Index

_

__init__() (protflow.jobstarters.JobStarter method) (protflow.jobstarters.LocalJobStarter method) (protflow.jobstarters.SbatchArrayJobstarter method) (protflow.metrics.fpocket.FPocket method) (protflow.metrics.protparam.ProtParam 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.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) __str__() (protflow.runners.Runner method) (protflow.tools.boltz.Boltz 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) 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) from_selection() (protflow.residues.ResidueSelection method)

G

generate_yaml_files() (protflow.tools.boltz.BoltzParams method) generic_run_setup() (protflow.runners.Runner method) 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)

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

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.protparam) module protflow protflow.config_template protflow.jobstarters protflow.metrics protflow.metrics.fpocket 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.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) 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.protparam.ProtParam 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.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.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) 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) 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_include_center() (protflow.tools.residue_selectors.DistanceSelector method) set_jobstarter() (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_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) set_poses() (protflow.poses.Poses method) (protflow.tools.residue_selectors.ResidueSelector 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.MotifRMSD method) (protflow.metrics.rmsd.MotifSeparateSuperpositionRMSD method) singular_violinplot() (in module protflow.utils.plotting) 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.ResidueSelection method)

to_list() (protflow.residues.ResidueSelection method) to_rfdiffusion_contig() (protflow.residues.ResidueSelection method) to_string() (protflow.residues.ResidueSelection 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)