioSimSpace._Exceptions.MissingSoftwareError method)
(BioSimSpace._Exceptions.ParameterisationError method)
(BioSimSpace._Exceptions.ThirdPartyError method)
workDir() (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)