Index

_

__add__() (protflow.residues.AtomSelection method) __init__() (protflow.jobstarters.JobStarter method) (protflow.jobstarters.LocalJobStarter method) (protflow.jobstarters.SbatchArrayJobstarter method) (protflow.metrics.fpocket.FPocket method) (protflow.metrics.generic_metric_runner.GenericMetric method) (protflow.metrics.protparam.ProtParam method) (protflow.metrics.rmsd.AtomRMSD method) (protflow.metrics.rmsd.BackboneRMSD method) (protflow.metrics.rmsd.MotifRMSD method) (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) (protflow.metrics.tmscore.TMalign method) (protflow.metrics.tmscore.TMscore method) (protflow.poses.Poses method) (protflow.residues.AtomSelection method) (protflow.tools.attnpacker.AttnPacker method) (protflow.tools.boltz.Boltz method) (protflow.tools.boltz.BoltzParams method) (protflow.tools.colabfold.Colabfold method) (protflow.tools.esmfold.ESMFold method) (protflow.tools.ligandmpnn.LigandMPNN method) (protflow.tools.protein_edits.ChainAdder method) (protflow.tools.protein_edits.ChainRemover method) (protflow.tools.protein_edits.SequenceAdder method) (protflow.tools.protein_edits.SequenceRemover method) (protflow.tools.protein_generator.ProteinGenerator method) (protflow.tools.residue_selectors.ChainSelector method) (protflow.tools.residue_selectors.DistanceSelector method) (protflow.tools.residue_selectors.NotSelector method) (protflow.tools.residue_selectors.ResidueSelector method) (protflow.tools.residue_selectors.TrueSelector method) (protflow.tools.rfdiffusion.RFdiffusion method) (protflow.tools.rosetta.Rosetta method) (protflow.utils.plotting.PlottingTrajectory method)

__init_subclass__() (protflow.runners.Runner class method) __iter__() (protflow.residues.AtomSelection method) __len__() (protflow.residues.AtomSelection method) __str__() (protflow.residues.AtomSelection method) (protflow.runners.Runner method) (protflow.tools.boltz.Boltz method) __sub__() (protflow.residues.AtomSelection method)

A

add() (protflow.utils.plotting.PlottingTrajectory method) add_and_plot() (protflow.utils.plotting.PlottingTrajectory method) add_chain() (in module protflow.utils.biopython_tools) (protflow.tools.protein_edits.ChainAdder method) add_constraint() (protflow.tools.boltz.BoltzParams method) add_dna() (protflow.tools.boltz.BoltzParams method) add_group_statistics() (in module protflow.utils.utils) add_ligand() (protflow.tools.boltz.BoltzParams method) add_property() (protflow.tools.boltz.BoltzParams method)

add_protein() (protflow.tools.boltz.BoltzParams method) add_rna() (protflow.tools.boltz.BoltzParams method) add_sequence() (protflow.tools.protein_edits.ChainAdder method) add_template() (protflow.tools.boltz.BoltzParams method) add_timestamp() (in module protflow.jobstarters) all_against_all_sequence_identity() (in module protflow.utils.metrics) AtomRMSD (class in protflow.metrics.rmsd) atoms (protflow.residues.AtomSelection attribute) AtomSelection (class in protflow.residues) AttnPacker (class in protflow.tools.attnpacker)

B

BackboneRMSD (class in protflow.metrics.rmsd) biopython_load_protein() (in module protflow.utils.biopython_tools) Boltz (class in protflow.tools.boltz) boltz_path (protflow.tools.boltz.Boltz attribute)

boltz_python (protflow.tools.boltz.Boltz attribute) boltz_yaml_reader() (in module protflow.tools.boltz) boltz_yaml_writer() (in module protflow.tools.boltz) BoltzParams (class in protflow.tools.boltz)

C

calc_all_atom_rmsd() (protflow.metrics.rmsd.BackboneRMSD method) calc_interchain_contacts() (in module protflow.utils.metrics) calc_interchain_contacts_pdb() (in module protflow.utils.metrics) calc_ligand_clashes() (in module protflow.utils.metrics) calc_ligand_clashes_vdw() (in module protflow.utils.metrics) calc_ligand_contacts() (in module protflow.utils.metrics) calc_rog() (in module protflow.utils.metrics) calc_rog_of_pdb() (in module protflow.utils.metrics) calc_sc_tm() (in module protflow.utils.metrics) calc_sequence_identity() (in module protflow.utils.metrics) calculate_composite_score() (protflow.poses.Poses method) calculate_max_score() (protflow.poses.Poses method) calculate_mean_score() (protflow.poses.Poses method) calculate_median_score() (protflow.poses.Poses method) calculate_min_score() (protflow.poses.Poses method) calculate_poses_interaction_pae() (in module protflow.tools.colabfold) calculate_std_score() (protflow.poses.Poses method) chain (protflow.tools.residue_selectors.ChainSelector attribute) ChainAdder (class in protflow.tools.protein_edits) ChainRemover (class in protflow.tools.protein_edits) chains (protflow.tools.residue_selectors.ChainSelector attribute) ChainSelector (class in protflow.tools.residue_selectors) change_poses_dir() (protflow.poses.Poses method) check_data_formatting() (protflow.runners.RunnerOutput method) check_for_batch_run() (protflow.tools.ligandmpnn.LigandMPNN method) check_for_col_in_df() (in module protflow.utils.plotting) check_for_existing_scorefile() (protflow.runners.Runner method)

check_for_prefix() (protflow.runners.Runner method) check_poses_df_integrity() (protflow.poses.Poses method) check_prefix() (protflow.poses.Poses method) class_in_df() (in module protflow.poses) clean_rosetta_scorefile() (in module protflow.tools.rosetta) col_in_df() (in module protflow.poses) (in module protflow.runners) Colabfold (class in protflow.tools.colabfold) collect_boltz_scores() (in module protflow.tools.boltz) collect_esmfold_scores() (in module protflow.tools.esmfold) collect_fpocket_output() (in module protflow.metrics.fpocket) collect_fpocket_scores() (in module protflow.metrics.fpocket) collect_scores() (in module protflow.tools.attnpacker) (in module protflow.tools.colabfold) (in module protflow.tools.ligandmpnn) (in module protflow.tools.rfdiffusion) (in module protflow.tools.rosetta) (protflow.metrics.tmscore.TMalign method) (protflow.metrics.tmscore.TMscore method) (protflow.tools.protein_generator.ProteinGenerator method) combine_dataframe_score_columns() (in module protflow.poses) convert_chain_seq_dict_to_yaml_dict() (in module protflow.tools.boltz) convert_pdb_to_fasta() (protflow.poses.Poses method) convert_poses_to_boltz_yaml() (in module protflow.tools.boltz) convert_resselection_cols() (protflow.poses.Poses method) count_mutations() (in module protflow.utils.metrics) create_distance_conservation_bias_cmds() (in module protflow.tools.ligandmpnn)

D

default_jobstarter (protflow.poses.Poses attribute) description_from_path() (in module protflow.poses) determine_pose_type() (protflow.poses.Poses method)

determine_protparams() (in module protflow.utils.biopython_tools) df (protflow.poses.Poses attribute) DistanceSelector (class in protflow.tools.residue_selectors) duplicate_poses() (protflow.poses.Poses method)

E

edit_boltz_yaml() (in module protflow.tools.boltz) entropy() (in module protflow.utils.metrics)

ESMFold (class in protflow.tools.esmfold) expand_options_flags() (in module protflow.runners) extract_center() (protflow.tools.residue_selectors.DistanceSelector method)

F

fast_parse_selection() (in module protflow.residues) filter_dataframe_by_rank() (in module protflow.poses) filter_dataframe_by_value() (in module protflow.poses) filter_poses_by_rank() (protflow.poses.Poses method) filter_poses_by_value() (protflow.poses.Poses method) FlowSeq (class in protflow.tools.boltz) FPocket (class in protflow.metrics.fpocket) from_contig() (in module protflow.residues)

from_dict() (in module protflow.residues) (protflow.residues.AtomSelection static method) from_list() (protflow.residues.AtomSelection static method) from_rfd3_contig() (protflow.residues.AtomSelection static method) from_rfd3_input_selection() (protflow.residues.AtomSelection static method) from_rfd3_input_spec() (protflow.residues.AtomSelection static method) from_rfd3_ligand() (protflow.residues.AtomSelection static method) from_selection() (protflow.residues.ResidueSelection method)

G

generate_yaml_files() (protflow.tools.boltz.BoltzParams method) generic_run_setup() (protflow.runners.Runner method) GenericMetric (class in protflow.metrics.generic_metric_runner) get_atoms() (in module protflow.utils.biopython_tools) get_atoms_of_motif() (in module protflow.utils.biopython_tools) get_config() (in module protflow) get_format() (in module protflow.poses)

get_mutation_indeces() (in module protflow.utils.metrics) get_mutations_list() (in module protflow.utils.metrics) get_next_chain_id() (in module protflow.utils.biopython_tools) get_outfile_name() (in module protflow.metrics.fpocket) get_pose() (protflow.poses.Poses method) get_residue_mapping() (in module protflow.tools.rfdiffusion) get_sequence_from_pose() (in module protflow.utils.biopython_tools) get_SLURM_stats() (in module protflow.jobstarters)

H

history (protflow.runners.SbatchArrayRunnerTimer attribute)

I

idx_to_char() (in module protflow.tools.boltz) import_fasta() (in module protflow.utils.plotting)

index_layers (protflow.metrics.fpocket.FPocket attribute) (protflow.tools.boltz.Boltz attribute)

J

job_ids (protflow.runners.SbatchArrayRunnerTimer attribute) JobStarter (class in protflow.jobstarters) jobstarter (protflow.metrics.protparam.ProtParam attribute) (protflow.tools.boltz.Boltz attribute) (protflow.tools.protein_edits.ChainAdder attribute) (protflow.tools.protein_edits.ChainRemover attribute)

L

LigandMPNN (class in protflow.tools.ligandmpnn) load_poses() (in module protflow.poses) (protflow.poses.Poses method)

load_sequence_from_fasta() (in module protflow.utils.biopython_tools) load_structure_from_pdbfile() (in module protflow.utils.biopython_tools) LocalJobStarter (class in protflow.jobstarters)

M

main() (in module protflow.metrics.generic_metric_runner) (in module protflow.metrics.protparam) module protflow protflow.config_template protflow.jobstarters protflow.metrics protflow.metrics.fpocket protflow.metrics.generic_metric_runner protflow.metrics.protparam protflow.metrics.rmsd protflow.metrics.tmscore protflow.poses protflow.residues protflow.runners protflow.tools protflow.tools.attnpacker protflow.tools.boltz protflow.tools.colabfold protflow.tools.esmfold protflow.tools.ligandmpnn protflow.tools.protein_edits protflow.tools.protein_generator protflow.tools.residue_selectors protflow.tools.rfdiffusion protflow.tools.rosetta protflow.utils protflow.utils.biopython_tools protflow.utils.metrics protflow.utils.plotting protflow.utils.pymol_tools protflow.utils.utils

MotifRMSD (class in protflow.metrics.rmsd) MotifSeparateSuperpositionRMSD (class in protflow.metrics.rmsd) multi_cols_only() (protflow.tools.ligandmpnn.LigandMPNN method) multimerize() (protflow.tools.protein_edits.ChainAdder method) mutations_pymol_scriptwriter() (in module protflow.utils.pymol_tools) MyDumper (class in protflow.tools.boltz)

N

name (protflow.tools.boltz.Boltz attribute)

normalize_series() (in module protflow.poses) NotSelector (class in protflow.tools.residue_selectors)

O

one_to_three_AA_code() (in module protflow.utils.biopython_tools)

options_flags_to_string() (in module protflow.runners)

P

parse_chain() (in module protflow.tools.protein_edits) parse_cols_for_plotting() (in module protflow.utils.plotting) parse_descriptions() (protflow.poses.Poses method) parse_diffusion_trbfile() (in module protflow.tools.rfdiffusion) parse_fasta_to_dict() (in module protflow.utils.utils) parse_fpocket_outfile() (in module protflow.metrics.fpocket) parse_from_scorefile() (in module protflow.residues) parse_generic_options() (in module protflow.runners) parse_motif() (protflow.tools.protein_edits.ChainAdder method) parse_options() (protflow.jobstarters.SbatchArrayJobstarter method) parse_pose_opt_cols() (protflow.tools.ligandmpnn.LigandMPNN method) parse_poses() (protflow.poses.Poses method) parse_residue() (in module protflow.residues) parse_residues() (in module protflow.tools.ligandmpnn) parse_rfdiffusion_opts() (protflow.tools.rfdiffusion.RFdiffusion method) parse_selection() (in module protflow.residues) parse_trbfile() (protflow.tools.protein_generator.ProteinGenerator method) PlottingTrajectory (class in protflow.utils.plotting) Poses (class in protflow.poses) poses (protflow.tools.residue_selectors.ChainSelector attribute) (protflow.tools.residue_selectors.DistanceSelector attribute) (protflow.tools.residue_selectors.ResidueSelector attribute) poses_list() (protflow.poses.Poses method) pre_cmd (protflow.tools.boltz.Boltz attribute) prep_a3m_for_prediction() (protflow.tools.colabfold.Colabfold method) prep_chain_input() (protflow.tools.residue_selectors.ChainSelector method) prep_fastas_for_prediction() (protflow.tools.colabfold.Colabfold method) (protflow.tools.esmfold.ESMFold method) prep_fpocket_options() (protflow.metrics.fpocket.FPocket method) prep_motif_input() (in module protflow.tools.rfdiffusion) prep_pose_options() (protflow.runners.Runner method) prep_ref() (protflow.metrics.tmscore.TMalign method) prep_residue_selection() (protflow.tools.residue_selectors.NotSelector method) prepend_cmd() (in module protflow.runners) ProteinGenerator (class in protflow.tools.protein_generator) protflow module protflow.config_template module protflow.jobstarters module protflow.metrics module protflow.metrics.fpocket module protflow.metrics.generic_metric_runner module protflow.metrics.protparam module

protflow.metrics.rmsd module protflow.metrics.tmscore module protflow.poses module protflow.residues module protflow.runners module protflow.tools module protflow.tools.attnpacker module protflow.tools.boltz module protflow.tools.colabfold module protflow.tools.esmfold module protflow.tools.ligandmpnn module protflow.tools.protein_edits module protflow.tools.protein_generator module protflow.tools.residue_selectors module protflow.tools.rfdiffusion module protflow.tools.rosetta module protflow.utils module protflow.utils.biopython_tools module protflow.utils.metrics module protflow.utils.plotting module protflow.utils.pymol_tools module protflow.utils.utils module ProtParam (class in protflow.metrics.protparam) python (protflow.metrics.protparam.ProtParam attribute) (protflow.tools.protein_edits.ChainAdder attribute) (protflow.tools.protein_edits.ChainRemover attribute)

R

reduce_to_unique() (in module protflow.residues) regex_expand_options_flags() (in module protflow.runners) reindex_poses() (protflow.poses.Poses method) remap_motifs() (protflow.tools.rfdiffusion.RFdiffusion method) remove_non_residue_residues() (in module protflow.utils.biopython_tools) renumber_pdb_by_residue_mapping() (in module protflow.utils.biopython_tools) renumber_pose_by_residue_mapping() (in module protflow.utils.biopython_tools) report() (protflow.runners.SbatchArrayRunnerTimer method) require_config() (in module protflow) reset_poses() (protflow.poses.Poses method) residue_contacts() (in module protflow.utils.metrics) residue_selection() (in module protflow.residues) residues (protflow.residues.ResidueSelection attribute) ResidueSelection (class in protflow.residues) ResidueSelector (class in protflow.tools.residue_selectors) return_poses() (protflow.runners.RunnerOutput method) RFdiffusion (class in protflow.tools.rfdiffusion) Rosetta (class in protflow.tools.rosetta) run() (protflow.metrics.fpocket.FPocket method) (protflow.metrics.generic_metric_runner.GenericMetric method) (protflow.metrics.protparam.ProtParam method) (protflow.metrics.rmsd.AtomRMSD method) (protflow.metrics.rmsd.BackboneRMSD method) (protflow.metrics.rmsd.MotifRMSD method) (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) (protflow.metrics.tmscore.TMalign method) (protflow.metrics.tmscore.TMscore method) (protflow.runners.Runner method) (protflow.runners.SbatchArrayRunnerTimer method) (protflow.tools.attnpacker.AttnPacker method) (protflow.tools.boltz.Boltz method) (protflow.tools.colabfold.Colabfold method) (protflow.tools.esmfold.ESMFold method) (protflow.tools.ligandmpnn.LigandMPNN method) (protflow.tools.protein_edits.ChainAdder method) (protflow.tools.protein_edits.ChainRemover method) (protflow.tools.protein_edits.SequenceAdder method) (protflow.tools.protein_edits.SequenceRemover method) (protflow.tools.protein_generator.ProteinGenerator method) (protflow.tools.rfdiffusion.RFdiffusion method) (protflow.tools.rosetta.Rosetta method)

Runner (class in protflow.runners) runner (protflow.runners.SbatchArrayRunnerTimer attribute) Runner.CrashError RunnerOutput (class in protflow.runners)

S

save_poses() (protflow.poses.Poses method) save_runner_scorefile() (protflow.runners.Runner method) save_scores() (protflow.poses.Poses method) save_structure_to_pdbfile() (in module protflow.utils.biopython_tools) SbatchArrayJobstarter (class in protflow.jobstarters) SbatchArrayRunnerTimer (class in protflow.runners) scale_series() (in module protflow.poses) scatterplot() (in module protflow.utils.plotting) scorefile (protflow.poses.Poses attribute) search_path() (protflow.runners.Runner method) select() (protflow.tools.residue_selectors.ChainSelector method) (protflow.tools.residue_selectors.DistanceSelector method) (protflow.tools.residue_selectors.NotSelector method) (protflow.tools.residue_selectors.ResidueSelector method) (protflow.tools.residue_selectors.TrueSelector method) select_single() (protflow.tools.residue_selectors.ChainSelector method) (protflow.tools.residue_selectors.DistanceSelector method) (protflow.tools.residue_selectors.NotSelector method) (protflow.tools.residue_selectors.ResidueSelector method) (protflow.tools.residue_selectors.TrueSelector method) sequence_dict_to_fasta() (in module protflow.utils.utils) sequence_logo() (in module protflow.utils.plotting) SequenceAdder (class in protflow.tools.protein_edits) SequenceRemover (class in protflow.tools.protein_edits) session_start (protflow.runners.SbatchArrayRunnerTimer attribute) set_atoms() (protflow.metrics.rmsd.BackboneRMSD method) (protflow.metrics.rmsd.MotifRMSD method) set_center_atoms() (protflow.tools.residue_selectors.DistanceSelector method) set_centers() (protflow.tools.residue_selectors.DistanceSelector method) set_chain() (protflow.tools.residue_selectors.ChainSelector method) set_chains() (protflow.metrics.rmsd.BackboneRMSD method) (protflow.tools.residue_selectors.ChainSelector method) set_colormap() (protflow.utils.plotting.PlottingTrajectory method) set_contig() (protflow.tools.residue_selectors.NotSelector method) set_dims() (protflow.utils.plotting.PlottingTrajectory method) set_distance() (protflow.tools.residue_selectors.DistanceSelector method) set_function() (protflow.metrics.generic_metric_runner.GenericMetric method) set_include_center() (protflow.tools.residue_selectors.DistanceSelector method) set_jobstarter() (protflow.metrics.generic_metric_runner.GenericMetric method) (protflow.metrics.rmsd.BackboneRMSD method) (protflow.metrics.rmsd.MotifRMSD method) (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) (protflow.poses.Poses method) set_last_error_message() (protflow.jobstarters.JobStarter method) set_location() (protflow.utils.plotting.PlottingTrajectory method) set_logger() (protflow.poses.Poses method)

set_max_cores() (protflow.jobstarters.JobStarter method) set_module() (protflow.metrics.generic_metric_runner.GenericMetric method) set_motif() (protflow.poses.Poses method) set_noncenter_atoms() (protflow.tools.residue_selectors.DistanceSelector method) set_operator() (protflow.tools.residue_selectors.DistanceSelector method) set_options() (protflow.jobstarters.SbatchArrayJobstarter method) (protflow.metrics.generic_metric_runner.GenericMetric method) set_poses() (protflow.poses.Poses method) (protflow.tools.residue_selectors.ResidueSelector method) set_python_path() (protflow.metrics.generic_metric_runner.GenericMetric method) set_ref_col() (protflow.metrics.rmsd.BackboneRMSD method) (protflow.metrics.rmsd.MotifRMSD method) (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_ref_motif() (protflow.metrics.rmsd.MotifRMSD method) set_residue_selection() (protflow.tools.residue_selectors.NotSelector method) set_return_superimposed_poses() (protflow.metrics.rmsd.MotifRMSD method) set_rmsd_atoms() (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_rmsd_include_het_atoms() (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_rmsd_ref_motif() (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_rmsd_target_motif() (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_scorefile() (protflow.poses.Poses method) set_storage_format() (protflow.poses.Poses method) set_super_atoms() (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_super_include_het_atoms() (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_super_ref_motif() (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_super_target_motif() (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) set_target_motif() (protflow.metrics.rmsd.MotifRMSD method) set_work_dir() (protflow.poses.Poses method) set_y_label() (protflow.utils.plotting.PlottingTrajectory method) setup_batch_run() (protflow.tools.ligandmpnn.LigandMPNN method) setup_chain_list() (in module protflow.tools.protein_edits) setup_input_dict() (protflow.metrics.rmsd.AtomRMSD method) (protflow.metrics.rmsd.MotifRMSD method) (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) singular_violinplot() (in module protflow.utils.plotting) sort_residues_on_chain() (in module protflow.utils.biopython_tools) split_complex() (in module protflow.utils.biopython_tools) split_list() (in module protflow.jobstarters) split_multiline_fasta() (protflow.poses.Poses method) start() (protflow.jobstarters.JobStarter method) (protflow.jobstarters.LocalJobStarter method) (protflow.jobstarters.SbatchArrayJobstarter method) storage_format (protflow.poses.Poses attribute) superimpose() (in module protflow.utils.biopython_tools) superimpose_add_chain() (protflow.tools.protein_edits.ChainAdder method) superimpose_on_motif() (in module protflow.utils.biopython_tools)

T

three_to_one_AA_code() (in module protflow.utils.biopython_tools) TMalign (class in protflow.metrics.tmscore) TMscore (class in protflow.metrics.tmscore) to_dict() (protflow.residues.AtomSelection method) (protflow.residues.ResidueSelection method) to_list() (protflow.residues.AtomSelection method) (protflow.residues.ResidueSelection method)

to_rfdiffusion_contig() (protflow.residues.ResidueSelection method) to_string() (protflow.residues.ResidueSelection method) to_tuple() (protflow.residues.AtomSelection method) translate_entity() (in module protflow.utils.biopython_tools) TrueSelector (class in protflow.tools.residue_selectors)

U

update_motif_res_mapping() (in module protflow.tools.rfdiffusion)

V

vdw_radii() (in module protflow.utils.utils) violin_plot() (protflow.utils.plotting.PlottingTrajectory method)

violinplot_multiple_cols() (in module protflow.utils.plotting) violinplot_multiple_cols_dfs() (in module protflow.utils.plotting) violinplot_multiple_lists() (in module protflow.utils.plotting)

W

wait_for_job() (protflow.jobstarters.JobStarter method) (protflow.jobstarters.LocalJobStarter method) (protflow.jobstarters.SbatchArrayJobstarter method) work_dir (protflow.poses.Poses attribute) write_cmd() (protflow.metrics.tmscore.TMalign method) (protflow.metrics.tmscore.TMscore method) (protflow.tools.attnpacker.AttnPacker method) (protflow.tools.colabfold.Colabfold method) (protflow.tools.esmfold.ESMFold method) (protflow.tools.ligandmpnn.LigandMPNN method) (protflow.tools.protein_generator.ProteinGenerator method) (protflow.tools.rfdiffusion.RFdiffusion method) (protflow.tools.rosetta.Rosetta method)

write_fasta() (in module protflow.utils.plotting) write_to_json() (in module protflow.tools.ligandmpnn)