Index

A

AdvanceTraj() (in module movies) align_traj_on_density (module) AlignTrajectoryOnDensity() (in module align_traj_on_density) AlignTrajectoryOnFirstFrame() (in module align_traj_on_density) AnalyzeAreaPerLipid() (in module lipid_analysis) AnalyzeHydrophobicMoment() (in module hydrophobicity) AnalyzeLipidSplays() (in module lipid_analysis) AnalyzeLipidTiltAndSplay() (in module lipid_analysis) AnalyzeLipidTilts() (in module lipid_analysis)

AnalyzeMolecularOrderParameters() (in module lipid_order_parameters) AnalyzePoreRadii() (in module hole) AnalyzeSecondaryStructure() (in module secondary_structure) angles (module) AssignFloatPropToEntity() (in module entity_alg) AssignFloatPropToEntityResidues() (in module entity_alg) AssignNormalsToLipids() (in module lipid_analysis) AssignSecondaryStructure() (in module secondary_structure) AverageMembraneThickness() (in module trajectory_utilities)

B

BuildUnitCellVectors() (in module pbc_utilities)

C

CalculateCharge() (in module hydrophobicity) CalculateChargeWithSlidingWindow() (in module hydrophobicity) CalculateCovariance() (in module trajectory_utilities) CalculateCurvature() (in module surface_alg) CalculateGeneralizedCorrelations() (in module trajectory_utilities) CalculateHydrophobicity() (in module hydrophobicity) CalculateHydrophobicityWithSlidingWindow() (in module hydrophobicity) CalculateHydrophobicMoment() (in module hydrophobicity) CalculateHydrophobicMoment2() (in module hydrophobicity) CalculateHydrophobicMoment3() (in module hydrophobicity) CalculateHydrophobicMomentWithSlidingWindow() (in module hydrophobicity) CalculateInterfaceFromTraj() (in module trajectory_utilities) CalculateMolecularOrderParameters() (in module lipid_order_parameters) CalculateMutualInformation() (in module trajectory_utilities) CalculateNormals() (in module surface_alg) CalculateNormalsFast() (in module surface_alg) CalculateNormalsFast2() (in module surface_alg) CalculatePoreRadii() (in module hole) CalculatePrincipalComponents() (in module principal_components) CalculateSurface() (in module surface_alg)

CalculateSurface2() (in module surface_alg) CalculateVolumeFromDensityMap() (in module density_alg) CleanMaxDensitySurface() (in module surface_alg) CleanMaxDensitySurface2() (in module surface_alg) ClipObject() (in module movies) ClipScene() (in module movies) clustering (module) ClusterOnPairwiseDistance() (in module clustering) coarse_grained_conop (module) colvar (module) ConnectAtomsFromDict() (in module coarse_grained_conop) ConnectMartiniAtomsHeuristic() (in module coarse_grained_conop) ConnectMartiniProteinAtoms() (in module coarse_grained_conop) CreateDensityMapFromEntityView() (in module density_alg) CreateDensityMapFromTrajectory() (in module density_alg) CreateDensityMapFromTrajectoryWithPBC() (in module density_alg) CreateEntityFromVec3List() (in module entity_alg) CreatePerResidueCMTrajectory() (in module trajectory_utilities) CreateSequenceFromView() (in module sequence_alg)

D

density_alg (module)

DetermineAmphipathicity() (in module hydrophobicity)

E

entity_alg (module) ExtendEntityToNeighboringUnitCells() (in module pbc_utilities) ExtendEntityWithPBC() (in module pbc_utilities)

ExtendTrajectory() (in module trajectory_utilities) ExtendTrajectoryToNeighboringUnitCells() (in module trajectory_utilities) ExtractTiltAndSplayModuli() (in module lipid_analysis)

F

Fade() (in module movies) Fades() (in module movies) file_utilities (module) FindClosestAtom() (in module entity_alg) FindMotif() (in module sequence_alg)

FindSecStrucElements() (in module secondary_structure) FindWithinWithNonOrthogonalPBC() (in module pbc_utilities) FindWithinWithPBC() (in module pbc_utilities) FitSplayDistribution() (in module lipid_analysis) FitTiltDistribution() (in module lipid_analysis)

G

GenerateConnectivityDictFromITPFile() (in module coarse_grained_conop) GenerateCrystalPackingFromPDB() (in module entity_alg) GenerateSearchVectors() (in module pbc_utilities) GetBoundaryBetweenDensities() (in module density_alg) GetBoundaryBetweenViews() (in module lipid_analysis) GetCellAnglesList() (in module trajectory_utilities)

GetCellSizeList() (in module trajectory_utilities) GetCellVectorsList() (in module trajectory_utilities) GetMaxDensitySurface() (in module density_alg) GetResidueHydrophobicity() (in module hydrophobicity) GetUCellVectorSizeAndAngles() (in module pbc_utilities)

H

HierarchicalClusteringOnPairwiseDistance() (in module clustering) hole (module)

HoshenKopelman() (in module clustering) hydrophobicity (module)

I

IntegrateFloatList() (in module colvar)

InterpolateTrajectory() (in module movies)

L

lipid_analysis (module)

lipid_order_parameters (module)

M

MakeMovieAndCleanImageFiles() (in module movies)

movies (module)

O

OrientNormals() (in module surface_alg) OrientNormalsAlongDensity() (in module surface_alg)

OrientNormalsFast() (in module surface_alg)

P

ParsePDBForCubicPhase() (in module file_utilities) pbc_utilities (module) plot (module) PlotDistanceBetwAtoms() (in module plot) PlotFloatProp() (in module plot) PlotHistDistanceBetwAtoms() (in module plot) PlotList() (in module plot)

PlotMinDistance() (in module plot) PlotSecStructureList() (in module secondary_structure) principal_components (module) ProjectOnPrincipalComponent() (in module principal_components) ProjectOnPrincipalComponentsAtomWise() (in module principal_components) ProjectVectorOnUnitCellVectors() (in module pbc_utilities)

R

ReadColvarFile() (in module colvar) ReadFile() (in module file_utilities) ReadFloatListFile() (in module file_utilities) ReadMissingResiduesFromPDB() (in module file_utilities) ReadNamdSMDFile() (in module colvar) ReadSymmetryFromPDB() (in module file_utilities)

ReadUnitCellFromPDB() (in module file_utilities) ReconstructTrajFromPrincipalComponents() (in module principal_components) RenderFrames() (in module movies) RenderTrajSimple() (in module movies) RepresentPrincipalComponentOnStruccture() (in module principal_components) Rotate() (in module movies)

S

secondary_structure (module) sequence_alg (module) SimplifySecStructure() (in module secondary_structure)

SimplifySecStructureList() (in module secondary_structure) SmoothAverageMembrane() (in module trajectory_utilities) surface_alg (module)

T

trajectory_utilities (module) TransformViewWithPeriodicBoundaries() (in module align_traj_on_density)

TranslateFrames() (in module trajectory_utilities)

V

VectorsToNeighboringUnitCells() (in module pbc_utilities)

W

WrapFloatList() (in module trajectory_utilities) WrapTrajectoryInPeriodicCell() (in module trajectory_utilities) WrapTransformedView() (in module align_traj_on_density) WriteFloatList() (in module file_utilities)

WriteListOfListsInColumns() (in module file_utilities) WriteListOfListsInLines() (in module file_utilities) WriteSplayDict() (in module lipid_analysis) WriteTiltDict() (in module lipid_analysis)

Z

Zoom() (in module movies)

ZoomAndClip() (in module movies)