Index

Symbols | A | B | C | D | E | F | G | H | I | M | N | O | P | R | S | T | U | W

Symbols

A

B

C

  • core::alignment::MultipleSequenceAlignment
  • core::alignment::NWAligner
  • core::alignment::NWAlignerAnyGap
  • core::alignment::PairwiseAlignment
  • core::alignment::PairwiseSequenceAlignment
  • core::alignment::PairwiseStructureAlignment
  • core::alignment::scoring::AlignmentConstraints
  • core::alignment::scoring::AlignmentScoreBase
  • core::alignment::scoring::AlignmentTMScoring
  • core::alignment::scoring::CombinedScore
  • core::alignment::scoring::FrequencyScaledGapPenalty
  • core::alignment::scoring::LocalStructure5
  • core::alignment::scoring::LocalStructure7
  • core::alignment::scoring::LocalStructureMatch
  • core::alignment::scoring::NcbiSimilarityMatrixFactory
  • core::alignment::scoring::Picasso3
  • core::alignment::scoring::QuickSequenceIdentity
  • core::alignment::scoring::QuickSequenceIdentity16
  • core::alignment::scoring::QuickSequenceIdentity8
  • core::alignment::scoring::SecondarySimilarity
  • core::alignment::scoring::SimilarityMatrix
  • core::alignment::scoring::SimilarityMatrixScore
  • core::alignment::SemiglobalAligner
  • core::alignment::SWAligner
  • core::alignment::Target
  • core::alignment::tasks::TrimStructureByAlignment
  • core::alignment::Template
  • core::alignment::TMAlign
  • core::BioShellEnvironment
  • core::BioShellVersion
  • core::calc::clustering::AverageLink
  • core::calc::clustering::CentroidLink
  • core::calc::clustering::ClusterMergingRule
  • core::calc::clustering::CompleteLink
  • core::calc::clustering::DistanceByValues
  • core::calc::clustering::HierarchicalCluster
  • core::calc::clustering::HierarchicalClustering
  • core::calc::clustering::MedianLink
  • core::calc::clustering::Medoid
  • core::calc::clustering::SingleLink
  • core::calc::clustering::WardsMethod
  • core::calc::numeric::CatmullRomInterpolator
  • core::calc::numeric::CubicInterpolator
  • core::calc::numeric::DerivableFunction
  • core::calc::numeric::Function
  • core::calc::numeric::Function1D
  • core::calc::numeric::Interpolate1D
  • core::calc::numeric::Interpolate2D
  • core::calc::numeric::InterpolatePeriodic1D
  • core::calc::numeric::InterpolatePeriodic2D
  • core::calc::numeric::LBFGS
  • core::calc::numeric::LinearInterpolator
  • core::calc::numeric::Pca3
  • core::calc::statistics::BayesianClassifier2D
  • core::calc::statistics::BivariateNormal
  • core::calc::statistics::Cart
  • core::calc::statistics::Combined_1D_2D_Normal
  • core::calc::statistics::GiniImpuritySplit
  • core::calc::statistics::Hexbins
  • core::calc::statistics::Histogram
  • core::calc::statistics::KDE_1D
  • core::calc::statistics::LabelledObservationVector
  • core::calc::statistics::NormalDistribution
  • core::calc::statistics::ObservationVector
  • core::calc::statistics::OnlineStatistics
  • core::calc::statistics::OptimizePrediction
  • core::calc::statistics::P2QuantileEstimation
  • core::calc::statistics::PDF
  • core::calc::statistics::Random
  • core::calc::statistics::RandomSequenceIterator
  • core::calc::statistics::TrivariateNormal
  • core::calc::statistics::VonMisesDistribution
  • core::calc::structural::AssignHEC
  • core::calc::structural::BackboneHBondGeometry
  • core::calc::structural::BackboneHBondMap
  • core::calc::structural::ContactMap
  • core::calc::structural::HydrogenBondGeometry
  • core::calc::structural::LocalBackboneProperties
  • core::calc::structural::LocalBackbonePropertyDef
  • core::calc::structural::PairwiseResidueMap
  • core::calc::structural::ProteinArchitecture
  • core::calc::structural::RotamerGeometry
  • core::calc::structural::SaturatedRing6Geometry
  • core::calc::structural::TorsionBinType
  • core::calc::structural::transformations::CartesianToSpherical
  • core::calc::structural::transformations::Crmsd
  • core::calc::structural::transformations::PairwiseCrmsd
  • core::calc::structural::transformations::PairwiseStructureComparison
  • core::calc::structural::transformations::PairwiseTMScore
  • core::calc::structural::transformations::Rototranslation
  • core::calc::structural::transformations::StructureSuperpositionSeed
  • core::calc::structural::transformations::TMScore
  • core::chemical::AAHydrophobicity
  • core::chemical::AtomicElement
  • core::chemical::Bond
  • core::chemical::BondType
  • core::chemical::ChiAnglesDefinition
  • core::chemical::CompareDihedralAngles
  • core::chemical::ComparePlanarAngles
  • core::chemical::HydrogenBond
  • core::chemical::Molecule
  • core::chemical::Monomer
  • core::chemical::PKaValues
  • core::data::basic::Array2D
  • core::data::basic::Array2DStatic
  • core::data::basic::Array2DSymmetric
  • core::data::basic::Array3D
  • core::data::basic::BitSetGeneric
  • core::data::basic::BoundedPriorityQueue
  • core::data::basic::SparseMap2D
  • core::data::basic::SparseMap2D::const_iterator
  • core::data::basic::SparseMap2D::iterator
  • core::data::basic::ThreadSafeMap
  • core::data::basic::Vec3
  • core::data::basic::Vec3Cubic
  • core::data::io::AlignmentOutputLines
  • core::data::io::Atom
  • core::data::io::Cif
  • core::data::io::Conect
  • core::data::io::DataBlock
  • core::data::io::DataTable
  • core::data::io::DBRef
  • core::data::io::DsspData
  • core::data::io::DsspDataLine
  • core::data::io::Header
  • core::data::io::HelixField
  • core::data::io::Hetatm
  • core::data::io::Hsp
  • core::data::io::JsonArray
  • core::data::io::JsonValue
  • core::data::io::Keywords
  • core::data::io::Modres
  • core::data::io::NamedDataTable
  • core::data::io::Pdb
  • core::data::io::PdbField
  • core::data::io::Remark290
  • core::data::io::Remark465
  • core::data::io::Seqres
  • core::data::io::SheetField
  • core::data::io::TableRow
  • core::data::io::TVect
  • core::data::io::XML
  • core::data::io::XMLElement
  • core::data::sequence::ByUnknownRatio
  • core::data::sequence::FindInSequenceName
  • core::data::sequence::HecFractions
  • core::data::sequence::IsNotTooSimple
  • core::data::sequence::IsNucleicSequence
  • core::data::sequence::IsProteinSequence
  • core::data::sequence::NoShorterThan
  • core::data::sequence::PirEntry
  • core::data::sequence::PirEntryType
  • core::data::sequence::ReduceSequenceAlphabet
  • core::data::sequence::SecondaryStructure
  • core::data::sequence::SecondaryStructureAnnotation
  • core::data::sequence::Sequence
  • core::data::sequence::SequenceFilter
  • core::data::sequence::SequenceProfile
  • core::data::structural::AtomSelector
  • core::data::structural::Chain
  • core::data::structural::Chain::atom_const_iterator
  • core::data::structural::Chain::atom_iterator
  • core::data::structural::ChainSelector
  • core::data::structural::CompositeSelector
  • core::data::structural::Helix
  • core::data::structural::HelixTypes
  • core::data::structural::IsAA
  • core::data::structural::IsAlternateLocation
  • core::data::structural::IsAromaticAA
  • core::data::structural::IsBB
  • core::data::structural::IsBBCB
  • core::data::structural::IsCA
  • core::data::structural::IsCB
  • core::data::structural::IsElement
  • core::data::structural::IsFirstResidue
  • core::data::structural::IsHydrogen
  • core::data::structural::IsLastResidue
  • core::data::structural::IsNamedAtom
  • core::data::structural::IsNT
  • core::data::structural::IsSC
  • core::data::structural::LogicalANDSelector
  • core::data::structural::NotHydrogen
  • core::data::structural::PdbAtom
  • core::data::structural::ProperlyConnectedCA
  • core::data::structural::Residue
  • core::data::structural::ResidueHasAllHeavyAtoms
  • core::data::structural::ResidueHasBB
  • core::data::structural::ResidueHasBBCB
  • core::data::structural::ResidueHasCA
  • core::data::structural::ResidueIndex
  • core::data::structural::ResidueIndexer
  • core::data::structural::ResidueIsTerminal
  • core::data::structural::ResidueSelector
  • core::data::structural::SecondaryStructureElement
  • core::data::structural::SelectAllAtoms
  • core::data::structural::SelectChainBreaks
  • core::data::structural::SelectChainResidueAtom
  • core::data::structural::SelectChainResidues
  • core::data::structural::SelectClashingResidues
  • core::data::structural::SelectContiguousResidues
  • core::data::structural::SelectEverything
  • core::data::structural::SelectPlanarCAGeometry
  • core::data::structural::SelectResidueByName
  • core::data::structural::SelectResidueRange
  • core::data::structural::Strand
  • core::data::structural::StrandPairing
  • core::data::structural::StrandTypes
  • core::data::structural::Structure
  • core::data::structural::Structure::atom_const_iterator
  • core::data::structural::Structure::atom_iterator
  • core::data::structural::Structure::residue_const_iterator
  • core::data::structural::Structure::residue_iterator
  • core::protocols::AbstractSequenceProtocol
  • core::protocols::AlignmentPValuesProtocol
  • core::protocols::PairwiseSequenceIdentityProtocol
  • core::protocols::SequenceWeightingProtocol
  • core::protocols::StructureAlignmentProtocol
  • cpplexer
  • cpplexer::CFamilyLexer
  • cpplexer::CLexer
  • cpplexer::CppLexer
  • cpplexer::IdlLexer

D

  • doxyrest::HighlightedText
  • doxyrest::RefCodeBlock
  • doxyrest::RefTransform

E

F

G

H

  • How to compile BioShell package
  • How to get bioshell on your machine?

I

M

N

O

P

R

  • README-How_to_add_examples
  • README-Wlasne_aplikacje_jak_zaczac

S

  • sampling
  • scoring
  • sequence
  • simulations
  • simulations::cartesian::ff::mf::R12
  • simulations::evaluators::CallEvaluator
  • simulations::evaluators::cartesian::CM
  • simulations::evaluators::cartesian::CrmsdEvaluator
  • simulations::evaluators::cartesian::REndSquare
  • simulations::evaluators::cartesian::RgSquare
  • simulations::evaluators::EchoEvaluator
  • simulations::evaluators::Evaluator
  • simulations::evaluators::Timer
  • simulations::forcefield::cartesian::DihedralsAlongChain
  • simulations::forcefields::ByAtomEnergy
  • simulations::forcefields::ByResidueEnergy
  • simulations::forcefields::cabs::CabsA13
  • simulations::forcefields::cabs::CabsBackboneEnergy
  • simulations::forcefields::cabs::CabsR13
  • simulations::forcefields::cabs::CabsR15
  • simulations::forcefields::cabs::CabsRotamersEnergy
  • simulations::forcefields::cabs::CabsT14
  • simulations::forcefields::cabs::CGRotamersLibrary
  • simulations::forcefields::cabs::CGRotamersPairwise
  • simulations::forcefields::CalculateEnergyBase
  • simulations::forcefields::cartesian::ContactEnergy
  • simulations::forcefields::cartesian::ContactMapEnergy
  • simulations::forcefields::cartesian::DSSPEnergy
  • simulations::forcefields::cartesian::ExcludedVolumePenalty
  • simulations::forcefields::cartesian::HarmonicEnergy
  • simulations::forcefields::cartesian::LJEnergySW
  • simulations::forcefields::cartesian::LJEnergySWHomogenic
  • simulations::forcefields::cartesian::RamachandranFF
  • simulations::forcefields::cartesian::RgEnergy
  • simulations::forcefields::cartesian::SimplePolymerBonds
  • simulations::forcefields::cartesian::TauRamachandranFF
  • simulations::forcefields::ConstEnergy
  • simulations::forcefields::ForceFieldConfig
  • simulations::forcefields::LongRangeByResidues
  • simulations::forcefields::mf::BoundedMFComponent
  • simulations::forcefields::mf::MeanFieldDistribution2D
  • simulations::forcefields::mf::MeanFieldDistributions
  • simulations::forcefields::mf::ShortRangeMFBase
  • simulations::forcefields::mf::SSWeightedShortRangeMFBase
  • simulations::forcefields::mm::AtomIndexType
  • simulations::forcefields::mm::ExcludedPairsList
  • simulations::forcefields::mm::MMAtomTyping
  • simulations::forcefields::mm::MMBondedParameters
  • simulations::forcefields::mm::MMBondEnergy
  • simulations::forcefields::mm::MMBondEnergy::CompareMMBondTerms
  • simulations::forcefields::mm::MMBondTerm
  • simulations::forcefields::mm::MMDihedralEnergy
  • simulations::forcefields::mm::MMDihedralEnergy::CompareMMDihedralTerms
  • simulations::forcefields::mm::MMDihedralEnergy::MMDihedralTerm
  • simulations::forcefields::mm::MMNonBonded
  • simulations::forcefields::mm::MMNonBondedParameters
  • simulations::forcefields::mm::MMNonBondedSW
  • simulations::forcefields::mm::MMPlanarEnergy
  • simulations::forcefields::mm::MMPlanarEnergy::CompareMMPlanarTerms
  • simulations::forcefields::mm::MMPlanarEnergy::MMPlanarTerm
  • simulations::forcefields::mm::MMResidueAngle
  • simulations::forcefields::mm::MMResidueAtom
  • simulations::forcefields::mm::MMResidueBond
  • simulations::forcefields::mm::MMResidueDihedral
  • simulations::forcefields::mm::MMResidueImproper
  • simulations::forcefields::mm::MMResidueRotatableBond
  • simulations::forcefields::mm::MMResidueType
  • simulations::forcefields::NeighborList
  • simulations::forcefields::ShortRangeEnergyBase
  • simulations::forcefields::surpass::SurpassA13
  • simulations::forcefields::surpass::SurpassCentrosymetricEnergy
  • simulations::forcefields::surpass::SurpassContactEnergy
  • simulations::forcefields::surpass::SurpassHBNeighborList
  • simulations::forcefields::surpass::SurpassHelixStifnessEnergy
  • simulations::forcefields::surpass::SurpassHydrogenBond
  • simulations::forcefields::surpass::SurpassHydrogenBond::AcceptorH
  • simulations::forcefields::surpass::SurpassLocalRepulsionEnergy
  • simulations::forcefields::surpass::SurpassPromotedContact
  • simulations::forcefields::surpass::SurpassR12
  • simulations::forcefields::surpass::SurpassR13
  • simulations::forcefields::surpass::SurpassR14
  • simulations::forcefields::surpass::SurpassR15
  • simulations::forcefields::TotalEnergy
  • simulations::forcefields::TotalEnergyByResidue
  • simulations::movers::AType
  • simulations::movers::BackrubMover
  • simulations::movers::cabs::CabsPhiPsiMover
  • simulations::movers::cabs::CabsRotamerChanger
  • simulations::movers::cabs::CabsRotamerMover
  • simulations::movers::ising::SingleFlip2D
  • simulations::movers::ising::WolffMove2D
  • simulations::movers::LigandTossingMover

T

U

  • ui::www::Route
  • ui::www::WebServer
  • utils
  • utils::exceptions::AtomNotFound
  • utils::exceptions::NoSuchFile
  • utils::Logger
  • utils::LogLevel
  • utils::LogManager
  • utils::options::Option
  • utils::options::OptionParser
  • utils::options::PrintHelp
  • utils::options::PrintMarkdownHelp
  • utils::options::SetDBPath
  • utils::options::VerbosityLevel
  • utils::Profiler
  • utils::ProfilingManager
  • utils::ThreadPool
  • utils::UnitTests

W