Index

_

__init__() (choppa.align.AlignFactory method) (choppa.IO.input.ComplexFactory method) (choppa.IO.input.FitnessFactory method) (choppa.logoplots.LogoPlot method) (choppa.render.InteractiveView method) (choppa.render.PublicationView method)

A

align_fitness() (choppa.align.AlignFactory method), [1]

AlignFactory (class in choppa.align), [1] alignment_idx_to_original_idx() (choppa.align.AlignFactory method), [1]

B

biopython_to_mda() (in module choppa.utils), [1]

build_logoplot() (choppa.logoplots.LogoPlot method)

C

check_validity() (choppa.IO.input.ComplexFactory method) (choppa.IO.input.FitnessFactory method) choppa module choppa.align module, [1] choppa.cli module choppa.cli.cli module choppa.cli.utils module choppa.data module choppa.IO module choppa.IO.convert module

choppa.IO.input module choppa.logoplots module, [1] choppa.render module, [1] choppa.tests module choppa.tests.test_choppa module choppa.utils module, [1] command() (choppa.cli.utils.SpecialHelpOrder method) complex_get_seq() (choppa.align.AlignFactory method), [1] complex_get_seqidcs() (choppa.align.AlignFactory method), [1] ComplexFactory (class in choppa.IO.input) count_fit_residues() (choppa.render.PublicationView method), [1]

D

divide_fitness_types() (choppa.logoplots.LogoPlot method), [1]

E

extract_ligands() (choppa.IO.input.ComplexFactory method)

F

fill_aligned_fitness() (choppa.align.AlignFactory method), [1] fitness_get_seq() (choppa.align.AlignFactory method), [1]

fitness_get_seqidcs() (choppa.align.AlignFactory method), [1] fitness_reset_keys() (choppa.align.AlignFactory method), [1] FitnessFactory (class in choppa.IO.input)

G

get_alignment() (choppa.align.AlignFactory method), [1] get_confidence_limits() (choppa.render.InteractiveView method), [1] get_contacts_mda() (in module choppa.utils), [1] get_fitness_alignment_shift_dict() (choppa.align.AlignFactory method), [1] get_fitness_basedict() (choppa.IO.input.FitnessFactory method)

get_help() (choppa.cli.utils.SpecialHelpOrder method) get_interaction_dict() (choppa.render.InteractiveView method), [1] get_ligand_resnames_from_pdb_str() (in module choppa.utils), [1] get_logoplot_dict() (choppa.render.InteractiveView method), [1] get_pdb_components() (in module choppa.utils), [1] get_surface_coloring_dict() (choppa.render.InteractiveView method), [1]

I

inject_stuff_in_template() (choppa.render.InteractiveView method), [1]

InteractiveView (class in choppa.render), [1]

L

list_commands_for_help() (choppa.cli.utils.SpecialHelpOrder method) load_pdb() (choppa.IO.input.ComplexFactory method)

load_pdb_rdkit() (choppa.IO.input.ComplexFactory method) LogoPlot (class in choppa.logoplots), [1]

M

module choppa choppa.align, [1] choppa.cli choppa.cli.cli choppa.cli.utils choppa.data choppa.IO choppa.IO.convert choppa.IO.input choppa.logoplots, [1] choppa.render, [1] choppa.tests choppa.tests.test_choppa choppa.utils, [1]

N

nextstrain_to_csv() (in module choppa.IO.convert)

P

phylo_json_to_df() (in module choppa.IO.convert) process_ligand() (in module choppa.utils), [1] process_protein() (in module choppa.utils), [1] PublicationView (class in choppa.render), [1] pymol_add_interactions() (choppa.render.PublicationView method), [1] pymol_color_by_fitness() (choppa.render.PublicationView method), [1]

pymol_color_coder() (choppa.render.PublicationView method), [1] pymol_prettify_system() (choppa.render.PublicationView method), [1] pymol_select_components() (choppa.render.PublicationView method), [1] pymol_setup_system() (choppa.render.PublicationView method), [1] pymol_start_session() (choppa.render.PublicationView method), [1] pymol_write_session() (choppa.render.PublicationView method), [1]

R

read_fitness_csv() (choppa.IO.input.FitnessFactory method) remove_waters() (choppa.IO.input.ComplexFactory method) render() (choppa.render.InteractiveView method) (choppa.render.PublicationView method), [1]

render_logoplot() (choppa.logoplots.LogoPlot method), [1] render_singleres_logoplot() (in module choppa.logoplots), [1]

S

sdf_str_from_pdb() (in module choppa.utils), [1] show_contacts() (in module choppa.utils), [1]

SpecialHelpOrder (class in choppa.cli.utils) split_pdb_str() (in module choppa.utils), [1] surface_coloring_dict_to_js() (choppa.render.InteractiveView method), [1]

T

test_choppa_correct_custom_columns() (in module choppa.tests.test_choppa) test_choppa_imported() (in module choppa.tests.test_choppa) test_choppa_incorrect_custom_columns() (in module choppa.tests.test_choppa)

test_choppa_render_toy_mac1_full() (in module choppa.tests.test_choppa) test_choppa_render_toy_mac1_sectioned() (in module choppa.tests.test_choppa) test_choppa_render_toy_mac1_sectioned_noconf() (in module choppa.tests.test_choppa) test_choppa_render_toy_mac1_truncated() (in module choppa.tests.test_choppa)

V

validate_alignment() (choppa.align.AlignFactory method), [1]