Index

A

alignAllMol() (in module molFit_quaternions) append() (selText.SelText method) appendDCD() (dcdReader.DCDReader method)

appendLOG() (logReader.LOGReader method) appendPDB() (dcdParser.NAMDDCD method) applyRotation() (in module molFit_quaternions) astype() (selText.SelText method)

C

ChordDiag (class in DistanceChordDiagram) compAutoCorrel() (HydrogenBonds.HydrogenBonds method) compDensity() (RadialDensity.RadialNumberDensity method) (RadialDensity.ResidueWiseWaterDensity method) compDSF() (IncoherentScat.IncoherentScat method) compHBNumber() (HydrogenBonds.HydrogenBonds method) compIntermediateFunc() (IncoherentScat.IncoherentScat method) compMSD() (IncoherentScat.IncoherentScat method)

compOrientationalProb() (Rotations.Rotations method) compOrientations() (Rotations.WaterAtProtSurface method) compResidenceTime() (ResidenceTime.ResidenceTime method) compResidueWiseResidenceTime() (ResidenceTime.ResidenceTime method) compRotationalRelaxation() (Rotations.Rotations method) compScatteringFunc() (IncoherentScat.IncoherentScat method) ConstantsAndModels (module) convertScatFunctoEISF() (IncoherentScat.IncoherentScat method) coordinates() (selText.SelText method)

D

Dataset (class in Dataset) (module) dcdParser (module)

DCDReader (class in dcdReader) dcdReader (module) DistanceChordDiagram (module)

G

generateVolMap() (Rotations.WaterAtProtSurface method) (VolMapDensity.WaterVolNumberDensity method) getAlignedCenterOfMass() (dcdParser.NAMDDCD method) getAlignedData() (dcdParser.NAMDDCD method) getAtom() (selText.SelText method) getAtomsMasses() (psfParser.NAMDPSF method) getAutoCorr() (Rotations.WaterAtProtSurface method) getBoundAtoms() (psfParser.NAMDPSF method) getCenterOfMass() (dcdParser.NAMDDCD method) getCharges() (selText.SelText method) getCoor() (pdbParser.NAMDPDB method) getDataDistribution() (logParser.NAMDLOG method) getDataSeries() (logParser.NAMDLOG method) getDistances() (dcdParser.NAMDDCD method) getDistEntropy() (Rotations.WaterAtProtSurface method) getDistribution() (VolMapDensity.WaterVolNumberDensity method) getGyrationRadius() (dcdParser.NAMDDCD method) getHBAcceptors() (psfParser.NAMDPSF method) getHBDonors() (psfParser.NAMDPSF method) getIndices() (selText.SelText method) getKineticEnergyDistribution() (velParser.NAMDVEL method) getMasses() (selText.SelText method) getName() (selText.SelText method)

getOrientations() (Rotations.WaterAtProtSurface method) getPBC() (dcdParser.NAMDDCD method) getProtVolume() (dcdParser.NAMDDCD method) getRandomVec() (in module ConstantsAndModels) getResidues() (selText.SelText method) getResName() (selText.SelText method) getRMSDperAtom() (dcdParser.NAMDDCD method) getRMSDperFrame() (dcdParser.NAMDDCD method) getRMSDperResidue() (dcdParser.NAMDDCD method) getSameResidueAs() (psfParser.NAMDPSF method) getSegName() (selText.SelText method) getSelection() (psfParser.NAMDPSF method) getSpecVolume() (dcdParser.NAMDDCD method) getSTDperAtom() (dcdParser.NAMDDCD method) getSubSelection() (selText.SelText method) getUniqueAtom() (selText.SelText method) getUniqueName() (selText.SelText method) getUniqueResidues() (selText.SelText method) getUniqueResName() (selText.SelText method) getUniqueSegName() (selText.SelText method) getWithin() (dcdParser.NAMDDCD method) getWithin_kdTree (module) getWithin_kdTree() (in module getWithin_kdTree) getWithinCOM() (dcdParser.NAMDDCD method)

H

HydrogenBonds (class in HydrogenBonds) (module)

HydroproReader (class in HydroproReader) (module)

I

importDCDFile() (dcdReader.DCDReader method) importFile() (Dataset.Dataset method) importLOGFile() (logReader.LOGReader method)

importPDBFile() (pdbReader.PDBReader method) importVELFile() (velReader.VELReader method) IncoherentScat (class in IncoherentScat) (module)

L

logParser (module)

LOGReader (class in logReader) logReader (module)

M

molFit_quaternions (module)

N

NAMDDCD (class in dcdParser) NAMDLOG (class in logParser)

NAMDPDB (class in pdbParser) NAMDPSF (class in psfParser) NAMDVEL (class in velParser)

P

pdbParser (module) PDBReader (class in pdbReader) pdbReader (module) periodic_kdtree (module) PeriodicCKDTree (class in periodic_kdtree) plotAutoCorr() (Rotations.WaterAtProtSurface method) plotAutoCorrel() (HydrogenBonds.HydrogenBonds method) plotAveragedDistances_chordDiagram() (dcdParser.NAMDDCD method) plotAveragedDistances_parallelPlot() (dcdParser.NAMDDCD method) plotDataDistribution() (logParser.NAMDLOG method) plotDataSeries() (logParser.NAMDLOG method) plotDensity() (RadialDensity.RadialNumberDensity method) (RadialDensity.ResidueWiseWaterDensity method) plotDistEntropy() (Rotations.WaterAtProtSurface method) plotDistribution() (VolMapDensity.WaterVolNumberDensity method) plotDSF() (IncoherentScat.IncoherentScat method)

plotIntermediateFunc() (IncoherentScat.IncoherentScat method) plotKineticEnergyDistribution() (velParser.NAMDVEL method) plotOrientationalProb() (Rotations.Rotations method) plotOrientations() (Rotations.WaterAtProtSurface method) plotResidenceTime() (ResidenceTime.ResidenceTime method) plotResidueWiseResidenceTime() (ResidenceTime.ResidenceTime method) plotRMSDperAtom() (dcdParser.NAMDDCD method) plotRMSDperFrame() (dcdParser.NAMDDCD method) plotRMSDperResidue() (dcdParser.NAMDDCD method) plotRotationalRelaxation() (Rotations.Rotations method) plotScatteringFunc() (IncoherentScat.IncoherentScat method) plotSTDperAtom() (dcdParser.NAMDDCD method) process() (DistanceChordDiagram.ChordDiag method) (selParser.SelParser method) psfParser (module) psfReader (module)

Q

query() (periodic_kdtree.PeriodicCKDTree method)

query_ball_point() (periodic_kdtree.PeriodicCKDTree method)

R

RadialDensity (module) RadialNumberDensity (class in RadialDensity) readFile() (HydroproReader.HydroproReader method) ResidenceTime (class in ResidenceTime) (module)

ResidueWiseWaterDensity (class in RadialDensity) rotate() (dcdParser.NAMDDCD method) Rotations (class in Rotations) (module)

S

selection() (Dataset.Dataset method) SelParser (class in selParser) selParser (module)

SelText (class in selText) selText (module) show() (DistanceChordDiagram.ChordDiag method)

V

velParser (module) VELReader (class in velReader)

velReader (module) VolMapDensity (module)

W

WaterAtProtSurface (class in Rotations) WaterVolNumberDensity (class in VolMapDensity)

writePDB() (selText.SelText method) writeVolMap() (Rotations.WaterAtProtSurface method) (VolMapDensity.WaterVolNumberDensity method)