rstoolbox
1.0.0
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An introduction to rstoolbox
Highlighted works
Installing and Getting Started
Available direct executables
Tutorials
API reference
RosettaScripts
What’s new
Contributing
Page
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
adapt_length() (in module rstoolbox.utils)
add_column() (in module rstoolbox.utils)
add_fragments() (rstoolbox.components.FragmentFrame method)
add_left_title() (in module rstoolbox.utils)
add_quality_measure() (rstoolbox.components.FragmentFrame method)
add_reference() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
add_reference_sequence() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
add_reference_shift() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
add_reference_structure() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
add_right_title() (in module rstoolbox.utils)
add_source_file() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.FragmentFrame method)
add_source_files() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
add_top_title() (in module rstoolbox.utils)
add_white_to_cmap() (in module rstoolbox.utils)
apply_resfile() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
B
baseline() (in module rstoolbox.utils)
binary_overlap() (in module rstoolbox.analysis)
binary_similarity() (in module rstoolbox.analysis)
C
clean_rosetta_suffix() (rstoolbox.components.DesignFrame method)
coerce() (rstoolbox.components.FragmentFrame method)
color_variant() (in module rstoolbox.utils)
concat_fragments() (in module rstoolbox.utils)
cumulative() (in module rstoolbox.analysis)
D
delete_empty() (rstoolbox.components.SequenceFrame method)
delete_extra() (rstoolbox.components.SequenceFrame method)
delete_reference() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
DesignFrame (class in rstoolbox.components)
DesignSeries (class in rstoolbox.components)
distribution_quality() (in module rstoolbox.plot)
E
edit_legend_text() (in module rstoolbox.utils)
F
format_Ipython() (in module rstoolbox.utils)
FragmentFrame (class in rstoolbox.components)
G
generate_mutant_variants() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
generate_mutants_from_matrix() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
generate_wt_reversions() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_available_labels() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_available_references() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
get_available_sequences() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_available_structure_predictions() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_available_structures() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_dihedrals() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_id() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_identified_mutants() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_key_residues() (rstoolbox.components.SequenceFrame method)
get_label() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_mutation_count() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_mutation_positions() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_mutations() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_phi() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_psi() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_reference_sequence() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
get_reference_shift() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
get_reference_structure() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
get_selection() (in module rstoolbox.components)
get_sequence() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_sequence_and_structure() (in module rstoolbox.io)
get_sequence_with() (rstoolbox.components.DesignFrame method)
get_sequential_data() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_source_files() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_structure() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
get_structure_prediction() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
H
has_reference_sequence() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
has_reference_structure() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
has_source_file() (rstoolbox.components.FragmentFrame method)
has_source_files() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
highlight() (in module rstoolbox.utils)
I
identify_mutants() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
is_comparable() (rstoolbox.components.FragmentFrame method)
is_empty() (rstoolbox.components.Selection method)
is_shifted() (rstoolbox.components.Selection method)
is_transposed() (rstoolbox.components.SequenceFrame method)
L
label_percentage() (in module rstoolbox.analysis)
label_sequence() (in module rstoolbox.analysis)
load_refdata() (in module rstoolbox.utils)
logo_plot() (in module rstoolbox.plot)
logo_plot_in_axis() (in module rstoolbox.plot)
M
make_frequency_network() (rstoolbox.components.FragmentFrame method)
make_per_position_frequency_network() (rstoolbox.components.FragmentFrame method)
make_redundancy_table() (in module rstoolbox.utils)
make_resfile() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
make_rosetta_app_path() (in module rstoolbox.utils)
make_sequence_matrix() (rstoolbox.components.FragmentFrame method)
make_structures() (in module rstoolbox.io)
map_to_sequences() (rstoolbox.components.Selection method)
multiple_distributions() (in module rstoolbox.plot)
mutations() (in module rstoolbox.utils)
O
open_rosetta_file() (in module rstoolbox.io)
order() (rstoolbox.components.FragmentFrame method)
P
parse_master_file() (in module rstoolbox.io)
parse_rosetta_contacts() (in module rstoolbox.io)
parse_rosetta_file() (in module rstoolbox.io)
parse_rosetta_fragments() (in module rstoolbox.io)
parse_rosetta_json() (in module rstoolbox.io)
parse_rosetta_pdb() (in module rstoolbox.io)
per_residue_matrix_score_plot() (in module rstoolbox.plot)
plot_96wells() (in module rstoolbox.plot)
plot_alignment() (in module rstoolbox.plot)
plot_CD() (in module rstoolbox.plot)
plot_dssp_vs_psipred() (in module rstoolbox.plot)
plot_fragment_profiles() (in module rstoolbox.plot)
plot_fragments() (in module rstoolbox.plot)
plot_in_context() (in module rstoolbox.plot)
plot_MALS() (in module rstoolbox.plot)
plot_ramachandran() (in module rstoolbox.plot)
plot_ramachandran_single() (in module rstoolbox.plot)
plot_SPR() (in module rstoolbox.plot)
plot_thermal_melt() (in module rstoolbox.plot)
positional_enrichment() (in module rstoolbox.analysis)
positional_sequence_similarity() (in module rstoolbox.analysis)
positional_sequence_similarity_plot() (in module rstoolbox.plot)
positional_structural_count() (in module rstoolbox.analysis)
positional_structural_identity() (in module rstoolbox.analysis)
positional_structural_similarity_plot() (in module rstoolbox.plot)
pymol_mutant_selector() (in module rstoolbox.io)
Q
quick_consensus_secondary_structure() (rstoolbox.components.FragmentFrame method)
quick_consensus_sequence() (rstoolbox.components.FragmentFrame method)
R
random_fastq() (in module rstoolbox.tests.helper)
random_frequency_matrix() (in module rstoolbox.tests.helper)
random_proteins() (in module rstoolbox.tests.helper)
read_CD() (in module rstoolbox.io)
read_fasta() (in module rstoolbox.io)
read_fastq() (in module rstoolbox.io)
read_hmmsearch() (in module rstoolbox.io)
read_MALS() (in module rstoolbox.io)
read_SPR() (in module rstoolbox.io)
renumber() (rstoolbox.components.FragmentFrame method)
replace_source_files() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
report() (in module rstoolbox.utils)
retrieve_sequences_from_pdbs() (rstoolbox.components.DesignFrame method)
rstoolbox.components.description (module)
rstoolbox.core.core_init (module)
S
sample_top_neighbors() (rstoolbox.components.FragmentFrame method)
score_by_pssm() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
secondary_structure_percentage() (in module rstoolbox.analysis)
select_quantile() (rstoolbox.components.FragmentFrame method)
Selection (class in rstoolbox.components)
SelectionContainer (class in rstoolbox.components)
selector_percentage() (in module rstoolbox.analysis)
seqID() (rstoolbox.components.Selection method)
sequence_bits() (rstoolbox.components.DesignFrame method)
sequence_distance() (rstoolbox.components.DesignFrame method)
sequence_frequencies() (rstoolbox.components.DesignFrame method)
sequence_frequency_plot() (in module rstoolbox.plot)
sequence_similarity() (in module rstoolbox.analysis)
SequenceFrame (class in rstoolbox.components)
sequencing_enrichment() (in module rstoolbox.utils)
sequential_frequencies() (in module rstoolbox.analysis)
shift() (rstoolbox.components.Selection method)
(rstoolbox.components.SelectionContainer method)
slice_region() (rstoolbox.components.FragmentFrame method)
split_dataframe_rows() (in module rstoolbox.utils)
split_values() (in module rstoolbox.utils)
structure_bits() (rstoolbox.components.DesignFrame method)
structure_frequencies() (rstoolbox.components.DesignFrame method)
T
to_bits() (rstoolbox.components.SequenceFrame method)
to_list() (rstoolbox.components.Selection method)
to_string() (rstoolbox.components.Selection method)
top_limit() (rstoolbox.components.FragmentFrame method)
transfer_reference() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
(rstoolbox.components.SequenceFrame method)
translate_3frames() (in module rstoolbox.utils)
translate_dna_sequence() (in module rstoolbox.utils)
U
unshift() (rstoolbox.components.Selection method)
(rstoolbox.components.SelectionContainer method)
use_qgrid() (in module rstoolbox.utils)
V
view_mutants_alignment() (rstoolbox.components.DesignFrame method)
(rstoolbox.components.DesignSeries method)
W
write_clustalw() (in module rstoolbox.io)
write_fasta() (in module rstoolbox.io)
write_fragment_sequence_profiles() (in module rstoolbox.io)
write_mutant_alignments() (in module rstoolbox.io)
write_rosetta_fragments() (in module rstoolbox.io)