Index

Symbols

'read' command line option 'zero' command line option - command line option, [1] -- command line option --add_atom_types command line option --add_index_map command line option --add_templates command line option --all_dlg_poses command line option --bad_charge_ok command line option --blunt_ends command line option --box_center command line option --box_center_off_reactive_res command line option --box_enveloping command line option --box_size command line option --cache_templates command line option --charge_model command line option, [1] --compute_charges command line option --config_file command line option, [1] --config_preset command line option --debug_fn command line option --default_altloc command line option --delete_bad_res command line option --delete_bad_res_from_box_radius command line option --delete_residues command line option --double_bond_penalty command line option --eps_12 command line option --flexible_amides command line option --flexres command line option --hydrate command line option --keep_chorded_rings command line option --keep_equivalent_rings command line option --keep_flexres_sdf command line option --load_atom_params command line option --macrocycle_allow_A command line option --merge_these_atom_types command line option --min_ring_size command line option --mol command line option --multimol_outdir command line option --multimol_prefix command line option --multimol_targz command line option --multimol_targz_size command line option --name_from_prop command line option --out command line option --output_basename command line option --padding command line option --r_eq_12 command line option --r_eq_13_scaling command line option --r_eq_14_scaling command line option

--reactive_flexres command line option --reactive_name command line option --reactive_name_specific command line option --reactive_smarts command line option --reactive_smarts_idx command line option --read_json command line option --read_pdb command line option --read_pqr command line option --read_with_prody command line option --rec_residue command line option --receptor command line option --redirect_stdout command line option --remove_smiles command line option --rigid_macrocycles command line option --rigidify_bonds_indices command line option --rigidify_bonds_smarts command line option --rot_terminal_group command line option --set_template command line option --suffix command line option --tether_smarts command line option --tether_smarts_indices command line option --wanted_altloc command line option --write_gpf command line option --write_json command line option --write_pdb command line option, [1], [2] --write_pdbqt command line option --write_sdf command line option --write_vina_box command line option -a command line option -aa command line option -b command line option, [1] -c command line option -d command line option, [1] -f command line option -g command line option -i command line option, [1] -j command line option, [1] -k command line option -n command line option -o command line option, [1] -p command line option, [1], [2] -r command line option, [1] -s command line option, [1] -t command line option -v command line option -w command line option -z command line option `:5 command line option

C

can command line option command line option 'read' 'zero' -, [1] -- --add_atom_types --add_index_map --add_templates --all_dlg_poses --bad_charge_ok --blunt_ends --box_center --box_center_off_reactive_res --box_enveloping --box_size --cache_templates --charge_model, [1] --compute_charges --config_file, [1] --config_preset --debug_fn --default_altloc --delete_bad_res --delete_bad_res_from_box_radius --delete_residues --double_bond_penalty --eps_12 --flexible_amides --flexres --hydrate --keep_chorded_rings --keep_equivalent_rings --keep_flexres_sdf --load_atom_params --macrocycle_allow_A --merge_these_atom_types --min_ring_size --mol --multimol_outdir --multimol_prefix --multimol_targz --multimol_targz_size --name_from_prop --out --output_basename --padding --r_eq_12 --r_eq_13_scaling --r_eq_14_scaling --reactive_flexres --reactive_name --reactive_name_specific --reactive_smarts --reactive_smarts_idx --read_json --read_pdb --read_pqr --read_with_prody --rec_residue --receptor --redirect_stdout --remove_smiles --rigid_macrocycles --rigidify_bonds_indices --rigidify_bonds_smarts --rot_terminal_group --set_template --suffix --tether_smarts --tether_smarts_indices --wanted_altloc --write_gpf --write_json --write_pdb, [1], [2] --write_pdbqt --write_sdf --write_vina_box -a -aa -b, [1] -c -d, [1] -f -g -i, [1] -j, [1] -k -n -o, [1] -p, [1], [2] -r, [1] -s, [1] -t -v -w -z `:5 can cumulative Default, [1] docking_results_filename e.g. espaloma Flag for Log nagl on pre-calculated read] Specify, [1] the Turns which Write zero

cumulative command line option

D

Default command line option, [1]

docking_results_filename command line option

E

e.g. command line option

espaloma command line option

F

Flag command line option

for command line option

L

Log command line option

N

nagl command line option

O

on command line option

P

pre-calculated command line option

R

read] command line option

S

Specify command line option, [1]

T

the command line option

Turns command line option

W

which command line option

Write command line option

Z

zero command line option