- _ -

• __init__() : driver.pNAB
• _run() : driver.pNAB

- b -

• Backbone() : PNAB::Backbone
• Base() : PNAB::Base
• Bases() : PNAB::Bases
• BaseUnit() : PNAB::BaseUnit

- c -

• center() : PNAB::Backbone
• Chain() : PNAB::Chain
• computeHelicalParameters() : PNAB::HelicalParameters
• ConformationSearch() : PNAB::ConformationSearch

- d -

• deleteVectorAtom() : PNAB::Backbone , PNAB::Base

- f -

• fillConformerEnergyData() : PNAB::Chain

- g -

• generateConformerData() : PNAB::Chain
• GeneticAlgorithmSearch() : PNAB::ConformationSearch
• getBackboneIndexRange() : PNAB::BaseUnit
• getBackboneLinkers() : PNAB::BaseUnit
• getBaseConnectIndex() : PNAB::BaseUnit
• getBaseFromName() : PNAB::Bases
• getBaseIndexRange() : PNAB::BaseUnit
• getBasePairName() : PNAB::Base
• getBasesFromStrand() : PNAB::Bases
• getCode() : PNAB::Base
• getComplimentBasesFromStrand() : PNAB::Bases
• getFixedBonds() : PNAB::BaseUnit
• getGlobalRotationMatrix() : PNAB::HelicalParameters
• getGlobalTranslationVec() : PNAB::HelicalParameters
• getHead() : PNAB::Backbone
• getLinker() : PNAB::Backbone , PNAB::Base
• getMol() : PNAB::BaseUnit
• getMolecule() : PNAB::Backbone , PNAB::Base
• getName() : PNAB::Base
• getStepRotationMatrix() : PNAB::HelicalParameters
• getStepTranslationVec() : PNAB::HelicalParameters
• getTail() : PNAB::Backbone
• getVector() : PNAB::Backbone , PNAB::Base

- h -

• HelicalParameters() : PNAB::HelicalParameters

- m -

• measureDistance() : PNAB::ConformationSearch
• MonteCarloSearch() : PNAB::ConformationSearch

- o -

• operator<() : PNAB::ConformerData
• orderResidues() : PNAB::Chain

- p -

• printProgress() : PNAB::ConformationSearch

- r -

• RandomSearch() : PNAB::ConformationSearch
• ReferenceFrameToHelicalParameters() : PNAB::HelicalParameters
• reportData() : PNAB::ConformationSearch
• rodrigues_formula() : PNAB::HelicalParameters
• rotate() : PNAB::Backbone
• run() : driver.pNAB , PNAB::ConformationSearch
• RuntimeParameters() : PNAB::RuntimeParameters

- s -

• setCoordsForChain() : PNAB::Chain
• setupChain() : PNAB::Chain
• setupFFConstraints() : PNAB::Chain
• StepParametersToReferenceFrame() : PNAB::HelicalParameters
• SystematicSearch() : PNAB::ConformationSearch

- t -

• translate() : PNAB::Backbone

- v -

• validate() : PNAB::Backbone , PNAB::Base

- w -

• WeightedDistributions() : PNAB::ConformationSearch

- ~ -

• ~Chain() : PNAB::Chain