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SOAPify
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Index
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A
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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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W
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X
_
__init__() (SOAPify.classify.SOAPclassification method)
(SOAPify.classify.SOAPReferences method)
(SOAPify.engine.dscribeSOAPengineContainer method)
(SOAPify.engine.quippySOAPengineContainer method)
(SOAPify.engine.SOAPengineContainer method)
(SOAPify.transitions.tracker.StateTracker method)
A
applyClassification() (in module SOAPify.classify)
C
calculateResidenceTimes() (in module SOAPify.transitions)
calculateResidenceTimesFromClassification() (in module SOAPify.transitions)
calculateTransitionMatrix() (in module SOAPify.transitions)
centerMaskCreator() (in module SOAPify.engine)
centersMask (SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
createReferencesFromTrajectory() (in module SOAPify.classify)
createTrajectory() (in module SOAPify.cli)
createUniverseFromSlice() (in module SOAPify.HDF5er.HDF5To)
crossover (SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
D
distances (SOAPify.classify.SOAPclassification attribute)
dscribeSOAPengineContainer (class in SOAPify.engine)
E
engine (SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
exportChunk2HDF5() (in module SOAPify.HDF5er.HDF5erUtils)
F
features (SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
fillSOAPVectorFromdscribe() (in module SOAPify.utils)
G
getAddressesQuippyLikeDscribe() (in module SOAPify.utils)
getDictFromList() (in module SOAPify.cli)
getDistanceBetween() (in module SOAPify.classify)
getDistancesFromRef() (in module SOAPify.classify)
getDistancesFromRefNormalized() (in module SOAPify.classify)
getdscribeSOAPMapping() (in module SOAPify.utils)
getLocation() (SOAPify.engine.dscribeSOAPengineContainer method)
(SOAPify.engine.quippySOAPengineContainer method)
(SOAPify.engine.SOAPengineContainer method)
getquippySOAPMapping() (in module SOAPify.utils)
getReferencesFromDataset() (in module SOAPify.classify)
getResidenceTimesFromStateTracker() (in module SOAPify.transitions.tracker)
getSlicesFromAttrs() (in module SOAPify.utils)
getSoapEngine() (in module SOAPify.engine)
getSOAPSettings() (in module SOAPify.utils)
getTimeSOAPSimple() (in module SOAPify.analysis)
getXYZfromMDA() (in module SOAPify.HDF5er.HDF5To)
getXYZfromTrajGroup() (in module SOAPify.HDF5er.HDF5To)
H
HDF52AseAtomsChunckedwithSymbols() (in module SOAPify.HDF5er.HDF5To)
I
isTrajectoryGroup() (in module SOAPify.HDF5er.HDF5erUtils)
K
kernelSoap() (in module SOAPify.distances)
KNOWNSOAPENGINES (in module SOAPify.engine)
L
legend (SOAPify.classify.SOAPclassification attribute)
listNeighboursAlongTrajectory() (in module SOAPify.analysis)
lmax (SOAPify.classify.SOAPReferences attribute)
(SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
M
MDA2HDF5() (in module SOAPify.HDF5er.ToHDF5)
mergeReferences() (in module SOAPify.classify)
module
SOAPify
SOAPify.analysis
SOAPify.classify
SOAPify.cli
SOAPify.distances
SOAPify.engine
SOAPify.HDF5er
SOAPify.HDF5er.HDF5erUtils
SOAPify.HDF5er.HDF5To
SOAPify.HDF5er.ToHDF5
SOAPify.saponify
SOAPify.transitions
SOAPify.transitions.tracker
SOAPify.utils
N
names (SOAPify.classify.SOAPReferences attribute)
neighbourChangeInTime() (in module SOAPify.analysis)
nmax (SOAPify.classify.SOAPReferences attribute)
(SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
normalizeArray() (in module SOAPify.utils)
normalizeMatrixByRow() (in module SOAPify.transitions)
O
orderByZ() (in module SOAPify.utils)
P
patchBoxFromTopology() (in module SOAPify.HDF5er.HDF5erUtils)
Q
quippySOAPengineContainer (class in SOAPify.engine)
R
rcut (SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
references (SOAPify.classify.SOAPclassification attribute)
removeAtomIdentityFromEventTracker() (in module SOAPify.transitions.tracker)
S
saponifyMultipleTrajectories() (in module SOAPify.saponify)
saponifyTrajectory() (in module SOAPify.saponify)
saveReferences() (in module SOAPify.classify)
saveXYZfromTrajGroup() (in module SOAPify.HDF5er.HDF5To)
simpleKernelSoap() (in module SOAPify.distances)
simpleSOAPdistance() (in module SOAPify.distances)
SOAPclassification (class in SOAPify.classify)
SOAPdistance() (in module SOAPify.distances)
SOAPdistanceNormalized() (in module SOAPify.distances)
SOAPengine (SOAPify.engine.dscribeSOAPengineContainer attribute)
(SOAPify.engine.quippySOAPengineContainer attribute)
(SOAPify.engine.SOAPengineContainer attribute)
SOAPengineContainer (class in SOAPify.engine)
SOAPenginekind (SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
SOAPify
module
SOAPify.analysis
module
SOAPify.classify
module
SOAPify.cli
module
SOAPify.distances
module
SOAPify.engine
module
SOAPify.HDF5er
module
SOAPify.HDF5er.HDF5erUtils
module
SOAPify.HDF5er.HDF5To
module
SOAPify.HDF5er.ToHDF5
module
SOAPify.saponify
module
SOAPify.transitions
module
SOAPify.transitions.tracker
module
SOAPify.utils
module
SOAPReferences (class in SOAPify.classify)
species (SOAPify.engine.dscribeSOAPengineContainer property)
(SOAPify.engine.quippySOAPengineContainer property)
(SOAPify.engine.SOAPengineContainer property)
spectra (SOAPify.classify.SOAPReferences attribute)
StateTracker (class in SOAPify.transitions.tracker)
stride (SOAPify.transitions.tracker.StateTracker property)
T
timeSOAP() (in module SOAPify.analysis)
timeSOAPsimple() (in module SOAPify.analysis)
TRACK_CURSTATE (in module SOAPify.transitions.tracker)
TRACK_ENDSTATE (in module SOAPify.transitions.tracker)
TRACK_EVENTTIME (in module SOAPify.transitions.tracker)
TRACK_PREVSTATE (in module SOAPify.transitions.tracker)
trackStates() (in module SOAPify.transitions.tracker)
traj2SOAP() (in module SOAPify.cli)
transitionMatrixFromSOAPClassification() (in module SOAPify.transitions)
transitionMatrixFromSOAPClassificationNormalized() (in module SOAPify.transitions)
transitionMatrixFromStateTracker() (in module SOAPify.transitions.tracker)
U
universe2HDF5() (in module SOAPify.HDF5er.ToHDF5)
W
window (SOAPify.transitions.tracker.StateTracker property)
X
xyz2hdf5Converter() (in module SOAPify.HDF5er.ToHDF5)
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