Index

Symbols

--benchmark command line option --check_lig_matches command line option --config_file command line option --help command line option

--ref_ligase command line option --write_default command line option -h command line option

A

active_confs() (p4ward.tools.classes.ProtacPose method) (p4ward.tools.classes.Protein method)

active_poses() (p4ward.tools.classes.Protac method) arg_parser() (in module p4ward.config.config)

B

benchmark() (in module p4ward.benchmark.capri)

C

calc_fnat() (in module p4ward.benchmark.capri) calc_irms() (in module p4ward.benchmark.capri) calc_lrms() (in module p4ward.benchmark.capri) calc_rank() (in module p4ward.benchmark.capri) capture_rxdock_scores() (in module p4ward.run.protac_scoring) capture_scores() (in module p4ward.run.megadock) check_ligand_matches() (in module p4ward.run.protac_prep) check_linker_size() (in module p4ward.run.protac_prep) chimerax_view() (in module p4ward.analyse.summaries) Cluster (class in p4ward.tools.classes)

cluster() (in module p4ward.run.megadock) command line option --benchmark --check_lig_matches --config_file --help --ref_ligase --write_default -h conf_sampling() (in module p4ward.run.protac_run) crl_filters() (in module p4ward.run.protein_filter)

F

fix_proteins() (in module p4ward.run.md)

G

generate_protein_poses() (in module p4ward.analyse.rank) get_all_confs() (p4ward.tools.classes.Cluster method) get_atom_pairs() (in module p4ward.benchmark.capri) get_centroid() (p4ward.tools.classes.Cluster method) get_cl_from_pose() (p4ward.tools.classes.Cluster method) get_cl_size() (p4ward.tools.classes.Cluster method) get_coords_array() (in module p4ward.run.structure_tools) get_e3_modelfile() (in module p4ward.run.structure_tools) get_interface() (in module p4ward.benchmark.capri)

get_ligand_struct() (p4ward.tools.classes.Protein method) get_matches() (in module p4ward.run.protac_prep) get_pose() (p4ward.tools.classes.Protac method) get_protac_dist_cuttoff() (in module p4ward.run.structure_tools) get_protein_charges() (in module p4ward.run.md) get_protein_struct() (p4ward.tools.classes.Protein method) get_rmsd() (in module p4ward.run.structure_tools) get_rotated_struct() (p4ward.tools.classes.ProteinPose method) get_triad_points() (p4ward.tools.classes.Protein method)

I

interactive_plots() (in module p4ward.analyse.plot)

L

ligand_distances() (in module p4ward.run.protein_filter) LinkerConf (class in p4ward.tools.classes)

load_biopython_structures() (in module p4ward.run.structure_tools) load_run_objects() (in module p4ward.tools.run_tracker) load_tracker() (in module p4ward.tools.run_tracker)

M

make_config() (in module p4ward.config.config) make_indices_link() (in module p4ward.run.protac_prep) make_step_check() (in module p4ward.analyse.plot) make_structure() (in module p4ward.benchmark.capri) minimize_proteins() (in module p4ward.run.md) module p4ward.analyse.plot p4ward.analyse.rank p4ward.analyse.summaries p4ward.benchmark.capri p4ward.config.config p4ward.run.md p4ward.run.megadock p4ward.run.protac_prep p4ward.run.protac_run p4ward.run.protac_sampling p4ward.run.protac_scoring p4ward.run.protein_filter p4ward.run.structure_tools p4ward.tools.classes p4ward.tools.decorators p4ward.tools.logger p4ward.tools.run_tracker

P

p4ward.analyse.plot module p4ward.analyse.rank module p4ward.analyse.summaries module p4ward.benchmark.capri module p4ward.config.config module p4ward.run.md module p4ward.run.megadock module p4ward.run.protac_prep module p4ward.run.protac_run module p4ward.run.protac_sampling module p4ward.run.protac_scoring module p4ward.run.protein_filter module

p4ward.run.structure_tools module p4ward.tools.classes module p4ward.tools.decorators module p4ward.tools.logger module p4ward.tools.run_tracker module plot_funnel() (in module p4ward.analyse.plot) plot_pca() (in module p4ward.analyse.plot) plot_ppi() (in module p4ward.analyse.plot) plot_scatter() (in module p4ward.analyse.plot) prep_structures() (in module p4ward.run.megadock) Protac (class in p4ward.tools.classes) protac_prep() (in module p4ward.run.protac_prep) protac_sampling() (in module p4ward.run.protac_sampling) protac_summaries() (in module p4ward.analyse.summaries) ProtacPose (class in p4ward.tools.classes) Protein (class in p4ward.tools.classes) protein_poses() (in module p4ward.analyse.rank) ProteinPose (class in p4ward.tools.classes) pymol_align() (in module p4ward.run.structure_tools) pymol_combine() (in module p4ward.run.structure_tools)

R

rescore() (in module p4ward.analyse.rank) rotate_atoms() (in module p4ward.run.megadock)

run_docking() (in module p4ward.run.megadock) rxdock_rescore() (in module p4ward.run.protac_scoring)

S

sample_protac_pose() (in module p4ward.run.protac_sampling) sample_unbound_confs() (p4ward.tools.classes.Protac method) save_protein_objects() (in module p4ward.tools.run_tracker)

set_logging() (in module p4ward.tools.logger) structure_proximity() (in module p4ward.run.structure_tools) summary_csv() (in module p4ward.analyse.summaries)

T

top_protac() (p4ward.tools.classes.ProteinPose method)

track_run() (in module p4ward.tools.decorators)

U

user_choice() (in module p4ward.tools.decorators)

W

write_charges() (in module p4ward.run.structure_tools) write_crl_complex() (in module p4ward.analyse.summaries)

write_default_conf() (in module p4ward.config.config) write_unbound_confs() (p4ward.tools.classes.Protac method)