Index

A

aas (isambard.specifications.coiledcoil.CoiledCoil attribute) (isambard.specifications.solenoid.HelixPair attribute) accept_proposed_value() (isambard.optimisation.mmc_optimizer.MMCParameter method) align_nab() (in module isambard.modelling.non_canonical) apply_trans_rot() (in module isambard.modelling.non_canonical)

assign_fitnesses() (isambard.optimisation.base_evo_opt.BaseOptimizer method) ax_unit (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) axis (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) axis_distances (isambard.specifications.solenoid.HelixPair attribute)

B

base_sequence (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) BaseOptimizer (class in isambard.optimisation.base_evo_opt) basis_set_sequences (isambard.specifications.coiledcoil.CoiledCoil attribute) best_energy (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation attribute), [1] best_model (isambard.optimisation.base_evo_opt.BaseOptimizer attribute) (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation attribute), [1] best_parameters (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation attribute), [1]

build (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) build() (isambard.specifications.coiledcoil.CoiledCoil method) (isambard.specifications.helix.HelicalHelix method) (isambard.specifications.helix.Helix method) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand method) (isambard.specifications.solenoid.HelixPair method) (isambard.specifications.solenoid.Solenoid method)

C

c_n_bonds (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) c_n_ca_angles (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) c_o_bonds (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) ca_c_bonds (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) ca_c_n_angles (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) ca_c_o_angles (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) calculate_contact_order() (in module isambard.evaluation.contact_order) calculate_hydrophobic_fitness() (in module isambard.evaluation.hydrophobic_fitness)

check_move() (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation static method) CMAES (class in isambard.optimisation.evo_optimizers) CoiledCoil (class in isambard.specifications.coiledcoil) compute_params() (isambard.optimisation.evo_optimizers.CMAES method) convert_pro_to_hyp() (in module isambard.modelling.non_canonical) current_energy (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation attribute), [1] current_value (isambard.optimisation.mmc_optimizer.MMCParameter attribute) curve (isambard.specifications.helix.HelicalHelix attribute) curve_primitive (isambard.specifications.helix.HelicalHelix attribute)

D

DE (class in isambard.optimisation.evo_optimizers) default_build() (in module isambard.optimisation.base_evo_opt) default_value (isambard.optimisation.base_evo_opt.Parameter attribute) DISCRETE_RANGE (isambard.optimisation.mmc_optimizer.MMCParameterType attribute)

DNADuplex (class in isambard.specifications.nucleic_acid_duplex) dssp_available() (in module isambard.evaluation.dssp) DYNAMIC (isambard.optimisation.base_evo_opt.ParameterType attribute) dynamic() (isambard.optimisation.base_evo_opt.Parameter class method)

E

eval_function (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation attribute)

extract_all_ss_dssp() (in module isambard.evaluation.dssp)

F

find_ss_regions() (in module isambard.evaluation.dssp) float_f() (in module isambard.optimisation.mmc_optimizer) from_parameters() (isambard.specifications.coiledcoil.CoiledCoil class method) from_polymers() (isambard.specifications.coiledcoil.CoiledCoil class method) from_polypeptide() (isambard.specifications.ta_polypeptide.TAPolypeptide class method)

from_sequence() (isambard.specifications.nucleic_acid_duplex.DNADuplex class method) from_start_and_end() (isambard.specifications.helix.HelicalHelix class method) (isambard.specifications.helix.Helix class method) (isambard.specifications.nucleic_acid_duplex.DNADuplex class method) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand class method) funnel_rebuild() (isambard.optimisation.base_evo_opt.BaseOptimizer static method)

G

GA (class in isambard.optimisation.evo_optimizers) generate_antisense_sequence() (in module isambard.specifications.nucleic_acid_duplex)

generate_complementary_strand() (isambard.specifications.nucleic_acid_duplex.DNADuplex static method) get_number_within() (in module isambard.evaluation.hydrophobic_fitness) get_orient_angle() (isambard.specifications.helix.HelicalHelix method)

H

handedness (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) (isambard.specifications.solenoid.Solenoid attribute) HelicalHelix (class in isambard.specifications.helix) Helix (class in isambard.specifications.helix) helix_end (isambard.specifications.helix.HelicalHelix attribute) (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute)

helix_length (isambard.specifications.helix.HelicalHelix attribute) (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) helix_start (isambard.specifications.helix.HelicalHelix attribute) (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) helix_type (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) HelixPair (class in isambard.specifications.solenoid)

I

initialize_cma_es() (isambard.optimisation.evo_optimizers.CMAES method) isambard.evaluation.contact_order (module) isambard.evaluation.dssp (module) isambard.evaluation.hydrophobic_fitness (module) isambard.modelling.non_canonical (module) isambard.modelling.scwrl (module) isambard.optimisation.base_evo_opt (module)

isambard.optimisation.evo_optimizers (module) isambard.optimisation.mmc_optimizer (module) isambard.specifications.coiledcoil (module) isambard.specifications.helix (module) isambard.specifications.nucleic_acid_duplex (module) isambard.specifications.nucleic_acid_strand (module) isambard.specifications.solenoid (module) isambard.specifications.ta_polypeptide (module)

L

label (isambard.optimisation.mmc_optimizer.MMCParameter attribute)

LIST (isambard.optimisation.mmc_optimizer.MMCParameterType attribute) log_results() (isambard.optimisation.base_evo_opt.BaseOptimizer method)

M

major_axis (isambard.specifications.helix.HelicalHelix attribute) major_handedness (isambard.specifications.coiledcoil.CoiledCoil attribute) (isambard.specifications.helix.HelicalHelix attribute) major_pitch (isambard.specifications.helix.HelicalHelix attribute) major_pitches (isambard.specifications.coiledcoil.CoiledCoil attribute) major_radii (isambard.specifications.coiledcoil.CoiledCoil attribute) major_radius (isambard.specifications.helix.HelicalHelix attribute) major_rise_per_monomer (isambard.specifications.helix.HelicalHelix attribute) make_energy_funnel_data() (isambard.optimisation.base_evo_opt.BaseOptimizer method) make_helix() (isambard.specifications.solenoid.HelixPair static method) minor_handedness (isambard.specifications.helix.HelicalHelix attribute)

minor_helix_type (isambard.specifications.helix.HelicalHelix attribute) minor_helix_types (isambard.specifications.coiledcoil.CoiledCoil attribute) minor_repeat (isambard.specifications.helix.HelicalHelix attribute) minor_repeats (isambard.specifications.coiledcoil.CoiledCoil attribute) minor_residues_per_turn() (isambard.specifications.helix.HelicalHelix method) minor_rise_per_residue (isambard.specifications.helix.HelicalHelix attribute) MMCParameter (class in isambard.optimisation.mmc_optimizer) MMCParameterOptimisation (class in isambard.optimisation.mmc_optimizer) MMCParameterType (class in isambard.optimisation.mmc_optimizer) move_to() (isambard.specifications.helix.HelicalHelix method) (isambard.specifications.helix.Helix method) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand method)

N

n_ca_bonds (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) n_ca_c_angles (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) NORMAL_DIST (isambard.optimisation.mmc_optimizer.MMCParameterType attribute) NucleicAcidStrand (class in isambard.specifications.nucleic_acid_strand)

nucleotides_per_turn (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) num_monomers (isambard.specifications.helix.HelicalHelix attribute) (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) num_of_repeats (isambard.specifications.solenoid.Solenoid attribute)

O

o_c_n_angles (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) off_plane (isambard.specifications.solenoid.HelixPair attribute)

oligomeric_state (isambard.specifications.coiledcoil.CoiledCoil attribute) orientation (isambard.specifications.helix.HelicalHelix attribute) orientations (isambard.specifications.coiledcoil.CoiledCoil attribute)

P

pack_side_chains_scwrl() (in module isambard.modelling.scwrl) Parameter (class in isambard.optimisation.base_evo_opt) parameter_type (isambard.optimisation.mmc_optimizer.MMCParameter attribute) parameters (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation attribute) ParameterType (class in isambard.optimisation.base_evo_opt) parse_individual() (isambard.optimisation.base_evo_opt.BaseOptimizer method) parse_scwrl_out() (in module isambard.modelling.scwrl)

phi_c_alpha (isambard.specifications.helix.HelicalHelix attribute) phi_c_alphas (isambard.specifications.coiledcoil.CoiledCoil attribute) phis (isambard.specifications.solenoid.HelixPair attribute) phos_3_prime (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) planar_residue() (in module isambard.specifications.ta_polypeptide) proposed_value (isambard.optimisation.mmc_optimizer.MMCParameter attribute) PSO (class in isambard.optimisation.evo_optimizers)

R

rad_unit (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) radius (isambard.specifications.solenoid.Solenoid attribute) randomise_proposed_value() (isambard.optimisation.mmc_optimizer.MMCParameter method) reject_proposed_value() (isambard.optimisation.mmc_optimizer.MMCParameter method) repeat_unit (isambard.specifications.solenoid.Solenoid attribute) residues_per_turn (isambard.specifications.helix.Helix attribute) rise (isambard.specifications.solenoid.Solenoid attribute) rise_per_nucleotide (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) rise_per_residue (isambard.specifications.helix.Helix attribute)

rot_ang (isambard.specifications.solenoid.Solenoid attribute) rotate() (isambard.specifications.helix.HelicalHelix method) (isambard.specifications.helix.Helix method) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand method) rotate_monomers() (isambard.specifications.helix.HelicalHelix method) rotational_offsets (isambard.specifications.coiledcoil.CoiledCoil attribute) run_dssp() (in module isambard.evaluation.dssp) run_hf_loop() (in module isambard.evaluation.hydrophobic_fitness) run_opt() (isambard.optimisation.base_evo_opt.BaseOptimizer method) run_scwrl() (in module isambard.modelling.scwrl)

S

scwrl_available() (in module isambard.modelling.scwrl) sequences (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation attribute) Solenoid (class in isambard.specifications.solenoid) specification (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation attribute) splays (isambard.specifications.solenoid.HelixPair attribute)

start_optimisation() (isambard.optimisation.mmc_optimizer.MMCParameterOptimisation method) starting_value (isambard.optimisation.mmc_optimizer.MMCParameter attribute) STATIC (isambard.optimisation.base_evo_opt.ParameterType attribute) static() (isambard.optimisation.base_evo_opt.Parameter class method) static_dist_or_list (isambard.optimisation.mmc_optimizer.MMCParameter attribute) STATIC_VALUE (isambard.optimisation.mmc_optimizer.MMCParameterType attribute)

T

tag_dssp_data() (in module isambard.evaluation.dssp) tan_unit (isambard.specifications.helix.Helix attribute) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand attribute) TAPolypeptide (class in isambard.specifications.ta_polypeptide)

torsion_angles (isambard.specifications.ta_polypeptide.TAPolypeptide attribute) translate() (isambard.specifications.helix.HelicalHelix method) (isambard.specifications.helix.Helix method) (isambard.specifications.nucleic_acid_strand.NucleicAcidStrand method) tropocollagen() (isambard.specifications.coiledcoil.CoiledCoil class method)

U

UNIFORM_DIST (isambard.optimisation.mmc_optimizer.MMCParameterType attribute)

update() (isambard.optimisation.evo_optimizers.CMAES method) update_particle() (isambard.optimisation.evo_optimizers.PSO method)

Z

z_shifts (isambard.specifications.coiledcoil.CoiledCoil attribute) (isambard.specifications.solenoid.HelixPair attribute)