Index

A

addToSystem() (cvpack.Angle method) (cvpack.AtomicFunction method) (cvpack.AttractionStrength method) (cvpack.CentroidFunction method) (cvpack.CompositeRMSD method) (cvpack.Distance method) (cvpack.HelixAngleContent method) (cvpack.HelixHBondContent method) (cvpack.HelixRMSDContent method) (cvpack.HelixTorsionContent method) (cvpack.MetaCollectiveVariable method) (cvpack.NumberOfContacts method) (cvpack.OpenMMForceWrapper method) (cvpack.PathInCVSpace method) (cvpack.PathInRMSDSpace method) (cvpack.RadiusOfGyration method) (cvpack.RadiusOfGyrationSq method) (cvpack.ResidueCoordination method) (cvpack.RMSD method) (cvpack.SheetRMSDContent method) (cvpack.ShortestDistance method) (cvpack.Torsion method) (cvpack.TorsionSimilarity method)

Angle (class in cvpack) AtomicFunction (class in cvpack) AttractionStrength (class in cvpack)

C

CentroidFunction (class in cvpack)

CompositeRMSD (class in cvpack) CVWriter (class in cvpack.reporting)

D

deserialize() (in module cvpack.serialization)

Distance (class in cvpack)

F

fromOpenMMForce() (cvpack.AtomicFunction class method)

G

getEffectiveMass() (cvpack.Angle method) (cvpack.AtomicFunction method) (cvpack.AttractionStrength method) (cvpack.CentroidFunction method) (cvpack.CompositeRMSD method) (cvpack.Distance method) (cvpack.HelixAngleContent method) (cvpack.HelixHBondContent method) (cvpack.HelixRMSDContent method) (cvpack.HelixTorsionContent method) (cvpack.MetaCollectiveVariable method) (cvpack.NumberOfContacts method) (cvpack.OpenMMForceWrapper method) (cvpack.PathInCVSpace method) (cvpack.PathInRMSDSpace method) (cvpack.RadiusOfGyration method) (cvpack.RadiusOfGyrationSq method) (cvpack.ResidueCoordination method) (cvpack.RMSD method) (cvpack.SheetRMSDContent method) (cvpack.ShortestDistance method) (cvpack.Torsion method) (cvpack.TorsionSimilarity method) getHeaders() (cvpack.reporting.CVWriter method) (cvpack.reporting.MetaCVWriter method) getInnerEffectiveMasses() (cvpack.MetaCollectiveVariable method) getInnerValues() (cvpack.MetaCollectiveVariable method) getInnerVariables() (cvpack.MetaCollectiveVariable method) getMassUnit() (cvpack.Angle method) (cvpack.AtomicFunction method) (cvpack.AttractionStrength method) (cvpack.CentroidFunction method) (cvpack.CompositeRMSD method) (cvpack.Distance method) (cvpack.HelixAngleContent method) (cvpack.HelixHBondContent method) (cvpack.HelixRMSDContent method) (cvpack.HelixTorsionContent method) (cvpack.MetaCollectiveVariable method) (cvpack.NumberOfContacts method) (cvpack.OpenMMForceWrapper method) (cvpack.PathInCVSpace method) (cvpack.PathInRMSDSpace method) (cvpack.RadiusOfGyration method) (cvpack.RadiusOfGyrationSq method) (cvpack.ResidueCoordination method) (cvpack.RMSD method) (cvpack.SheetRMSDContent method) (cvpack.ShortestDistance method) (cvpack.Torsion method) (cvpack.TorsionSimilarity method) getName() (cvpack.Angle method) (cvpack.AtomicFunction method) (cvpack.AttractionStrength method) (cvpack.CentroidFunction method) (cvpack.CompositeRMSD method) (cvpack.Distance method) (cvpack.HelixAngleContent method) (cvpack.HelixHBondContent method) (cvpack.HelixRMSDContent method) (cvpack.HelixTorsionContent method) (cvpack.MetaCollectiveVariable method) (cvpack.NumberOfContacts method) (cvpack.OpenMMForceWrapper method) (cvpack.PathInCVSpace method) (cvpack.PathInRMSDSpace method) (cvpack.RadiusOfGyration method) (cvpack.RadiusOfGyrationSq method) (cvpack.ResidueCoordination method) (cvpack.RMSD method) (cvpack.SheetRMSDContent method) (cvpack.ShortestDistance method) (cvpack.Torsion method) (cvpack.TorsionSimilarity method) getNullBondForce() (cvpack.RMSD method)

getParameterDefaultValues() (cvpack.MetaCollectiveVariable method) getParameterDerivatives() (cvpack.MetaCollectiveVariable method) getParameterValues() (cvpack.MetaCollectiveVariable method) getPeriodicBounds() (cvpack.Angle method) (cvpack.AtomicFunction method) (cvpack.AttractionStrength method) (cvpack.CentroidFunction method) (cvpack.CompositeRMSD method) (cvpack.Distance method) (cvpack.HelixAngleContent method) (cvpack.HelixHBondContent method) (cvpack.HelixRMSDContent method) (cvpack.HelixTorsionContent method) (cvpack.MetaCollectiveVariable method) (cvpack.NumberOfContacts method) (cvpack.OpenMMForceWrapper method) (cvpack.PathInCVSpace method) (cvpack.PathInRMSDSpace method) (cvpack.RadiusOfGyration method) (cvpack.RadiusOfGyrationSq method) (cvpack.ResidueCoordination method) (cvpack.RMSD method) (cvpack.SheetRMSDContent method) (cvpack.ShortestDistance method) (cvpack.Torsion method) (cvpack.TorsionSimilarity method) getReferenceValue() (cvpack.ResidueCoordination method) getUnit() (cvpack.Angle method) (cvpack.AtomicFunction method) (cvpack.AttractionStrength method) (cvpack.CentroidFunction method) (cvpack.CompositeRMSD method) (cvpack.Distance method) (cvpack.HelixAngleContent method) (cvpack.HelixHBondContent method) (cvpack.HelixRMSDContent method) (cvpack.HelixTorsionContent method) (cvpack.MetaCollectiveVariable method) (cvpack.NumberOfContacts method) (cvpack.OpenMMForceWrapper method) (cvpack.PathInCVSpace method) (cvpack.PathInRMSDSpace method) (cvpack.RadiusOfGyration method) (cvpack.RadiusOfGyrationSq method) (cvpack.ResidueCoordination method) (cvpack.RMSD method) (cvpack.SheetRMSDContent method) (cvpack.ShortestDistance method) (cvpack.Torsion method) (cvpack.TorsionSimilarity method) getValue() (cvpack.Angle method) (cvpack.AtomicFunction method) (cvpack.AttractionStrength method) (cvpack.CentroidFunction method) (cvpack.CompositeRMSD method) (cvpack.Distance method) (cvpack.HelixAngleContent method) (cvpack.HelixHBondContent method) (cvpack.HelixRMSDContent method) (cvpack.HelixTorsionContent method) (cvpack.MetaCollectiveVariable method) (cvpack.NumberOfContacts method) (cvpack.OpenMMForceWrapper method) (cvpack.PathInCVSpace method) (cvpack.PathInRMSDSpace method) (cvpack.RadiusOfGyration method) (cvpack.RadiusOfGyrationSq method) (cvpack.ResidueCoordination method) (cvpack.RMSD method) (cvpack.SheetRMSDContent method) (cvpack.ShortestDistance method) (cvpack.Torsion method) (cvpack.TorsionSimilarity method) getValues() (cvpack.reporting.CVWriter method) (cvpack.reporting.MetaCVWriter method)

H

HelixAngleContent (class in cvpack) HelixHBondContent (class in cvpack)

HelixRMSDContent (class in cvpack) HelixTorsionContent (class in cvpack)

M

MetaCollectiveVariable (class in cvpack)

MetaCVWriter (class in cvpack.reporting)

N

NumberOfContacts (class in cvpack)

O

OpenMMForceWrapper (class in cvpack)

P

PathInCVSpace (class in cvpack)

PathInRMSDSpace (class in cvpack)

R

RadiusOfGyration (class in cvpack) RadiusOfGyrationSq (class in cvpack)

ResidueCoordination (class in cvpack) RMSD (class in cvpack)

S

serialize() (in module cvpack.serialization) setReferenceValue() (cvpack.ResidueCoordination method)

SheetRMSDContent (class in cvpack) ShortestDistance (class in cvpack) StateDataReporter (class in cvpack.reporting)

T

Torsion (class in cvpack)

TorsionSimilarity (class in cvpack)