Home
Trees
Indices
Help
CSB v1.2.5.d7fd331
[
frames
] |
no frames
]
[
Identifiers
|
Bugs
|
Deprecations
]
Identifier Index
[
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
_
]
A
a
(in
Color
)
add_header()
(in
PDBFileBuilder
)
append()
(in
TransitionTable
)
a
(in
GeneralizedInverseGaussian
)
add_hmm()
(in
HHMFileBuilder
)
append()
(in
ChainResiduesCollection
)
A3M
(in
AlignmentFormats
)
add_hsp()
(in
ClansEntry
)
append()
(in
DisorderedAtom
)
A3MAlignment
(in
csb.bio.sequence
)
add_hsp_block()
(in
ClansFileBuilder
)
append()
(in
EnsembleModelsCollection
)
A3MOutputBuilder
(in
csb.bio.io.fasta
)
add_hsp_block()
(in
ClansFileWriter
)
append()
(in
ResidueAtomsTable
)
A3MSequenceIterator
(in
csb.bio.io.fasta
)
add_initial_state()
(in
TrajectoryBuilder
)
append()
(in
SecondaryStructure
)
ABCMeta
add_intermediate_state()
(in
ShortTrajectoryBuilder
)
append()
(in
StructureChainsTable
)
AbstractAlignment
(in
csb.bio.sequence
)
add_intermediate_state()
(in
TrajectoryBuilder
)
append()
(in
CollectionContainer
)
AbstractAlignmentAlgorithm
(in
csb.bio.sequence.alignment
)
add_many()
(in
OutputBuilder
)
append()
(in
DictionaryContainer
)
AbstractContainer
(in
csb.core
)
add_param_block()
(in
ClansFileBuilder
)
append_groups_from()
(in
Clans
)
AbstractDensity
(in
csb.statistics.pdf
)
add_param_block()
(in
ClansFileWriter
)
AppExit
(in
csb.apps
)
AbstractEnsembleMC
(in
csb.statistics.samplers.mc.multichain
)
add_peaks()
(in
XeasyFileBuilder
)
Application
(in
csb.apps
)
AbstractEntity
(in
csb.bio.structure
)
add_pos_block()
(in
ClansFileBuilder
)
approx_psi()
(in
csb.numeric
)
AbstractEstimator
(in
csb.statistics.pdf
)
add_pos_block()
(in
ClansFileWriter
)
AppRunner
(in
csb.apps
)
AbstractExchangeMC
(in
csb.statistics.samplers.mc.multichain
)
add_position()
(in
OutputBuilder
)
AppRunner
(in
csb.apps.bfit
)
AbstractGradient
(in
csb.numeric.integrators
)
add_positional_argument()
(in
ArgHandler
)
AppRunner
(in
csb.apps.bfite
)
AbstractHeatWorkJacobianLogger
(in
csb.statistics.samplers.mc.neqsteppropagator
)
add_residue()
(in
ExtendedOutputBuilder
)
AppRunner
(in
csb.apps.buildhmm
)
AbstractIndexer
(in
csb.core
)
add_residue()
(in
OutputBuilder
)
AppRunner
(in
csb.apps.csfrag
)
AbstractIntegrator
(in
csb.numeric.integrators
)
add_rotmtx_block()
(in
ClansFileBuilder
)
AppRunner
(in
csb.apps.embd
)
AbstractMC
(in
csb.statistics.samplers.mc
)
add_rotmtx_block()
(in
ClansFileWriter
)
AppRunner
(in
csb.apps.helloworld
)
AbstractMCPropagation
(in
csb.statistics.samplers.mc.neqsteppropagator
)
add_scalar_option()
(in
ArgHandler
)
AppRunner
(in
csb.apps.hhfrag
)
AbstractMCPropagator
(in
csb.statistics.samplers.mc.propagators
)
add_separator()
(in
OutputBuilder
)
AppRunner
(in
csb.apps.hhsearch
)
AbstractMDPropagation
(in
csb.statistics.samplers.mc.neqsteppropagator
)
add_seq_block()
(in
ClansFileBuilder
)
AppRunner
(in
csb.apps.precision
)
AbstractNCMCPropagator
(in
csb.statistics.samplers.mc.propagators
)
add_seq_block()
(in
ClansFileWriter
)
AppRunner
(in
csb.apps.promix
)
AbstractNCMCSampler
(in
csb.statistics.samplers.mc.singlechain
)
add_seqgroups_block()
(in
ClansFileBuilder
)
apps
(in
csb
)
AbstractNIContainer
(in
csb.core
)
add_seqgroups_block()
(in
ClansFileWriter
)
Ar
(in
ChemElements
)
AbstractParameter
(in
csb.statistics.pdf.parameterized
)
add_sequence()
(in
A3MOutputBuilder
)
ARG
(in
ProteinAlphabet
)
AbstractPerturbation
(in
csb.statistics.samplers.mc.neqsteppropagator
)
add_sequence()
(in
FASTAOutputBuilder
)
ARG
(in
StdProteinAlphabet
)
AbstractPerturbationParam
(in
csb.statistics.samplers.mc.neqsteppropagator
)
add_sequence()
(in
OutputBuilder
)
ArgHandler
(in
csb.apps
)
AbstractPropagation
(in
csb.statistics.samplers.mc.neqsteppropagator
)
add_sequence()
(in
PIROutputBuilder
)
args
(in
AppRunner
)
AbstractPropagationParam
(in
csb.statistics.samplers.mc.neqsteppropagator
)
add_sequences_line()
(in
ClansFileWriter
)
args
(in
Application
)
AbstractPropagationResult
(in
csb.statistics.samplers.mc
)
add_spectrum()
(in
XeasyFileBuilder
)
ARGUMENT_ERROR
(in
ExitCodes
)
AbstractPropagator
(in
csb.statistics.samplers.mc.propagators
)
add_structure()
(in
FileBuilder
)
ArgumentError
(in
csb.apps.csfrag
)
AbstractRENS
(in
csb.statistics.samplers.mc.multichain
)
add_structure()
(in
PDBEnsembleFileBuilder
)
ArgumentError
(in
csb.apps.hhfrag
)
AbstractRENSSwapParameterInfo
(in
csb.statistics.samplers.mc.multichain
)
add_structure()
(in
PDBFileBuilder
)
ArgumentError
(in
csb.apps.precision
)
AbstractResidueMapper
(in
csb.bio.io.wwpdb
)
add_target()
(in
PIROutputBuilder
)
ArgumentIOError
(in
csb.apps.csfrag
)
AbstractSampler
(in
csb.statistics.samplers
)
add_template()
(in
PIROutputBuilder
)
ArgumentIOError
(in
csb.apps.hhfrag
)
AbstractScoringMatrix
(in
csb.bio.sequence.alignment
)
add_template()
(in
FileSystemStructureProvider
)
ArgumentIOError
(in
csb.apps.precision
)
AbstractSequence
(in
csb.bio.sequence
)
add_transition_pseudocounts()
(in
ProfileHMM
)
array()
(in
Expression
)
AbstractSingleChainMC
(in
csb.statistics.samplers.mc.singlechain
)
add_transition_pseudocounts()
(in
PseudocountBuilder
)
ars
(in
csb.statistics
)
AbstractState
(in
csb.statistics.samplers
)
addall()
(in
PredictionBuilder
)
ARS
(in
csb.statistics.ars
)
AbstractStepRENS
(in
csb.statistics.samplers.mc.multichain
)
Adenine
(in
NucleicAlphabet
)
ARSPosteriorAlpha
(in
csb.statistics.scalemixture
)
AbstractStepStatistics
(in
csb.statistics.samplers.mc.neqsteppropagator
)
AFTER
(in
SecStructureScoring
)
As
(in
ChemElements
)
AbstractStructureMixture
(in
csb.statistics.mixtures
)
AFTER_PREDICTED
(in
SecStructureScoring
)
as_tuple()
(in
TorsionPredictionInfo
)
AbstractStructureParser
(in
csb.bio.io.wwpdb
)
Ag
(in
ChemElements
)
ASN
(in
ProteinAlphabet
)
AbstractSwapCommunicator
(in
csb.statistics.samplers.mc.multichain
)
Al
(in
ChemElements
)
ASN
(in
StdProteinAlphabet
)
AbstractSwapParameterInfo
(in
csb.statistics.samplers.mc.multichain
)
ALA
(in
ProteinAlphabet
)
ASP
(in
ProteinAlphabet
)
AbstractSwapScheme
(in
csb.statistics.samplers.mc.multichain
)
ALA
(in
StdProteinAlphabet
)
ASP
(in
StdProteinAlphabet
)
AbstractSystemInfo
(in
csb.statistics.samplers.mc.neqsteppropagator
)
align()
(in
AbstractAlignmentAlgorithm
)
assertAlmostEqual()
(in
Case
)
AbstractTestBuilder
(in
csb.test
)
align()
(in
Chain
)
assertFasterThan()
(in
Case
)
AbstractWHAM
(in
csb.statmech.wham
)
AlignedSequenceAdapter
(in
csb.bio.sequence
)
AssertionError
Ac
(in
ChemElements
)
aligner
(in
HHfrag
)
assign()
(in
ChemShiftTarget
)
acceptance_probability
(in
AbstractSwapCommunicator
)
alignment
(in
HHpredHit
)
assign()
(in
Target
)
acceptance_rate
(in
SingleSwapStatistics
)
alignment
(in
ProfileHMM
)
assign()
(in
TargetResidue
)
acceptance_rate
(in
AbstractMCPropagator
)
alignment
(in
csb.bio.sequence
)
assignall()
(in
Target
)
acceptance_rate
(in
AbstractSingleChainMC
)
alignment()
(in
AlignmentResult
)
Assignment
(in
csb.bio.fragments
)
acceptance_rates
(in
AbstractExchangeMC
)
AlignmentArgumentLengthError
(in
csb.bio.structure
)
assignment()
(in
AssignmentFactory
)
acceptance_rates
(in
SwapStatistics
)
AlignmentFormats
(in
csb.bio.sequence
)
assignment()
(in
ChemShiftAssignmentFactory
)
accepted
(in
AbstractSwapCommunicator
)
AlignmentResult
(in
csb.bio.sequence.alignment
)
AssignmentFactory
(in
csb.bio.fragments
)
accepted_swaps
(in
SingleSwapStatistics
)
AlignmentRowsTable
(in
csb.bio.sequence
)
assignments
(in
TargetResidue
)
accession
(in
Target
)
alignments
(in
HHOutputParser
)
assignments()
(in
BenchmarkAdapter
)
accession
(in
RosettaFragment
)
AlignmentTypes
(in
csb.bio.sequence
)
assignments_sec_structure()
(in
BenchmarkAdapter
)
accession
(in
EntryID
)
all
(in
Expression
)
ASX
(in
ProteinAlphabet
)
accession
(in
Chain
)
ALL()
(in
Filters
)
AsyncParseResult
(in
csb.bio.io.wwpdb
)
accession
(in
Structure
)
ALL_ALPHABETS
(in
SequenceAlphabets
)
AsyncStructureParser
(in
csb.bio.io.wwpdb
)
accumulate()
(in
AbstractHeatWorkJacobianLogger
)
all_layers
(in
ProfileHMM
)
At
(in
ChemElements
)
accumulate()
(in
TrivialHeatWorkJacobianLogger
)
alpha
(in
HeaderInfo
)
at()
(in
RosettaFragmentMap
)
add()
(in
MatchTable
)
alpha
(in
Dirichlet
)
at()
(in
SecondaryStructure
)
add()
(in
PredictionBuilder
)
alpha
(in
Gamma
)
ATOM
(in
ChemShiftReader
)
add()
(in
ClansSeqgroup
)
alpha
(in
GeneralizedNormal
)
Atom
(in
csb.bio.structure
)
add()
(in
CustomStructureProvider
)
alpha
(in
InverseGamma
)
ATOM3
(in
ChemShift3Reader
)
add()
(in
FileSystemStructureProvider
)
ALPHA_SIGMA
(in
GaussianMixture
)
atom_contacts()
(in
ContactMap
)
add()
(in
NOESpectrum
)
alphabet
(in
AbstractSequence
)
atom_matrix()
(in
ContactMap
)
add()
(in
AbstractAlignment
)
alphabet
(in
SequenceAdapter
)
atom_name
(in
Label
)
add()
(in
Backend
)
alphabet
(in
Chain
)
AtomConnectivity
(in
csb.bio.nmr
)
add_alignment()
(in
HHpredHit
)
alternate
(in
Atom
)
AtomNotFoundError
(in
csb.bio.structure
)
add_alignment()
(in
A3MOutputBuilder
)
AlternatingAdjacentSwapScheme
(in
csb.statistics.samplers.mc.multichain
)
atoms
(in
ResidueInfo
)
add_alignment()
(in
FASTAOutputBuilder
)
alternative
(in
ClusterRep
)
atoms
(in
ContactMap
)
add_alignment()
(in
OutputBuilder
)
Am
(in
ChemElements
)
atoms
(in
Residue
)
add_alignment()
(in
PIROutputBuilder
)
amax
(in
HeaderInfo
)
attfactor
(in
ClansParams
)
add_array_argument()
(in
ArgHandler
)
amean
(in
HeaderInfo
)
Attributes
(in
csb.test
)
add_array_option()
(in
ArgHandler
)
amin
(in
HeaderInfo
)
attvalpow
(in
ClansParams
)
add_boolean_option()
(in
ArgHandler
)
Amino
(in
NucleicAlphabet
)
Au
(in
ChemElements
)
add_comment()
(in
OutputBuilder
)
anchored_around()
(in
Assignment
)
augment_state()
(in
csb.statistics.samplers.mc
)
add_emission_pseudocounts()
(in
ProfileHMM
)
AngleUnits
(in
csb.bio.structure
)
autoclose
(in
EntryWriter
)
add_emission_pseudocounts()
(in
PseudocountBuilder
)
anneal()
(in
GaussianMixture
)
autocorrelation()
(in
csb.statistics
)
add_entry()
(in
Clans
)
Any
(in
NucleicAlphabet
)
AutoFlushStream
(in
csb.io
)
add_final_state()
(in
TrajectoryBuilder
)
AnyTestBuilder
(in
csb.test
)
AUTONUMBER
(in
Chart
)
add_fragment()
(in
OutputBuilder
)
app
(in
csb.test
)
average_structure()
(in
csb.bio.utils
)
add_group()
(in
Clans
)
append()
(in
RosettaFragmentMap
)
avgfoldchange
(in
ClansParams
)
add_header()
(in
XeasyFileBuilder
)
append()
(in
EmissionTable
)
axis_and_angle()
(in
csb.numeric
)
add_header()
(in
FileBuilder
)
append()
(in
HMMLayer
)
Home
Trees
Indices
Help
CSB v1.2.5.d7fd331
Generated by Epydoc 3.0.1 on Tue Jul 4 20:19:03 2017
http://epydoc.sourceforge.net