Index

Symbols | A | C | D | E | F | H | O | P | R | S

Symbols

-addbox <distance> [No Default]
receptor_setup command line option
-allowed_clashes
POSIT command line option
-allowedClashes
combine_receptors command line option
-annotate_scores [Default: false]
fred command line option
hybrid command line option
scorepose command line option
-bound_ligand <bound ligand file> [No Default]
receptor_setup command line option
-box <box file> [No Default]
receptor_setup command line option
-clashed_molecule_file <filename>
POSIT command line option
-clear_score_cache [Default: false]
receptor_toolbox command line option
-conftest <test type> [Default: isomeric]
POSIT command line option
fred command line option
hybrid command line option
scorepose command line option
-dbase <filename>
POSIT command line option
-dbase <input filename1> [<input filename2> ... ] [No Default: Required Parameter]
fred command line option
-dbase <input filename1> [<input filename2> ...] [No Default: Required Parameter]
hybrid command line option
-dbase <input filename1> [<input filename2> ...] [No Default: Required Parameter]
scorepose command line option
-disable_all_custom_constraints [Default: false]
receptor_toolbox command line option
-disable_all_protein_constraints [Default: false]
receptor_toolbox command line option
-disable_custom_constraint <constraint> [<constraint> ...] [No Default]
receptor_toolbox command line option
-disable_protein_constraint <name> [<name> ...] [No Default]
receptor_toolbox command line option
-dock_resolution <setting> [Default: Standard]
fred command line option
hybrid command line option
-docked_molecule_file <filename>
POSIT command line option
-docked_molecule_file <filename> [Default: docked.oeb.gz]
hybrid command line option
-docked_molecule_file <filename> [Default: docked.oeb.gz]
fred command line option
-docked_poses <filename> [No Default: Required Parameter]
docking_report command line option
-enable_all_custom_constraints [Default: false]
receptor_toolbox command line option
-enable_all_protein_constraints [Default: false]
receptor_toolbox command line option
-enable_custom_constraint <constraint> [<constraint> ...] [No Default]
receptor_toolbox command line option
-enable_protein_constraint <name> [<name> ...] [No Default]
receptor_toolbox command line option
-extract_bound_ligand <filename> [No Default]
receptor_toolbox command line option
-extract_custom_constraints <filename> [No Default]
receptor_toolbox command line option
-extract_extra_molecules <filename> [No Default]
receptor_toolbox command line option
-extract_protein <filename> [No Default]
receptor_toolbox command line option
-force_planar_aromatic
POSIT command line option
-hitlist_size
POSIT command line option
-hitlist_size <num> [Default: 500]
scorepose command line option
-hitlist_size <num> [Default: 500]
fred command line option
hybrid command line option
-ignore_nitrogen_stereo
POSIT command line option
-in <filename>
POSIT command line option
-ligand_residue <residue identifier> [No Default]
pdb2receptor command line option
-minimum_probability
POSIT command line option
-molnames
POSIT command line option
-molnames <input filename> [No Default]
fred command line option
hybrid command line option
scorepose command line option
-mpi_hostfile <filename>
POSIT command line option
-mpi_np <n>
POSIT command line option
-names <molecule name> [<molecule name> ...] [No Default]
docking_report command line option
-no_dots
POSIT command line option
-no_dots [Default: false]
fred command line option
hybrid command line option
scorepose command line option
-no_extra_output_files
POSIT command line option
-no_extra_output_files [Default: false]
hybrid command line option
scorepose command line option
-no_extra_output_files [Default: false]
fred command line option
-no_strip_water [Default: false]
receptor_setup command line option
-num_poses
POSIT command line option
-num_poses <num> [Default: 1]
fred command line option
hybrid command line option
-optimize <level> [No Default]
scorepose command line option
-outputall
POSIT command line option
-outputdir
combine_receptors command line option
-param
POSIT command line option
-param <filename>
combine_receptors command line option
-param <parameter filename> [No Default]
fred command line option
hybrid command line option
scorepose command line option
-pdb <filename> [No Default: Required Parameter]
apopdb2receptor command line option
pdb2receptor command line option
-prealigned
combine_receptors command line option
-prefix
POSIT command line option
combine_receptors command line option
-prefix <value> [Default: hybrid]
hybrid command line option
-prefix <value> [Default: fred]
fred command line option
-prefix <value> [Default: rescore]
scorepose command line option
-prepare_score_cache <fred, scorepose or hybrid> [No Default]
receptor_toolbox command line option
-protein <input filename> [No Default: Required Parameter]
receptor_setup command line option
-receptor <filename> [Default: receptor.oeb.gz]
pdb2receptor command line option
receptor_setup command line option
-receptor <filename> [Default: receptor.oeb.gz]
apopdb2receptor command line option
-receptor <filename> [<filename> ...] [No Default: Required Parameter]
docking_report command line option
-receptor <filenames>
POSIT command line option
-receptor <receptor file1> [<receptor file2> ...] [No Default: Required Parameter]
hybrid command line option
-receptor <receptor file> [No Default: Required Parameter]
fred command line option
receptor_toolbox command line option
scorepose command line option
-receptors <filenames>
combine_receptors command line option
-rejected_file
POSIT command line option
-report_file
POSIT command line option
-report_file <filename> [Default: docking_report.pdf]
docking_report command line option
-report_file <filename> [Default: report.txt]
fred command line option
hybrid command line option
scorepose command line option
-rescored_mol_output_file <output filename> [Default: scored.oeb.gz]
scorepose command line option
-save_component_scores [Default: false]
fred command line option
hybrid command line option
scorepose command line option
-score_file
POSIT command line option
-score_file <filename> [Default: score.txt]
fred command line option
hybrid command line option
scorepose command line option
-score_tag
POSIT command line option
-score_tag <score tag> [No Default]
fred command line option
-score_tag <tag> [No Default]
scorepose command line option
-score_tag <tag> [No Default]
hybrid command line option
-sd_tags <Tag> [<Tag> ...] [No Default]
docking_report command line option
-set_bound_ligand_title <title> [No Default]
receptor_toolbox command line option
-set_custom_constraints <filename> [No Default]
receptor_toolbox command line option
-set_receptor_title <title> [No Default]
receptor_toolbox command line option
-settings_file
POSIT command line option
-settings_file <filename> [Default: settings.param]
fred command line option
hybrid command line option
scorepose command line option
-site_residue <residue identifier> [No Default: Required Parameter]
apopdb2receptor command line option
-smiles_file <filename> [No Default]
docking_report command line option
-solvent_residues <name> [<name> ...] [Default: HOH]
apopdb2receptor command line option
-solvent_residues <name> [<name> ...] [Default: HOH]
pdb2receptor command line option
-sort_poses [Default: false]
scorepose command line option
-sortby
POSIT command line option
-status_file
POSIT command line option
-status_file <filename> [Default: status.txt]
fred command line option
hybrid command line option
scorepose command line option
-turn_inner_contour <on or off> [No Default]
receptor_toolbox command line option
-undocked_molecule_file
POSIT command line option
-undocked_molecule_file <filename> [Default: undocked.oeb.gz]
fred command line option
hybrid command line option
-verbose
combine_receptors command line option

A

apopdb2receptor command line option
-pdb <filename> [No Default: Required Parameter]
-receptor <filename> [Default: receptor.oeb.gz]
-site_residue <residue identifier> [No Default: Required Parameter]
-solvent_residues <name> [<name> ...] [Default: HOH]
APPNAME_OE_ARCH

C

combine_receptors command line option
-allowedClashes
-outputdir
-param <filename>
-prealigned
-prefix
-receptors <filenames>
-verbose

D

docking_report command line option
-docked_poses <filename> [No Default: Required Parameter]
-names <molecule name> [<molecule name> ...] [No Default]
-receptor <filename> [<filename> ...] [No Default: Required Parameter]
-report_file <filename> [Default: docking_report.pdf]
-sd_tags <Tag> [<Tag> ...] [No Default]
-smiles_file <filename> [No Default]

E

environment variable
APPNAME_OE_ARCH
OE_ARCH, [1], [2], [3]
OE_LICENSE
PATH, [1], [2], [3], [4]

F

fred command line option
-annotate_scores [Default: false]
-conftest <test type> [Default: isomeric]
-dbase <input filename1> [<input filename2> ... ] [No Default: Required Parameter]
-dock_resolution <setting> [Default: Standard]
-docked_molecule_file <filename> [Default: docked.oeb.gz]
-hitlist_size <num> [Default: 500]
-molnames <input filename> [No Default]
-no_dots [Default: false]
-no_extra_output_files [Default: false]
-num_poses <num> [Default: 1]
-param <parameter filename> [No Default]
-prefix <value> [Default: fred]
-receptor <receptor file> [No Default: Required Parameter]
-report_file <filename> [Default: report.txt]
-save_component_scores [Default: false]
-score_file <filename> [Default: score.txt]
-score_tag <score tag> [No Default]
-settings_file <filename> [Default: settings.param]
-status_file <filename> [Default: status.txt]
-undocked_molecule_file <filename> [Default: undocked.oeb.gz]

H

hybrid command line option
-annotate_scores [Default: false]
-conftest <test type> [Default: isomeric]
-dbase <input filename1> [<input filename2> ...] [No Default: Required Parameter]
-dock_resolution <setting> [Default: Standard]
-docked_molecule_file <filename> [Default: docked.oeb.gz]
-hitlist_size <num> [Default: 500]
-molnames <input filename> [No Default]
-no_dots [Default: false]
-no_extra_output_files [Default: false]
-num_poses <num> [Default: 1]
-param <parameter filename> [No Default]
-prefix <value> [Default: hybrid]
-receptor <receptor file1> [<receptor file2> ...] [No Default: Required Parameter]
-report_file <filename> [Default: report.txt]
-save_component_scores [Default: false]
-score_file <filename> [Default: score.txt]
-score_tag <tag> [No Default]
-settings_file <filename> [Default: settings.param]
-status_file <filename> [Default: status.txt]
-undocked_molecule_file <filename> [Default: undocked.oeb.gz]

O

OE_ARCH, [1], [2], [3]
OE_LICENSE

P

PATH, [1], [2], [3], [4]
pdb2receptor command line option
-ligand_residue <residue identifier> [No Default]
-pdb <filename> [No Default: Required Parameter]
-receptor <filename> [Default: receptor.oeb.gz]
-solvent_residues <name> [<name> ...] [Default: HOH]
POSIT command line option
-allowed_clashes
-clashed_molecule_file <filename>
-conftest <test type> [Default: isomeric]
-dbase <filename>
-docked_molecule_file <filename>
-force_planar_aromatic
-hitlist_size
-ignore_nitrogen_stereo
-in <filename>
-minimum_probability
-molnames
-mpi_hostfile <filename>
-mpi_np <n>
-no_dots
-no_extra_output_files
-num_poses
-outputall
-param
-prefix
-receptor <filenames>
-rejected_file
-report_file
-score_file
-score_tag
-settings_file
-sortby
-status_file
-undocked_molecule_file

R

receptor_setup command line option
-addbox <distance> [No Default]
-bound_ligand <bound ligand file> [No Default]
-box <box file> [No Default]
-no_strip_water [Default: false]
-protein <input filename> [No Default: Required Parameter]
-receptor <filename> [Default: receptor.oeb.gz]
receptor_toolbox command line option
-clear_score_cache [Default: false]
-disable_all_custom_constraints [Default: false]
-disable_all_protein_constraints [Default: false]
-disable_custom_constraint <constraint> [<constraint> ...] [No Default]
-disable_protein_constraint <name> [<name> ...] [No Default]
-enable_all_custom_constraints [Default: false]
-enable_all_protein_constraints [Default: false]
-enable_custom_constraint <constraint> [<constraint> ...] [No Default]
-enable_protein_constraint <name> [<name> ...] [No Default]
-extract_bound_ligand <filename> [No Default]
-extract_custom_constraints <filename> [No Default]
-extract_extra_molecules <filename> [No Default]
-extract_protein <filename> [No Default]
-prepare_score_cache <fred, scorepose or hybrid> [No Default]
-receptor <receptor file> [No Default: Required Parameter]
-set_bound_ligand_title <title> [No Default]
-set_custom_constraints <filename> [No Default]
-set_receptor_title <title> [No Default]
-turn_inner_contour <on or off> [No Default]

S

scorepose command line option
-annotate_scores [Default: false]
-conftest <test type> [Default: isomeric]
-dbase <input filename1> [<input filename2> ...] [No Default: Required Parameter]
-hitlist_size <num> [Default: 500]
-molnames <input filename> [No Default]
-no_dots [Default: false]
-no_extra_output_files [Default: false]
-optimize <level> [No Default]
-param <parameter filename> [No Default]
-prefix <value> [Default: rescore]
-receptor <receptor file> [No Default: Required Parameter]
-report_file <filename> [Default: report.txt]
-rescored_mol_output_file <output filename> [Default: scored.oeb.gz]
-save_component_scores [Default: false]
-score_file <filename> [Default: score.txt]
-score_tag <tag> [No Default]
-settings_file <filename> [Default: settings.param]
-sort_poses [Default: false]
-status_file <filename> [Default: status.txt]