Index

_

__init__() (modlamp.analysis.GlobalAnalysis method) (modlamp.core.BaseDescriptor method) (modlamp.core.BaseSequence method) (modlamp.datasets.Bunch method) (modlamp.descriptors.PeptideDescriptor method) (modlamp.sequences.AMPngrams method) (modlamp.sequences.MixedLibrary method) (modlamp.wetlab.CD method)

A

aa_energies() (in module modlamp.core) aa_formulas() (in module modlamp.core) aa_weights() (in module modlamp.core)

aliphatic_index() (modlamp.descriptors.GlobalDescriptor method) AmphipathicArc (class in modlamp.sequences) AMPngrams (class in modlamp.sequences) aromaticity() (modlamp.descriptors.GlobalDescriptor method)

B

BaseDescriptor (class in modlamp.core) BaseSequence (class in modlamp.core)

boman_index() (modlamp.descriptors.GlobalDescriptor method) Bunch (class in modlamp.datasets)

C

calc_aa_freq() (modlamp.analysis.GlobalAnalysis method) calc_charge() (modlamp.analysis.GlobalAnalysis method) calc_H() (modlamp.analysis.GlobalAnalysis method) calc_len() (modlamp.analysis.GlobalAnalysis method) calc_meanres_ellipticity() (modlamp.wetlab.CD method) calc_molar_ellipticity() (modlamp.wetlab.CD method) calc_uH() (modlamp.analysis.GlobalAnalysis method) calculate_all() (modlamp.descriptors.GlobalDescriptor method) calculate_arc() (modlamp.descriptors.PeptideDescriptor method) calculate_autocorr() (modlamp.descriptors.PeptideDescriptor method) calculate_charge() (modlamp.descriptors.GlobalDescriptor method) calculate_crosscorr() (modlamp.descriptors.PeptideDescriptor method)

calculate_global() (modlamp.descriptors.PeptideDescriptor method) calculate_moment() (modlamp.descriptors.PeptideDescriptor method) calculate_MW() (modlamp.descriptors.GlobalDescriptor method) calculate_profile() (modlamp.descriptors.PeptideDescriptor method) CD (class in modlamp.wetlab) Centrosymmetric (class in modlamp.sequences) charge_density() (modlamp.descriptors.GlobalDescriptor method) clean() (modlamp.core.BaseSequence method) count_aa() (modlamp.core.BaseDescriptor method) count_aas() (in module modlamp.core) count_ngrams() (in module modlamp.core) (modlamp.core.BaseDescriptor method)

D

dichroweb() (modlamp.wetlab.CD method)

F

feature_scaling() (modlamp.core.BaseDescriptor method) feature_shuffle() (modlamp.core.BaseDescriptor method) filter_aa() (modlamp.core.BaseDescriptor method) (modlamp.core.BaseSequence method)

filter_duplicates() (modlamp.core.BaseDescriptor method) (modlamp.core.BaseSequence method) filter_sequences() (modlamp.core.BaseDescriptor method) filter_values() (modlamp.core.BaseDescriptor method) formula() (modlamp.descriptors.GlobalDescriptor method)

G

generate_sequences() (modlamp.sequences.AmphipathicArc method) (modlamp.sequences.AMPngrams method) (modlamp.sequences.Centrosymmetric method) (modlamp.sequences.Helices method) (modlamp.sequences.HelicesACP method) (modlamp.sequences.Hepahelices method) (modlamp.sequences.Kinked method) (modlamp.sequences.MixedLibrary method) (modlamp.sequences.Oblique method) (modlamp.sequences.Random method)

GlobalAnalysis (class in modlamp.analysis) GlobalDescriptor (class in modlamp.descriptors)

H

helical_wheel() (in module modlamp.plot) Helices (class in modlamp.sequences) HelicesACP (class in modlamp.sequences)

helicity() (modlamp.wetlab.CD method) Hepahelices (class in modlamp.sequences) hydrophobic_ratio() (modlamp.descriptors.GlobalDescriptor method)

I

instability_index() (modlamp.descriptors.GlobalDescriptor method)

isoelectric_point() (modlamp.descriptors.GlobalDescriptor method)

K

keep_natural_aa() (modlamp.core.BaseDescriptor method) (modlamp.core.BaseSequence method)

Kinked (class in modlamp.sequences)

L

length() (modlamp.descriptors.GlobalDescriptor method) load_ACPvsRandom() (in module modlamp.datasets) load_ACPvsTM() (in module modlamp.datasets) load_AMPvsTM() (in module modlamp.datasets)

load_AMPvsUniProt() (in module modlamp.datasets) load_custom() (in module modlamp.datasets) load_descriptordata() (modlamp.core.BaseDescriptor method) load_scale() (in module modlamp.core) (modlamp.descriptors.PeptideDescriptor method)

M

make_H_gradient() (modlamp.sequences.AmphipathicArc method) minmax_selection() (modlamp.core.BaseDescriptor method) MixedLibrary (class in modlamp.sequences) modlamp.analysis (module) modlamp.core (module) modlamp.database (module)

modlamp.datasets (module) modlamp.descriptors (module) modlamp.ml (module) modlamp.plot (module) modlamp.sequences (module) modlamp.wetlab (module) mutate_AA() (modlamp.core.BaseSequence method)

N

ngrams_apd() (in module modlamp.core)

O

Oblique (class in modlamp.sequences)

P

PeptideDescriptor (class in modlamp.descriptors) plot() (modlamp.wetlab.CD method) plot_2_features() (in module modlamp.plot) plot_3_features() (in module modlamp.plot) plot_aa_distr() (in module modlamp.plot) plot_feature() (in module modlamp.plot)

plot_pde() (in module modlamp.plot) plot_profile() (in module modlamp.plot) plot_summary() (modlamp.analysis.GlobalAnalysis method) plot_validation_curve() (in module modlamp.ml) plot_violin() (in module modlamp.plot) predict() (in module modlamp.ml) prune_library() (modlamp.sequences.MixedLibrary method)

Q

query_apd() (in module modlamp.database)

query_camp() (in module modlamp.database) query_database() (in module modlamp.database)

R

Random (class in modlamp.sequences) random_selection() (modlamp.core.BaseDescriptor method)

read_fasta() (in module modlamp.core) (modlamp.core.BaseDescriptor method)

S

save_descriptor() (modlamp.core.BaseDescriptor method) save_fasta() (in module modlamp.core) (modlamp.core.BaseDescriptor method) (modlamp.core.BaseSequence method)

score_cv() (in module modlamp.ml) score_testset() (in module modlamp.ml) sequence_order_shuffle() (modlamp.core.BaseDescriptor method)

T

train_best_model() (in module modlamp.ml)