Here is a list of all class members with links to the classes they belong to:

- _ -

• __init__() : driver.pNAB
• _is_helical : driver.pNAB
• _options : driver.pNAB
• _run() : driver.pNAB
• _verbose : driver.pNAB

- a -

• accepted : PNAB::ConformerData
• all_angles_ : PNAB::Chain
• all_bases_pair : PNAB::Bases
• all_torsions_ : PNAB::Chain
• angleE : PNAB::ConformerData

- b -

• Backbone() : PNAB::Backbone
• backbone : PNAB::Backbone
• backbone_ : PNAB::ConformationSearch
• backbone_index_range : PNAB::BaseUnit
• backbone_interconnects : PNAB::BaseUnit
• backbone_range_ : PNAB::ConformationSearch
• Base() : PNAB::Base
• base : PNAB::Base
• base_connect_index : PNAB::BaseUnit
• base_index_range : PNAB::BaseUnit
• Bases() : PNAB::Bases
• bases : PNAB::Bases
• bases_ : PNAB::ConformationSearch
• BaseUnit() : PNAB::BaseUnit
• bondE : PNAB::ConformerData
• bu_a_mol : PNAB::ConformationSearch
• buckle : PNAB::HelicalParameters
• build_strand : PNAB::RuntimeParameters
• build_strand_ : PNAB::Chain

- c -

• center() : PNAB::Backbone
• Chain() : PNAB::Chain
• chain_length_ : PNAB::Chain
• code : PNAB::Base
• combined_chain_ : PNAB::Chain
• computeHelicalParameters() : PNAB::HelicalParameters
• ConformationSearch() : PNAB::ConformationSearch
• constraintsAng_ : PNAB::Chain
• constraintsBond_ : PNAB::Chain
• constraintsTor_ : PNAB::Chain
• constraintsTot_ : PNAB::Chain
• conv_ : PNAB::ConformationSearch
• coords : PNAB::ConformationSearch
• crossover_rate : PNAB::RuntimeParameters

- d -

• deleteVectorAtom() : PNAB::Backbone , PNAB::Base
• dihedral_angles : PNAB::ConformerData
• dihedral_step : PNAB::RuntimeParameters
• distance : PNAB::ConformerData

- e -

• energy_filter : PNAB::RuntimeParameters

- f -

• ff_type : PNAB::RuntimeParameters
• ff_type_ : PNAB::Chain
• file_path : PNAB::Backbone , PNAB::Base
• fillConformerEnergyData() : PNAB::Chain
• fixed_bonds : PNAB::Backbone , PNAB::BaseUnit

- 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
• glbl_rot_ : PNAB::ConformationSearch
• glbl_translate_ : PNAB::ConformationSearch
• glycosidic_bond_distance : PNAB::RuntimeParameters
• glycosidic_bond_distance_ : PNAB::Chain

- h -

• h_rise : PNAB::HelicalParameters
• h_twist : PNAB::HelicalParameters
• head : PNAB::ConformationSearch
• header : driver.pNAB
• helical_params_ : PNAB::ConformationSearch
• HelicalParameters() : PNAB::HelicalParameters
• hexad_ : PNAB::Chain

- i -

• inclination : PNAB::HelicalParameters
• index : PNAB::ConformerData
• interconnects : PNAB::Backbone
• is_fixed_bond : PNAB::Chain
• is_helical : PNAB::HelicalParameters
• is_hexad : PNAB::RuntimeParameters
• isKCAL_ : PNAB::Chain

- l -

• linker : PNAB::Backbone , PNAB::Base

- m -

• max_distance : PNAB::RuntimeParameters
• measureDistance() : PNAB::ConformationSearch
• molecule : PNAB::ConformerData
• monomer_bb_index_range_ : PNAB::Chain
• monomer_coord : PNAB::ConformerData
• monomer_num_coords_ : PNAB::ConformationSearch
• monte_carlo_temperature : PNAB::RuntimeParameters
• MonteCarloSearch() : PNAB::ConformationSearch
• mutation_rate : PNAB::RuntimeParameters

- n -

• n_chains_ : PNAB::Chain
• name : PNAB::Base
• name_base_map : PNAB::Bases
• num_candidates : PNAB::RuntimeParameters
• num_steps : PNAB::RuntimeParameters
• number_of_candidates : PNAB::ConformationSearch

- o -

• opening : PNAB::HelicalParameters
• operator<() : PNAB::ConformerData
• options : driver.pNAB
• orderResidues() : PNAB::Chain
• output_string : PNAB::ConformationSearch

- p -

• pair_name : PNAB::Base
• pFF_ : PNAB::Chain
• population_size : PNAB::RuntimeParameters
• prefix : driver.pNAB
• prefix_ : PNAB::ConformationSearch
• printProgress() : PNAB::ConformationSearch
• propeller : PNAB::HelicalParameters

- r -

• RandomSearch() : PNAB::ConformationSearch
• ReferenceFrameToHelicalParameters() : PNAB::HelicalParameters
• reportData() : PNAB::ConformationSearch
• results : driver.pNAB
• rise : PNAB::HelicalParameters
• rl : PNAB::ConformationSearch
• rmsd : PNAB::ConformerData
• rng_ : PNAB::ConformationSearch
• rodrigues_formula() : PNAB::HelicalParameters
• roll : PNAB::HelicalParameters
• rotate() : PNAB::Backbone
• rotor_vector : PNAB::ConformationSearch
• run() : driver.pNAB , PNAB::ConformationSearch
• runtime_params_ : PNAB::ConformationSearch
• RuntimeParameters() : PNAB::RuntimeParameters

- s -

• search_algorithm : PNAB::RuntimeParameters
• seed : PNAB::RuntimeParameters
• setCoordsForChain() : PNAB::Chain
• setupChain() : PNAB::Chain
• setupFFConstraints() : PNAB::Chain
• shear : PNAB::HelicalParameters
• shift : PNAB::HelicalParameters
• slide : PNAB::HelicalParameters
• stagger : PNAB::HelicalParameters
• step_rot_ : PNAB::ConformationSearch
• step_translate_ : PNAB::ConformationSearch
• StepParametersToReferenceFrame() : PNAB::HelicalParameters
• strand : PNAB::RuntimeParameters
• strand_orientation : PNAB::RuntimeParameters
• strand_orientation_ : PNAB::Chain
• stretch : PNAB::HelicalParameters
• SystematicSearch() : PNAB::ConformationSearch

- t -

• tail : PNAB::ConformationSearch
• tilt : PNAB::HelicalParameters
• tip : PNAB::HelicalParameters
• torsionE : PNAB::ConformerData
• total_energy : PNAB::ConformerData
• translate() : PNAB::Backbone
• twist : PNAB::HelicalParameters

- u -

• unit : PNAB::BaseUnit , PNAB::ConformationSearch

- v -

• v_base_coords_vec_ : PNAB::Chain
• v_bb_start_index_ : PNAB::Chain
• v_chain_ : PNAB::Chain
• v_deleted_atoms_ids_ : PNAB::Chain
• v_fixed_bonds : PNAB::Chain
• v_new_bond_ids_ : PNAB::Chain
• v_num_bu_A_mol_atoms_ : PNAB::Chain
• validate() : PNAB::Backbone , PNAB::Base
• VDWE : PNAB::ConformerData
• vector_atom_deleted : PNAB::Backbone , PNAB::Base
• verbose_ : PNAB::ConformationSearch

- w -

• WeightedDistributions() : PNAB::ConformationSearch
• weighting_temperature : PNAB::RuntimeParameters

- x -

• x_displacement : PNAB::HelicalParameters

- y -

• y_displacement : PNAB::HelicalParameters

- ~ -

• ~Chain() : PNAB::Chain