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Identifier Index

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C

C (in ChemElements)	close() (in TempFolder)	Connection (in BenchmarkAdapter)
c_alpha (in ResidueAssignmentInfo)	close() (in RepositoryImp)	connection_string() (in BenchmarkAdapter)
Ca (in ChemElements)	close() (in SQLiteRepository)	consensus (in ProfileHMM)
calculate_history() (in ReplicaHistory)	closest() (in ChemShiftTargetResidue)	consistency (in ClusterRep)
calculate_image() (in Deconvolution)	closest() (in TargetResidue)	Console (in csb.build)
calculate_projected_trajectories() (in ReplicaHistory)	cluster2d (in ClansParams)	Console (in csb.test)
calculate_statistics() (in MaxentModel)	ClusterDivergingError (in csb.bio.fragments)	ContactMap (in csb.bio.nmr)
calculate_trajectories() (in ReplicaHistory)	ClusterEmptyError (in csb.bio.fragments)	ContactMapComparisonInfo (in csb.bio.nmr)
calibrate_hmm() (in ProfileBuilder)	ClusterExhaustedError (in csb.bio.fragments)	contacts (in ContactMap)
CALPHAS() (in Filters)	ClusterNode (in csb.bio.fragments)	Container (in csb.core)
CARBONS() (in Filters)	ClusterRep (in csb.bio.fragments)	contains() (in AtomConnectivity)
Case (in csb.test)	Cm (in ChemElements)	contains() (in SequenceAlphabets)
Cd (in ChemElements)	Co (in ChemElements)	content() (in TempFile)
Ce (in ChemElements)	CODEC (in FastResidueMapper)	Context (in csb.apps.hhsearch)
center_of_mass() (in csb.bio.utils)	Coil (in SecStructures)	convert() (in SecondaryShiftConverter)
centroid (in ClusterRep)	CollectionContainer (in csb.core)	convert_scores() (in ProfileHMM)
centroid() (in FragmentCluster)	CollectionIndexError (in csb.core)	convolve() (in csb.numeric)
centroids() (in BenchmarkAdapter)	collision_interval (in ThermostattedMDRENSSwapParameterInfo)	cooling (in ClansParams)
Cf (in ChemElements)	collision_probability (in ThermostattedMDRENSSwapParameterInfo)	coords (in ClansEntry)
chain (in RosettaFragment)	color (in ClansSeqgroup)	copy() (in ResidueInfo)
chain (in EntryID)	Color (in csb.bio.io.clans)	copy() (in TorsionAngles)
chain (in ResidueInfo)	colors (in ClansParams)	copy() (in ColumnInfo)
chain (in ContactMap)	column() (in Table)	core (in csb)
Chain (in csb.bio.structure)	ColumnIndexer (in csb.bio.sequence)	corr() (in Util)
chain() (in ProfileHMM)	ColumnInfo (in csb.bio.sequence)	correlate() (in csb.numeric)
chain_id (in Target)	ColumnInfo (in csb.io.tsv)	correlation (in Deconvolution)
ChainNotFoundError (in csb.bio.structure)	ColumnPositionError (in csb.bio.sequence)	count (in ClusterRep)
ChainResiduesCollection (in csb.bio.structure)	columns (in AbstractAlignment)	count (in FragmentCluster)
chains (in Structure)	columns (in AlignedSequenceAdapter)	count() (in RepositoryImp)
ChainSequence (in csb.bio.sequence)	columns (in Chart)	count() (in SQLiteRepository)
charge (in Atom)	columns (in DataRow)	CPU (in Options)
Chart (in csb.io.plots)	columns (in Table)	cpu (in HHsearch)
check_angle() (in TorsionAngles)	CombinedResidueMapper (in csb.bio.io.wwpdb)	Cr (in ChemElements)
check_equal_length() (in State)	command (in HHpredHitList)	CRASH (in ExitCodes)
check_flat_array() (in State)	command_line() (in AppRunner)	create() (in ProfileBuilder)
ChemElements (in csb.bio.structure)	command_line() (in AppRunner)	create() (in PredictionBuilder)
ChemicalShiftContainer (in csb.bio.io.vasco)	command_line() (in AppRunner)	create() (in ClusterNode)
ChemicalShiftNetwork (in csb.bio.nmr)	command_line() (in AppRunner)	create() (in ChemShiftReader)
ChemShift3Reader (in csb.bio.io.cs)	command_line() (in AppRunner)	create() (in OutputBuilder)
ChemShiftAssignment (in csb.bio.fragments)	command_line() (in AppRunner)	create() (in EntryID)
ChemShiftAssignmentFactory (in csb.bio.fragments)	command_line() (in AppRunner)	create() (in SparseChainSequence)
ChemShiftFormatError (in csb.bio.io.cs)	command_line() (in AppRunner)	create() (in ChainSequence)
ChemShiftInfo (in csb.bio.nmr)	command_line() (in AppRunner)	create() (in RichSequence)
ChemShiftReader (in csb.bio.io.cs)	command_line() (in AppRunner)	create() (in CompositeEntityIterator)
ChemShiftScoringModel (in csb.bio.nmr)	command_line() (in AppRunner)	create() (in Residue)
ChemShiftTarget (in csb.bio.fragments)	compare() (in ContactMap)	create() (in Enum)
ChemShiftTargetResidue (in csb.bio.fragments)	complement() (in RosettaFragmentMap)	create() (in RepositoryImp)
ChunkedReader (in SQLiteRepository)	complexatt (in ClansParams)	create() (in SQLiteRepository)
circmean() (in csb.statistics)	components() (in AbstractEntity)	create() (in TrajectoryBuilder)
circvar() (in csb.statistics)	CompositeEnsemble (in csb.statmech.ensembles)	create_deletion() (in StateFactory)
Cl (in ChemElements)	CompositeEntityIterator (in csb.bio.structure)	create_gap() (in AbstractResidueMapper)
clans (in csb.bio.io)	compute() (in TorsionAnglePredictor)	create_insertion() (in StateFactory)
Clans (in csb.bio.io.clans)	compute_single() (in TorsionAnglePredictor)	create_match() (in StateFactory)
clans_instance (in ClansParser)	compute_torsion() (in Chain)	create_parser() (in AbstractStructureParser)
ClansEntry (in csb.bio.io.clans)	compute_torsion() (in ProteinResidue)	cs (in csb.bio.io)
ClansEntryCollection (in csb.bio.io.clans)	conditional() (in MultivariateGaussian)	Cs (in ChemElements)
ClansFileBuilder (in csb.bio.io.clans)	confidence (in ClusterRep)	csb
ClansFileWriter (in csb.bio.io.clans)	config (in Case)	csfrag (in csb.apps)
ClansParams (in csb.bio.io.clans)	Config (in csb.test)	CSfrag (in csb.apps.csfrag)
ClansParser (in csb.bio.io.clans)	configure_input() (in FASTAProfileBuilder)	CSfragApp (in csb.apps.csfrag)
ClansSeqgroup (in csb.bio.io.clans)	configure_input() (in PDBProfileBuilder)	Cu (in ChemElements)
ClansSeqgroupCollection (in csb.bio.io.clans)	configure_input() (in ProfileBuilder)	Cumulative (in csb.statistics)
CLEAN (in ExitCodes)	ConfinedEntityIterator (in csb.bio.structure)	cumulative_density() (in Cumulative)
client_disposed() (in Backend)	ConformerMixture (in csb.statistics.mixtures)	currcool (in ClansParams)
clone() (in ChemShiftTarget)	connect() (in ChemicalShiftNetwork)	current_state (in SimpleProposalCommunicator)
clone() (in Target)	connect() (in ContactMap)	CUSTOM (in Attributes)
clone() (in ChemShiftInfo)	connect() (in NOESpectrum)	custom() (in csb.test)
clone() (in Atom)	connected() (in AtomConnectivity)	CustomStructureProvider (in csb.bio.io.wwpdb)
clone() (in Chain)	connected() (in ContactMap)	CustomTestBuilder (in csb.test)
clone() (in Residue)	connected_atoms() (in AtomConnectivity)	cutoff (in ContactMap)
clone() (in SecondaryStructure)	connected_dimensions() (in NOEPeak)	CYS (in ProteinAlphabet)
clone() (in State)	connected_dimensions() (in NOESpectrum)	CYS (in StdProteinAlphabet)
close() (in EntryWriter)	connected_shifts() (in ChemicalShiftNetwork)	Cytosine (in NucleicAlphabet)
close() (in TempFile)	connectedness (in FragmentCluster)