[ 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 _ ]

P

P (in ChemElements)	PDB_AMINOACIDS (in csb.bio.io.wwpdb)	probabilistic_fit() (in csb.bio.utils)
p (in GeneralizedInverseGaussian)	PDB_NUCLEOTIDES (in csb.bio.io.wwpdb)	probabilistic_or() (in csb.statistics)
Pa (in ChemElements)	PDBEnsembleFileBuilder (in csb.bio.io.wwpdb)	probabilistic_xor() (in csb.statistics)
package (in Version)	PDBFileBuilder (in csb.bio.io.wwpdb)	probability (in FragmentMatch)
pad() (in csb.numeric)	PDBHeaderParser (in csb.bio.io.wwpdb)	probability (in HHpredHit)
param (in AbstractPerturbation)	PDBParseError (in csb.bio.io.wwpdb)	Probability (in ScoreUnits)
param (in AbstractPropagation)	PDBProfileBuilder (in csb.apps.buildhmm)	probability (in Transition)
param (in HMCPropagation)	PDBS (in HHfrag)	probability_transform() (in csb.statistics.rand)
param_info (in AbstractSwapCommunicator)	pdbs25 (in HHfrag)	ProcessError (in csb.io)
param_info (in RENSTrajInfo)	PDBSequenceParser (in csb.bio.io.fasta)	procheck (in csb.bio.io)
param_infos (in AbstractExchangeMC)	pdf (in csb.statistics)	ProcheckParser (in csb.bio.io.procheck)
Parameter (in csb.statistics.pdf.parameterized)	PeakListFormatError (in csb.bio.io.noe)	product (in PredictionBuilder)
ParameterizationError (in csb.statistics.pdf.parameterized)	peek() (in Stack)	product (in ShortTrajectoryBuilder)
parameterized (in csb.statistics.pdf)	perturbation (in Step)	product (in TrajectoryBuilder)
ParameterizedDensity (in csb.statistics.pdf.parameterized)	PerturbationResult (in csb.statistics.samplers.mc.neqsteppropagator)	product_factory (in BaseSequenceParser)
ParameterNotFoundError (in csb.statistics.pdf)	perturbed_sys (in PerturbationResult)	product_type (in BaseSequenceParser)
parameters (in AbstractDensity)	PH (in Predicate)	product_type (in SequenceAlignmentReader)
ParameterValueError (in csb.statistics.pdf)	PHE (in ProteinAlphabet)	product_type (in StructureAlignmentFactory)
ParameterValueError (in csb.statistics.pdf.parameterized)	PHE (in StdProteinAlphabet)	ProfileBuilder (in csb.apps.buildhmm)
params (in Clans)	phi (in ResidueInfo)	ProfileHMM (in csb.bio.hmm)
params (in Expression)	phi (in TorsionAngles)	ProfileHMMRegion (in csb.bio.hmm)
params (in Predicate)	phi (in TorsionAnglesCollection)	ProfileHMMSegment (in csb.bio.hmm)
parent (in ClansEntry)	pi (in csb.statistics.pdf)	ProfileLength (in csb.bio.hmm)
PARENT (in csb.build)	PiHelix (in SecStructures)	program (in AppRunner)
parse() (in ArgHandler)	PIR (in AlignmentFormats)	program (in HHsearch)
parse() (in DSSPParser)	PIROutputBuilder (in csb.bio.io.fasta)	PROGRAM (in Console)
parse() (in StrideParser)	pk (in RepositoryImp)	program (in Console)
parse() (in HHProfileParser)	PK (in SQLiteRepository)	promix (in csb.apps)
parse() (in ProcheckParser)	pk (in SQLiteRepository)	ProMixApp (in csb.apps.promix)
parse() (in PSIPredParser)	pk (in Table)	propagation (in Step)
parse() (in VascoStructureParser)	PlainMDPropagation (in csb.statistics.samplers.mc.neqsteppropagator)	PropagationResult (in csb.statistics.samplers.mc)
parse() (in WhatCheckParser)	PlainMDPropagationParam (in csb.statistics.samplers.mc.neqsteppropagator)	propagators (in csb.statistics.samplers.mc)
parse() (in AbstractStructureParser)	plot (in Chart)	proposal_state (in SimpleProposalCommunicator)
parse() (in DegenerateID)	plot() (in LibrarySuperimposer)	Protein (in SequenceTypes)
parse() (in EntryID)	plots (in csb.io)	ProteinAlphabet (in csb.bio.sequence)
parse() (in SeqResID)	plots (in Chart)	ProteinResidue (in csb.bio.structure)
parse() (in StandardID)	PlotsCollection (in csb.io.plots)	protocol (in AbstractRENSSwapParameterInfo)
parse() (in Label)	Pm (in ChemElements)	protocol (in InterpolationFactory)
parse() (in A3MAlignment)	Po (in ChemElements)	protocol (in MDRENSSwapParameterInfo)
parse() (in SequenceAlignment)	polar() (in csb.numeric)	protocol (in NonequilibriumStepPropagator)
parse() (in StructureAlignment)	polar3d() (in csb.numeric)	Protocol (in csb.statistics.samplers.mc.neqsteppropagator)
parse() (in SimilarityMatrix)	POLL (in Shell)	protocol (in AbstractNCMCPropagator)
parse() (in SecondaryStructure)	position (in AbstractState)	protocol (in AbstractNCMCSampler)
parse() (in Enum)	position (in EnsembleState)	proton_dimensions (in NOESpectrum)
parse_async() (in AsyncStructureParser)	position (in State)	provider (in StructureAlignmentFactory)
parse_biomolecule() (in AbstractStructureParser)	position() (in ContactMap)	Proxy (in csb.core)
parse_file() (in ClansParser)	POSITIONAL (in Type)	PseudocountBuilder (in csb.bio.hmm.pseudocounts)
parse_file() (in BaseSequenceParser)	PositionError (in csb.bio.sequence)	pseudocounts (in ProfileHMM)
parse_file() (in HHOutputParser)	positive() (in ChemShiftScoringModel)	pseudocounts (in csb.bio.hmm)
parse_models() (in AbstractStructureParser)	power (in csb.statistics.pdf)	psi (in ResidueInfo)
parse_residue() (in AbstractStructureParser)	Pr (in ChemElements)	psi (in TorsionAngles)
parse_residue_safe() (in AbstractStructureParser)	precision (in csb.apps)	psi (in TorsionAnglesCollection)
parse_scores() (in PSIPredParser)	precision() (in TargetResidue)	psi (in csb.statistics.scalemixture)
parse_string() (in BaseSequenceParser)	PrecisionApp (in csb.apps.precision)	psi() (in csb.numeric)
parse_string() (in HHOutputParser)	predecessor (in Transition)	psipred (in ProfileHMM)
parse_structure() (in AbstractStructureParser)	predicate (in Expression)	psipred (in csb.bio.io)
parse_structure() (in AsyncStructureParser)	Predicate (in csb.io.tsv)	PSIPredParseError (in csb.bio.io.psipred)
parseArguments() (in Console)	prediction() (in BenchmarkAdapter)	PSIPredParser (in csb.bio.io.psipred)
parsename() (in Enum)	PredictionBuilder (in csb.apps.hhfrag)	PSIPredResidueInfo (in csb.bio.io.psipred)
parser (in ArgHandler)	prefix (in RemoteStructureProvider)	Pt (in ChemElements)
parser (in HHsearch)	principal_coordinates() (in csb.statistics)	Pu (in ChemElements)
path (in RevisionHandler)	prior (in ScaleMixture)	Purine (in NucleicAlphabet)
paths (in CustomStructureProvider)	PRO (in ProteinAlphabet)	push() (in Stack)
paths (in FileSystemStructureProvider)	PRO (in StdProteinAlphabet)	pval (in ClansParams)
PATTERN (in FastResidueMapper)	prob() (in MaxentModel)	pvalue (in HHpredHit)
Pb (in ChemElements)	prob_sum (in HHpredHit)	PYL (in ProteinAlphabet)
Pd (in ChemElements)	probabilistic_and() (in csb.statistics)	Pyrimidine (in NucleicAlphabet)