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Identifier Index

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S

S (in ChemElements)	SequenceParser (in csb.bio.io.fasta)	SS (in Options)
sample() (in ARS)	SequencePositionError (in csb.bio.sequence)	ss (in HHsearch)
sample() (in Envelope)	SequenceTypes (in csb.bio.sequence)	ss_score (in HHpredHit)
sample() (in AbstractSampler)	SER (in ProteinAlphabet)	SSCartoonBuilder (in csb.bio.io.svg)
sample() (in AbstractMC)	SER (in StdProteinAlphabet)	Stack (in csb.core)
sample() (in AbstractEnsembleMC)	serial_number (in Atom)	StandardID (in csb.bio.io.wwpdb)
sample() (in AbstractSingleChainMC)	serialize() (in ProfileHMM)	start (in Assignment)
sample_dirichlet() (in csb.statistics.rand)	serialize() (in ClansFileWriter)	start (in FragmentMatch)
sample_from_histogram() (in csb.statistics.rand)	series() (in GaussianMixture)	start (in RosettaFragment)
sample_sphere3d() (in csb.statistics.rand)	set() (in EmissionTable)	start (in HHpredHit)
sample_weights() (in MaxentModel)	set() (in TransitionTable)	start (in ProfileHMM)
sampler1 (in AbstractSwapCommunicator)	set() (in MaxentModel)	Start (in States)
sampler1 (in AbstractSwapParameterInfo)	set() (in AbstractParameter)	start (in AlignmentResult)
sampler2 (in AbstractSwapCommunicator)	set_default_params() (in ClansParams)	START (in LocalAlignmentAlgorithm)
sampler2 (in AbstractSwapParameterInfo)	set_default_rotmtx() (in Clans)	start (in SecondaryStructure)
samplers (in csb.statistics)	set_params() (in AbstractDensity)	start (in SecondaryStructureElement)
save() (in Chart)	set_perturbation_first() (in Step)	start() (in REMatchProxy)
Sb (in ChemElements)	set_propagation_first() (in Step)	start() (in Backend)
Sc (in ChemElements)	setDefaultDataRoot() (in Config)	start_index (in BaseCollectionContainer)
sc (in RevisionHandler)	setDefaultGeneratedDataRoot() (in Config)	start_insertion (in ProfileHMM)
scalar (in Expression)	setUp() (in Case)	start_marker (in EntryReader)
scalar() (in Table)	Sg (in ChemElements)	start_positions (in RosettaFragmentMap)
scale (in ProfileHMM)	shape (in InverseGaussian)	started (in Backend)
scale_and_fit() (in csb.bio.utils)	Shell (in csb.io)	starting_at() (in RosettaFragmentMap)
scale_estimator (in ScaleMixturePrior)	ShellInfo (in csb.io)	State (in csb.bio.hmm)
scalemixture (in csb.statistics)	SHIFT (in ChemShiftReader)	State (in csb.statistics.samplers)
ScaleMixture (in csb.statistics.scalemixture)	SHIFT3 (in ChemShift3Reader)	state (in AbstractMC)
ScaleMixturePrior (in csb.statistics.scalemixture)	ShiftInfo (in csb.bio.io.vasco)	StateExistsError (in csb.bio.hmm)
ScaleMixturePriorEstimator (in csb.statistics.scalemixture)	short (in Version)	StateFactory (in csb.bio.hmm)
scales (in GaussianMixture)	SHORT_PREFIX (in ArgHandler)	StateNotFoundError (in csb.bio.hmm)
scales (in ScaleMixture)	ShortTrajectoryBuilder (in csb.statistics.samplers.mc)	States (in csb.bio.hmm)
scan() (in SecondaryStructure)	show() (in Backend)	StaticHH (in FragmentTypes)
score (in Assignment)	show() (in Chart)	StatisticalEnsemble (in csb.statmech.ensembles)
score (in RosettaFragment)	showinfo (in ClansParams)	statistics (in csb)
score (in HHpredHit)	shrink() (in FragmentCluster)	statistics (in AbstractExchangeMC)
score (in AlignmentResult)	shrinkone() (in FragmentCluster)	statmech (in csb)
score (in SecondaryStructureElement)	Si (in ChemElements)	stats (in MaxentPosterior)
score() (in ScoringHelper)	sigma (in GaussianMixture)	stats (in SwapStatistics)
score() (in ChemShiftScoringModel)	sigma (in Normal)	stats (in NonequilibriumTrajectory)
score() (in AbstractScoringMatrix)	sign() (in csb.numeric)	StdProteinAlphabet (in csb.bio.sequence)
score() (in IdentityMatrix)	silent (in State)	Step (in csb.io.tsv)
score() (in SimilarityMatrix)	similarity (in HHpredHit)	Step (in csb.statistics.samplers.mc.neqsteppropagator)
score_units (in ProfileHMM)	SimilarityMatrix (in csb.bio.sequence.alignment)	steps (in Protocol)
scores() (in BenchmarkAdapter)	simple_secondary_shift() (in RandomCoil)	stepsize (in RWMCSampler)
ScoreUnits (in csb.bio.hmm)	SimpleProposalCommunicator (in csb.statistics.samplers.mc.singlechain)	STOP (in ProteinAlphabet)
scoring_matrix (in AbstractAlignmentAlgorithm)	simplify() (in SecondaryStructureElement)	stop() (in Backend)
ScoringHelper (in csb.apps.csfrag)	simpson_2d() (in csb.numeric)	Strand (in SecStructures)
Se (in ChemElements)	singlechain (in csb.statistics.samplers.mc)	stream (in EntryWriter)
searched_hmms (in HHpredHitList)	SingleSwapStatistics (in csb.statistics.samplers.mc.multichain)	strict (in SequenceAlignmentReader)
SEC (in ProteinAlphabet)	singleton() (in csb.core)	strict (in StructureAlignmentFactory)
sec_structure_at() (in Assignment)	size (in RosettaFragmentMap)	StrideParser (in csb.bio.io.dssp)
second_moments() (in csb.bio.utils)	size (in ClansSeqgroup)	strip() (in AbstractSequence)
secondary_shift() (in RandomCoil)	size (in AbstractAlignment)	strip() (in Sequence)
secondary_structure (in Assignment)	SIZE (in ChunkedReader)	strip() (in SequenceAdapter)
secondary_structure (in Chain)	skewness() (in csb.statistics)	Strong (in NucleicAlphabet)
secondary_structure (in Residue)	skip() (in csb.test)	structure (in csb.bio)
SecondaryShiftConverter (in csb.apps.csfrag)	slength (in HHpredHit)	Structure (in csb.bio.structure)
SecondaryShiftReader (in csb.apps.csfrag)	slice_query() (in HHfrag)	structure() (in BenchmarkAdapter)
SecondaryStructure (in csb.bio.structure)	SliceContext (in csb.apps.hhfrag)	structure() (in ProfileHMM)
SecondaryStructureElement (in csb.bio.structure)	SliceHelper (in csb.bio.sequence)	StructureAlignment (in csb.bio.sequence)
SecStructureFormatError (in csb.bio.io.wwpdb)	Sm (in ChemElements)	StructureAlignmentFactory (in csb.bio.io.fasta)
SecStructures (in csb.bio.structure)	Sn (in ChemElements)	StructureChainsTable (in csb.bio.structure)
SecStructureScoring (in csb.apps.hhsearch)	sort() (in RosettaFragmentMap)	StructureFormatError (in csb.bio.io.hhpred)
segment() (in ProfileHMM)	sort() (in HHpredHitList)	StructureFormatError (in csb.bio.io.wwpdb)
SegmentMixture (in csb.statistics.mixtures)	sort() (in Clans)	StructureNotFoundError (in csb.bio.io.wwpdb)
segments (in HHpredHitAlignment)	SOURCE (in BuildTypes)	StructureParser() (in csb.bio.io)
select (in Expression)	source_end (in ProfileHMMRegion)	StructureProvider (in csb.bio.io.wwpdb)
select() (in Operator)	source_end (in ProfileHMMSegment)	subject (in HHpredHitAlignment)
select() (in Table)	source_id (in Assignment)	subject (in AlignmentResult)
seq (in ClansEntry)	source_id (in FragmentMatch)	subregion() (in RosettaFragment)
seqgroups (in Clans)	source_id (in RosettaFragment)	subregion() (in ProfileHMM)
SeqResID (in csb.bio.io.wwpdb)	source_start (in ProfileHMMRegion)	subregion() (in AbstractAlignment)
sequence (in Assignment)	source_start (in ProfileHMMSegment)	subregion() (in AbstractSequence)
sequence (in Target)	sources (in RosettaFragmentMap)	subregion() (in Sequence)
sequence (in csb.bio)	SOURCETREE (in csb.build)	subregion() (in SequenceAdapter)
sequence (in AbstractSequence)	SparkyPeakListReader (in csb.bio.io.noe)	subregion() (in Chain)
Sequence (in csb.bio.sequence)	SparseChainSequence (in csb.bio.io.wwpdb)	subregion() (in SecondaryStructure)
sequence (in Sequence)	sql (in Between)	SubversionHandler (in csb.build)
sequence (in SequenceAdapter)	sql (in Equals)	successor (in Transition)
sequence (in Chain)	sql (in Greater)	suffix (in RemoteStructureProvider)
sequence_number (in ResidueInfo)	sql (in GreaterOrEquals)	superimpose() (in Chain)
sequence_number (in Residue)	sql (in In)	SuperimposeInfo (in csb.bio.structure)
SequenceAdapter (in csb.bio.sequence)	sql (in Lower)	surpasses() (in HHpredHit)
SequenceAlignment (in csb.bio.sequence)	sql (in LowerOrEquals)	svg (in csb.bio.io)
SequenceAlignmentReader (in csb.bio.io.fasta)	sql (in NotEquals)	swap() (in AbstractExchangeMC)
SequenceAlphabets (in csb.bio.sequence)	sql (in NotIn)	swap_all() (in AbstractSwapScheme)
SequenceCollection (in csb.bio.sequence)	sql (in Predicate)	swap_all() (in AlternatingAdjacentSwapScheme)
SequenceError (in csb.bio.sequence)	SQLiteRepository (in csb.io.tsv)	SwapStatistics (in csb.statistics.samplers.mc.multichain)
SequenceFormatError (in csb.bio.io.fasta)	sqrt (in csb.apps.embd)	sys (in AbstractPropagation)
SequenceIndexer (in csb.bio.sequence)	sqrt (in csb.statistics.pdf)	sys_after (in AbstractPerturbation)
SequenceNotFoundError (in csb.bio.sequence)	Sr (in ChemElements)	sys_before (in AbstractPerturbation)