homelette
latest
Installation
Docker
Tutorial 1: Basics
Tutorial 2: Model Generation
Tutorial 3: Model Evaluation
Tutorial 4: Extending homelette
Tutorial 5: Parallelization
Tutorial 6: Complex Modelling
Tutorial 7: Assembling Modelling Pipelines
Tutorial 8: Automatic Alignment Generation
Organization
Sequences and Alignments
Routines
Evaluation
PDB File interface
Extension Overview
homelette
Index
Edit on GitHub
Index
A
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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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M
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P
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R
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S
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T
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W
A
Alignment (class in homelette.alignment)
AlignmentGenerator (class in homelette.alignment)
AlignmentGenerator_from_aln (class in homelette.alignment)
AlignmentGenerator_hhblits (class in homelette.alignment)
AlignmentGenerator_pdb (class in homelette.alignment)
annotate() (homelette.alignment.Sequence method)
assemble_complex_aln() (in module homelette.alignment)
C
calc_coverage() (homelette.alignment.Alignment method)
calc_coverage_target() (homelette.alignment.Alignment method)
calc_identity() (homelette.alignment.Alignment method)
calc_identity_target() (homelette.alignment.Alignment method)
calc_pairwise_coverage_all() (homelette.alignment.Alignment method)
calc_pairwise_identity_all() (homelette.alignment.Alignment method)
D
download_pdb() (in module homelette.pdb_io)
E
evaluate() (homelette.evaluation.Evaluation_dope method)
(homelette.evaluation.Evaluation_mol_probity method)
(homelette.evaluation.Evaluation_qmean4 method)
(homelette.evaluation.Evaluation_qmean6 method)
(homelette.evaluation.Evaluation_qmeandisco method)
(homelette.evaluation.Evaluation_soap_pp method)
(homelette.evaluation.Evaluation_soap_protein method)
(homelette.extension.extension_foldx.Evaluation_foldx_alascan_buildmodels method)
(homelette.extension.extension_foldx.Evaluation_foldx_alascan_interaction method)
(homelette.extension.extension_foldx.Evaluation_foldx_interaction method)
(homelette.extension.extension_foldx.Evaluation_foldx_repairmodels method)
(homelette.extension.extension_foldx.Evaluation_foldx_stability method)
evaluate_models() (homelette.organization.Task method)
Evaluation_dope (class in homelette.evaluation)
Evaluation_foldx_alascan_buildmodels (class in homelette.extension.extension_foldx)
Evaluation_foldx_alascan_interaction (class in homelette.extension.extension_foldx)
Evaluation_foldx_interaction (class in homelette.extension.extension_foldx)
Evaluation_foldx_repairmodels (class in homelette.extension.extension_foldx)
Evaluation_foldx_stability (class in homelette.extension.extension_foldx)
Evaluation_mol_probity (class in homelette.evaluation)
Evaluation_qmean4 (class in homelette.evaluation)
Evaluation_qmean6 (class in homelette.evaluation)
Evaluation_qmeandisco (class in homelette.evaluation)
Evaluation_soap_pp (class in homelette.evaluation)
Evaluation_soap_protein (class in homelette.evaluation)
execute_routine() (homelette.organization.Task method)
F
from_fasta() (homelette.alignment.AlignmentGenerator class method)
(homelette.alignment.AlignmentGenerator_from_aln method)
(homelette.alignment.AlignmentGenerator_hhblits class method)
(homelette.alignment.AlignmentGenerator_pdb class method)
G
generate_models() (homelette.routines.Routine_altmod_default method)
(homelette.routines.Routine_altmod_slow method)
(homelette.routines.Routine_automodel_default method)
(homelette.routines.Routine_automodel_slow method)
(homelette.routines.Routine_complex_altmod_default method)
(homelette.routines.Routine_complex_altmod_slow method)
(homelette.routines.Routine_complex_automodel_default method)
(homelette.routines.Routine_complex_automodel_slow method)
(homelette.routines.Routine_loopmodel_default method)
(homelette.routines.Routine_loopmodel_slow method)
(homelette.routines.Routine_promod3 method)
get_annotation_pir() (homelette.alignment.Sequence method)
get_annotation_print() (homelette.alignment.Sequence method)
get_chains() (homelette.pdb_io.PdbObject method)
get_evaluation() (homelette.organization.Task method)
get_gaps() (homelette.alignment.Sequence method)
get_pdbs() (homelette.alignment.AlignmentGenerator method)
(homelette.alignment.AlignmentGenerator_from_aln method)
(homelette.alignment.AlignmentGenerator_hhblits method)
(homelette.alignment.AlignmentGenerator_pdb method)
get_sequence() (homelette.alignment.Alignment method)
(homelette.organization.Model method)
(homelette.pdb_io.PdbObject method)
get_suggestion() (homelette.alignment.AlignmentGenerator method)
(homelette.alignment.AlignmentGenerator_from_aln method)
(homelette.alignment.AlignmentGenerator_hhblits method)
(homelette.alignment.AlignmentGenerator_pdb method)
H
homelette.alignment
module
homelette.evaluation
module
homelette.extension.extension_foldx
module
homelette.organization
module
homelette.pdb_io
module
homelette.routines
module
I
initialize_task() (homelette.alignment.AlignmentGenerator method)
(homelette.alignment.AlignmentGenerator_from_aln method)
(homelette.alignment.AlignmentGenerator_hhblits method)
(homelette.alignment.AlignmentGenerator_pdb method)
M
Model (class in homelette.organization)
module
homelette.alignment
homelette.evaluation
homelette.extension.extension_foldx
homelette.organization
homelette.pdb_io
homelette.routines
P
parse_pdb() (homelette.organization.Model method)
parse_to_pd() (homelette.pdb_io.PdbObject method)
PdbObject (class in homelette.pdb_io)
print_clustal() (homelette.alignment.Alignment method)
R
read_pdb() (in module homelette.pdb_io)
remove_gaps() (homelette.alignment.Sequence method)
remove_redundant_gaps() (homelette.alignment.Alignment method)
remove_sequence() (homelette.alignment.Alignment method)
rename() (homelette.organization.Model method)
rename_sequence() (homelette.alignment.Alignment method)
replace_sequence() (homelette.alignment.Alignment method)
Routine_altmod_default (class in homelette.routines)
Routine_altmod_slow (class in homelette.routines)
Routine_automodel_default (class in homelette.routines)
Routine_automodel_slow (class in homelette.routines)
Routine_complex_altmod_default (class in homelette.routines)
Routine_complex_altmod_slow (class in homelette.routines)
Routine_complex_automodel_default (class in homelette.routines)
Routine_complex_automodel_slow (class in homelette.routines)
Routine_loopmodel_default (class in homelette.routines)
Routine_loopmodel_slow (class in homelette.routines)
Routine_promod3 (class in homelette.routines)
S
select_sequences() (homelette.alignment.Alignment method)
select_templates() (homelette.alignment.AlignmentGenerator method)
(homelette.alignment.AlignmentGenerator_from_aln method)
(homelette.alignment.AlignmentGenerator_hhblits method)
(homelette.alignment.AlignmentGenerator_pdb method)
Sequence (class in homelette.alignment)
show_suggestion() (homelette.alignment.AlignmentGenerator method)
(homelette.alignment.AlignmentGenerator_from_aln method)
(homelette.alignment.AlignmentGenerator_hhblits method)
(homelette.alignment.AlignmentGenerator_pdb method)
T
Task (class in homelette.organization)
transform_change_chain_id() (homelette.pdb_io.PdbObject method)
transform_concat() (homelette.pdb_io.PdbObject method)
transform_extract_chain() (homelette.pdb_io.PdbObject method)
transform_filter_res_name() (homelette.pdb_io.PdbObject method)
transform_filter_res_seq() (homelette.pdb_io.PdbObject method)
transform_remove_hetatm() (homelette.pdb_io.PdbObject method)
transform_renumber_residues() (homelette.pdb_io.PdbObject method)
W
write_clustal() (homelette.alignment.Alignment method)
write_fasta() (homelette.alignment.Alignment method)
write_pdb() (homelette.pdb_io.PdbObject method)
write_pir() (homelette.alignment.Alignment method)
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