Index

A

applyRotationMatrix() (in module newanalysis.helpers)

atomicCurrent() (in module newanalysis.helpers) atomsPerResidue() (in module newanalysis.functions)

B

bertholdHorn() (in module newanalysis.unfold)

buildNeighborList() (in module newanalysis.voro)

C

calcAngularDisplacement() (in module newanalysis.correl) (in module newanalysis.helpers) calcAngularMomentum() (in module newanalysis.helpers) calcAngularVelocityXCorrel() (in module newanalysis.correl) calcCN() (in module newanalysis.voro) calcCN_int8() (in module newanalysis.voro) calcDipDipEnergyAtomic() (in module newanalysis.helpers) calcEnergyAA() (in module newanalysis.helpers) calcEnergyAAhisto() (in module newanalysis.helpers) calcEnergyAAhisto1() (in module newanalysis.helpers) calcEnergyAApermind() (in module newanalysis.helpers) calcEnergyAApermindhisto() (in module newanalysis.helpers) calcEnergyAASep() (in module newanalysis.helpers) calcEnergyAtomic() (in module newanalysis.helpers) calcEnergyAtomicVoro() (in module newanalysis.helpers) calcEnergyDouble() (in module newanalysis.helpers) calcEnergyMuA() (in module newanalysis.helpers) calcFourierLaplaceTransform() (in module newanalysis.helpers) calcFrame() (newanalysis.gfunction.RDF method) (newanalysis.gfunction.RDF_voronoi method) calcHistoTS() (in module newanalysis.gfunction)

calcHistoTSVoro() (in module newanalysis.gfunction) calcInertiaTensor() (in module newanalysis.helpers) calcOctant() (in module newanalysis.helpers) calcRelativeAngDisp() (in module newanalysis.correl) calcResidenceTimeseries() (in module newanalysis.helpers) calcRotationMatrix() (in module newanalysis.helpers) calcTessellation() (in module newanalysis.functions) (in module newanalysis.voro) calcTessellationParallel() (in module newanalysis.voro) calcTessellationParallelAll() (in module newanalysis.voro) calcTessellationVolSurfAtomic() (in module newanalysis.voro) centerOfMassByResidue() (in module newanalysis.functions) centerOrientBox() (in module newanalysis.helpers) centerToPointOrientBox() (in module newanalysis.helpers) checkHBond() (in module newanalysis.helpers) collectiveDipoleMomentWaterShells() (in module newanalysis.helpers) comByResidue() (in module newanalysis.helpers) correlate() (in module newanalysis.correl) correlateParallel() (in module newanalysis.correl) crossDisplacementMdMj() (in module newanalysis.diffusion) CUDA (class in newanalysis.gfunction)

D

dipByResidue() (in module newanalysis.helpers) dipoleMoment() (in module newanalysis.functions) dipoleMomentByResidue() (in module newanalysis.functions) dipoleMomentNeutralSelection() (in module newanalysis.helpers)

dipTen() (in module newanalysis.helpers) dipTenCorrel() (in module newanalysis.helpers) dipTenInit() (in module newanalysis.helpers) drawTessellation() (in module newanalysis.voro)

F

f2c() (in module newanalysis.functions) findDS() (in module newanalysis.helpers)

findMinDist() (in module newanalysis.unfold) findNearestAtom() (in module newanalysis.helpers)

G

get_velocities() (in module newanalysis.functions)

M

minDist() (in module newanalysis.unfold) minDistBox() (in module newanalysis.unfold) minDistCenterBox() (in module newanalysis.unfold) minVec() (in module newanalysis.unfold) module newanalysis.correl newanalysis.diffusion newanalysis.functions newanalysis.gfunction newanalysis.helpers newanalysis.unfold newanalysis.voro

msdCOM() (in module newanalysis.diffusion) msdCOMvHnG() (in module newanalysis.diffusion) msdMJ() (in module newanalysis.diffusion) msdMJCharges() (in module newanalysis.diffusion) msdMJcrossterms() (in module newanalysis.diffusion) msdMJdecomp() (in module newanalysis.diffusion)

N

nearestNeighbor() (in module newanalysis.voro) newanalysis.correl module newanalysis.diffusion module newanalysis.functions module newanalysis.gfunction module

newanalysis.helpers module newanalysis.unfold module newanalysis.voro module nonGaussianParameter() (in module newanalysis.diffusion) NQRdipTen() (in module newanalysis.helpers) NQRself() (in module newanalysis.helpers) NQRselfAndB() (in module newanalysis.helpers)

P

pairDisplacement() (in module newanalysis.diffusion)

printInfo() (newanalysis.gfunction.RDF method) (newanalysis.gfunction.RDF_voronoi method)

R

RDF (class in newanalysis.gfunction) RDF_voronoi (class in newanalysis.gfunction) resetArrays() (newanalysis.gfunction.RDF method) (newanalysis.gfunction.RDF_voronoi method)

residueFirstAtom() (in module newanalysis.functions) rotationMatrixShellCorrelate() (in module newanalysis.correl) rotationMatrixShellCorrelateDist() (in module newanalysis.correl) rotationMatrixShellCorrelateTot() (in module newanalysis.correl) rotationMatrixShellCorrelateTotParts() (in module newanalysis.correl)

S

sparsecorrelate() (in module newanalysis.correl) sparsecrosscorrelate() (in module newanalysis.correl) sparsefullcorrelate() (in module newanalysis.correl) sparsefullcrosscorrelate() (in module newanalysis.correl) sparsefullnobulkcorrelate() (in module newanalysis.correl)

sparsefullnobulkthincorrelate() (in module newanalysis.correl) sparsefullnobulkthingreenkubo() (in module newanalysis.correl) SphereinCube() (in module newanalysis.helpers) sphHarmMatrix() (in module newanalysis.helpers) sumMDCage() (in module newanalysis.helpers) sumMDCageSingle() (in module newanalysis.helpers)

T

transform() (in module newanalysis.correl)

U

unfoldBox() (in module newanalysis.unfold) unfoldCharmmOcta() (in module newanalysis.unfold) unfoldOcta() (in module newanalysis.unfold)

unfoldTraj() (in module newanalysis.diffusion) update_box() (newanalysis.gfunction.RDF method) (newanalysis.gfunction.RDF_voronoi method)

V

vectorRotation() (in module newanalysis.correl)

velcomByResidue() (in module newanalysis.functions) (in module newanalysis.helpers)

W

waterRotationMatrix() (in module newanalysis.helpers)

write() (newanalysis.gfunction.RDF method) (newanalysis.gfunction.RDF_voronoi method)