Index

Symbols

-acolor <color> command line option -addbox <distance> [No Default] receptor_setup command line option -addfraglib omega command line option -addtorlib omega command line option -all <format> command line option -allowed_clashes posit command line option -allowedClashes combine_receptors command line option -am1bcc szybki command line option -annotate_scores [Default: false] fred command line option hybrid command line option scorepose command line option -apo_box <filename> command line option, [1] -apo_coords command line option -apo_grids command line option -apo_point_grid command line option -aromstyle <style> command line option rocs_report command line option -around <filename> command line option -around_mol <filename> command line option -astl <style> command line option rocs_report command line option -at_coords <filename> command line option, [1] -atomcolor <color> command line option -atomsstl <style> command line option -atomstereostyle <style> command line option -attachColor brood command line option -attachFrag brood command line option -attachmentCutoff (-attachcut) brood command line option -attachmentScale (-attach, -aScale) brood command line option -base <NAME> command line option -bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax> command line option -bcolor <color> command line option -besthits <N> eon command line option rocs command line option -besthits N command line option -biggerisbetter command line option -bondcolor <color> command line option -bondOrder (-bo) brood command line option -bondsstl <style> command line option -bondstereostyle <style> command line option -bound_ligand <bound ligand file> [No Default] receptor_setup command line option -boundary <number> command line option -boundary_radius <number> command line option -boundary_spacing <number> command line option -bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax> command line option -box <box file> [No Default] receptor_setup command line option -box_mol <filename> command line option, [1] -buildff makefraglib command line option omega command line option -bumpRadius brood command line option -by <number> command line option -calc <run_type> freeform command line option -canonOrder omega command line option -capAttach chomp command line option -ch3 tautomers command line option -chain <letter> command line option -charges eon command line option -checkBond (-checkbond) brood command line option -checkGeometry brood command line option -chemff <cff_file> checkcff command line option -chemff <cffname> rocs command line option -chunksize M command line option -clashed_molecule_file <filename> posit command line option -clean <bool> command line option -clear_score_cache [Default: false] receptor_toolbox command line option -cols <number> command line option -commentEnergy omega command line option -complex <filename> szybki command line option -conflabel rocs command line option -conftest <test type> [Default: isomeric] fred command line option hybrid command line option posit command line option scorepose command line option -coords <filename> command line option, [1] -count pkatyper command line option -countConfs command line option -cpddb brood command line option -cplx_grids command line option -csv brood command line option -current_charges szybki command line option -cutoff <F> rocs command line option -cutoff <number> command line option -cutoff <score> eon command line option -db (-database) brood command line option -dbase <filename> eon command line option posit command line option rocs command line option -dbase <input filename1> [<input filename2> ... ] fred command line option -dbase <input filename1> [<input filename2> ...] hybrid command line option scorepose command line option -dcutoff <number> command line option -default <number> command line option -default_value <number> command line option -deleteFixHydrogens omega command line option -dielectric omega command line option -dielectric_constant macrocycle command line option -dielectric_model <type> 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 -distance_cutoff <number> 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> docking_report command line option -dots brood command line option chomp command line option command line option -eganEgg (-egan) brood 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 -ensemble freeform command line option -entropy <type> szybki command line option -enumNitrogen flipper command line option omega command line option -enumRing omega command line option -eon_input rocs command line option -eon_input_file <filename> rocs command line option -eon_input_size <N> rocs command line option -eon_maxconfs <N> rocs command line option -eps_in <number> command line option -eps_out <number> command line option -erange omega command line option -ET (-et) brood command line option -ewindow eon command line option freeform command line option macrocycle command line option makefraglib command line option omega command line option -exact_vdw szybki command line option -exponent omega 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 -fail command line option -ff szybki command line option -ff <type> freeform command line option -fileChrg brood command line option -filter chomp command line option command line option -fix_elements command line option -fix_file <filename> szybki command line option -fix_smarts <file_name> szybki command line option -fixfile omega command line option -fixpka_dbase eon command line option -fixpka_query eon command line option -fixrms omega command line option -fixsmarts omega command line option -flex_file <filename> szybki command line option -flexdist <d> szybki command line option -flexlist <fn> szybki command line option -flextype <type> szybki command line option -flipN chomp command line option -flipper chomp command line option omega command line option -flipper_maxcenters omega command line option -flipper_warts omega command line option -forcefield brood command line option -forceflip flipper command line option -forceFlip chomp command line option -format brood command line option -fromCT brood command line option makefraglib command line option omega command line option -g <name> command line option -geq <number> command line option -geq_mask <number> command line option -grad_conv <c> szybki command line option -grid <name> command line option -grid1 <name> command line option -grid2 <name> command line option -grid3 <name> command line option -grid_spacing <number> command line option -grids <type> command line option -harm_constr1 <k> szybki command line option -harm_constr2 <d> szybki command line option -harm_smarts <file.txt> szybki command line option -heavy_rms szybki command line option -hitinterval brood 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 -hitlistProt brood command line option -hitsfile <filename> eon command line option rocs command line option -i <filename> command line option rocs_report command line option -i <filename> command line option, [1], [2], [3], [4] freeform command line option szybki command line option -idea (-cluster) brood command line option -ignore_nitrogen_stereo posit command line option -in command line option, [1] fixpa command line option flipper command line option macrocycle command line option makefraglib command line option molcharge command line option pkatyper command line option tautomers command line option -in (-i) chomp command line option -in <filename> checkcff command line option command line option, [1] freeform command line option makerocsdb command line option posit command line option rocs_report command line option szybki command line option -in1 (-i1) command line option -in1 <filename> command line option -in2 (-i2) command line option -in2 <filename> command line option -in3 <filename> command line option -includeInput omega command line option -info brood command line option command line option -inner_dielectric <d> szybki command line option -inner_dielectric <number> command line option -input <filename> command line option -input_file1 <filename> command line option -input_file2 <filename> command line option -input_file3 <filename> command line option -input_mol <filename> command line option, [1], [2], [3] -inscode <letter> command line option -int_method <value> command line option -interval brood command line option command line option -ionic <type> freeform command line option -ionize fixpa command line option -iteration_cycle_size macrocycle command line option -keep_alts command line option -keep_hydrogens command line option -keep_numbers command line option -keepFailures szybki command line option -l <filename> command line option, [1], [2] szybki command line option -largest_part szybki command line option -legend <bool> command line option -leq <number> command line option -leq_mask <number> command line option -lig_box <filename> command line option, [1] -lig_ch <char> command line option -lig_coords command line option -lig_end <int> command line option -lig_grids command line option -lig_ins <char> command line option -lig_model <int> command line option -lig_num <int> command line option -lig_point_grid command line option -lig_res <RES> command line option -ligand <filename> command line option, [1] -ligand_chain <char> command line option -ligand_inscode <char> command line option -ligand_model <int> command line option -ligand_res <RES> command line option -ligand_residue <residue identifier> pdb2receptor command line option -ligand_resnum <int> command line option -ligand_resnum_end <int> command line option -ligands <filename> szybki command line option -light_background command line option -light_bkg command line option -like_apo <filename> command line option -like_box <filename> command line option -like_lig <filename> command line option -like_std <filename> command line option -linkOnly (-linkonly, -struc, -struct) brood command line option -loadPG <filename> szybki command line option -log brood command line option command line option makefraglib command line option omega command line option -log <filename> command line option, [1] -log <prefix> szybki command line option -logfile <filename> command line option, [1] eon command line option rocs command line option -mask_cutoff <number> command line option, [1] -mask_vdw command line option -masked_point_cutoff <number> command line option -max pkatyper command line option -max_iter <m> szybki command line option -max_iterations macrocycle command line option -maxAromFJCt brood command line option -maxcenters flipper command line option -maxChiral chomp command line option -maxComplexity (-maxComp) brood command line option -maxConfRange omega command line option -maxconfs macrocycle command line option omega command line option -maxconfs <N> rocs command line option -maxconfs <value> freeform command line option -maxDegree chomp command line option -maxFrag brood command line option -maxFrequency (-maxFreq) brood command line option -maxFsp3C brood command line option -maxgenerated tautomers command line option -maxHit (-maxhit) brood command line option -maxhits <N> eon command line option rocs command line option -maxHvy chomp command line option -maxHvyAtom (-maxHeavyAtom) brood command line option -maxLipinski brood command line option -maxLipinskiAcc (-maxLipinskiAcceptors, -maxAcceptors) brood command line option -maxLipinskiDon (-maxLipinskiDonors, -maxDonors) brood command line option -maxLocalStrain brood command line option -maxlogp brood command line option -maxMartin (-maxAbbott, -maxABS) brood command line option -maxmatch omega command line option -maxMolWt chomp command line option -maxMolWt (-maxmolecularweight) brood command line option -maxpages rocs_report command line option -maxpsa (-maxtpsa) brood command line option -maxrot omega command line option -maxRotBond (-maxRotatableBond) brood command line option -maxtautomericatoms tautomers command line option -maxtime omega command line option tautomers command line option -maxtoreturn tautomers command line option -maxzonesize tautomers command line option -mcquery rocs command line option -merge <number> command line option -method <value> command line option -method {option} molcharge command line option -minAromFJCt brood command line option -minComplexity (-minComp) brood command line option -minDegree chomp command line option -minFrequency chomp command line option -minFrequency (-minFreq) brood command line option -minFsp3C brood command line option -minHvy chomp command line option -minHvyAtom (-minHeavyAtom) brood command line option -minimum_probability posit command line option

-minLipinski brood command line option -minLipinskiAcc (-minLipinskiAcceptors, -minAcceptors) brood command line option -minLipinskiDon (-minLipinskiDonors, -minDonors) brood command line option -minlogp brood command line option -minMartin (-minAbbott, -minABS) brood command line option -minMolWt (-minmolecularweight) brood command line option -minpsa (-mintpsa) brood command line option -minRotBond (-minRotatableBond) brood command line option -mod_vdw szybki command line option -model <type> command line option -mol <filename> 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 brood command line option macrocycle command line option -mpi_hostfile <filename> command line option eon command line option makefraglib command line option omega command line option posit command line option rocs command line option szybki command line option -mpi_np brood command line option macrocycle command line option -mpi_np <n> eon command line option makefraglib command line option omega command line option posit command line option rocs command line option szybki command line option -mpi_np <number> command line option -names <molecule name> [<molecule name> ...] [No Default] docking_report command line option -nchunks N command line option -neglect_frozen szybki command line option -neutralpH brood command line option -new_value <number> command line option -newrule 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_fixup command line option -no_pka_adjustment command line option -no_strip_water [Default: false] receptor_setup command line option -no_table command line option -noadj command line option -noCoulomb szybki command line option -nonsym command line option -nonsymmetrized_charges command line option -noqueryprot (-noqueryprotein) brood command line option -noqueryselectprot (-noqueryselectionprotein, -noqueryselection) brood command line option -normalize command line option -nostructs rocs command line option -num_orientations <number> command line option, [1] -num_poses posit command line option -num_poses <num> [Default: 1] fred command line option hybrid command line option -o <filename> command line option rocs_report command line option -o <filename.txt> command line option -o <filename> command line option, [1], [2], [3], [4] szybki command line option -oformat <extension> eon command line option rocs command line option -omega chomp command line option -op <value> command line option -operation <value> command line option -opt rocs command line option -optchem rocs command line option -optdof szybki command line option -optDOF szybki command line option -optGeometry <dof> szybki command line option -optimize <level> [No Default] scorepose command line option -optMethod <type> szybki command line option -out command line option, [1] fixpa command line option flipper command line option macrocycle command line option makefraglib command line option molcharge command line option pkatyper command line option tautomers command line option -out (-o) chomp command line option command line option -out <filename> command line option freeform command line option rocs_report command line option szybki command line option -out <oebfile> checkcff command line option -out <prefix> makerocsdb command line option -out_complex <filename> szybki command line option -out_protein <filename> szybki command line option -outer_dielectric <number> command line option -output <filename> command line option, [1] -output_all_format <format> command line option -output_grid <filename> command line option, [1] -output_lig <filename> command line option -output_mol <filename> command line option, [1], [2] -output_prot <filename> command line option -output_txt <filename.txt> command line option -output_waters <filename> command line option -outputall posit command line option -outputdir combine_receptors command line option -outputdir <dirname> rocs command line option -outputquery eon command line option rocs command line option -overwrite (-over) command line option -p <filename> command line option, [1], [2] szybki command line option -pad_zeros command line option -pagesize <size> command line option rocs_report command line option -param brood command line option command line option eon command line option macrocycle command line option makefraglib command line option molcharge command line option omega command line option pkatyper command line option posit command line option rocs command line option szybki command line option tautomers command line option -param <filename> combine_receptors command line option command line option, [1] freeform command line option -param <parameter filename> [No Default] fred command line option hybrid command line option scorepose command line option -paramfile molcharge command line option pkatyper command line option tautomers command line option -PBsolvent_dielectric <value> freeform command line option -pdb <filename> apopdb2receptor command line option pdb2receptor command line option -pendingFile omega command line option -pkanorm command line option tautomers command line option -point_grid command line option -prealigned combine_receptors command line option -prefix brood command line option chomp command line option combine_receptors command line option command line option macrocycle command line option makefraglib command line option molcharge command line option omega command line option pkatyper command line option posit command line option tautomers command line option -prefix <name> rocs command line option -prefix <p> freeform command line option -prefix <pn> szybki command line option -prefix <prefix> command line option, [1] eon command line option -prefix <text> 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 -primaryFrag chomp command line option -progress eon command line option makefraglib command line option omega command line option -progress <method> rocs command line option -progress <style> command line option, [1] -properties <type> command line option -property (-prop) brood command line option -prot (-protein) brood command line option -protein <filename> command line option, [1] szybki command line option -protein <input filename> receptor_setup command line option -protein_elec <m> szybki command line option -protein_vdw <r> szybki command line option -psize <size> rocs_report command line option -qconflabel rocs command line option -query <filename> eon command line option rocs command line option -queryFragment (-queryFrag) brood command line option -queryMol (-qMol) brood command line option -quickLook (-quick) brood command line option -radii <type> szybki command line option -randomstarts <N> rocs command line option -rangeIncrement omega command line option -rangeOffset brood command line option -rangeSize brood command line option -rank tautomers command line option -rankby <score> eon command line option rocs command line option -rankby <SD tag> command line option -readConfs chomp 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> ...] docking_report command line option -receptor <filenames> posit command line option -receptor <receptor file1> [<receptor file2> ...] hybrid command line option -receptor <receptor file> fred command line option receptor_toolbox command line option scorepose command line option -receptors <filenames> combine_receptors command line option -ref_tolerance macrocycle command line option -refmol <filename> rocs_report command line option -rejected_file posit command line option -removeDuplicates (-duplicates) command line option -report brood command line option rocs command line option szybki command line option -report <filename> checkcff command line option freeform 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 -reportfile <filename> eon command line option rocs command line option -reportFile <filename> szybki command line option -res <number> command line option -rescored_mol_output_file <output filename> [Default: scored.oeb.gz] scorepose command line option -residue_chain <letter> command line option -residue_insert <letter> command line option -residue_number <number> command line option -resolution <level> command line option -restrict_calc <level> command line option -results_set <type> command line option -ringOnly (-ring) brood command line option -rms eon command line option macrocycle command line option makefraglib command line option omega command line option -rms <value> freeform command line option -rmsd_deduplicate macrocycle command line option -rmsrange omega command line option -rot <number> command line option, [1] -rotorOffsetCompress omega command line option -rows <number> command line option -salt command line option eon command line option -salt <c> szybki command line option -salt <number> command line option -salt_conc <number> command line option -sampleHydrogens eon command line option omega command line option -save_component_scores [Default: false] fred command line option hybrid command line option scorepose command line option -savePG <filename> szybki command line option -scale <number> command line option -scdbase eon command line option rocs 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 -scoreonly eon command line option rocs command line option -sd_tags <Tag> [<Tag> ...] [No Default] docking_report command line option -sdEnergy omega command line option -sdtag brood command line option command line option -sdtag <string> szybki command line option -sdTags eon command line option rocs command line option -searchff omega command line option -select command line option -select (-selection) brood command line option -separate 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 -setfraglib omega 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 -settorlib omega command line option -shapeCutoff brood command line option -shapeonly rocs command line option -shefA <a> szybki command line option -shefB <b> szybki command line option -sheffield szybki command line option -silent szybki command line option -site_residue <residue identifier> apopdb2receptor command line option -size <size> command line option -skip makefraglib command line option -slice command line option -smarts chomp command line option -smiles_file <filename> [No Default] docking_report command line option -solv_dielectric <d> szybki command line option -solvcharges <type> freeform command line option -solvent <type> freeform command line option -solvent_residues <name> [<name> ...] [Default: HOH] apopdb2receptor command line option -solvent_residues <name> [<name> ...] [Default: HOH] pdb2receptor command line option -solventCA <s> szybki command line option -solventPB szybki command line option -sort_poses [Default: false] scorepose command line option -sortby posit command line option -sp3_aromatic <bool> command line option -sp3aromatic <bool> command line option -space <number> command line option -spacing eon command line option -split_lig command line option -stabilization command line option -stabilization <bool> command line option -standard_grids command line option -startfact makefraglib command line option -stats rocs command line option -status omega command line option rocs 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 -statusfile eon command line option -statusfile <filename> rocs command line option -stbl command line option -stbl <bool> command line option -std_box <filename> command line option, [1] -std_coords command line option -std_grids command line option -stereo tautomers command line option -strict omega command line option szybki command line option -strictatomtyping omega command line option -strictfrags omega command line option -strictstereo omega command line option -strip_water szybki command line option -subrocs rocs command line option -subtan rocs command line option -surf command line option -surface <bool> command line option -surface_points command line option -szmap_mpi_hostfile <filename> command line option -szmap_mpi_np <number> command line option -t szybki command line option -t <prop> command line option -table command line option -table <filename> command line option -tableFlag command line option -tag_set <set> command line option -tagname <prop> command line option -tanimoto_cutoff <F> rocs command line option -tautomer brood command line option -title brood command line option -title <text> command line option -to <number> command line option -tor_constr <fn> szybki command line option -torlibtype omega command line option -track <filename> freeform command line option -turn_inner_contour <on or off> [No Default] receptor_toolbox command line option -typecheck command line option -umatch omega 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 -unique command line option -use_apo_from <filename> command line option -userFrags chomp command line option -userUnique chomp command line option -v command line option, [1], [2], [3], [4], [5], [6], [7] -value_cutoff <number> command line option -vcutoff <number> command line option -vdw_cutoff szybki command line option -vdw_scale <number> command line option -veber (-gsk) brood command line option -verbose combine_receptors command line option command line option, [1], [2], [3], [4], [5], [6], [7] eon command line option makefraglib command line option omega command line option rocs command line option rocs_report command line option szybki command line option -verbose (-v) command line option -warn_if_missing_hydrogens command line option, [1] -warts flipper command line option omega command line option tautomers command line option -water_charge <type> command line option -waters <filename> command line option -writegrid eon command line option -zap_spacing <number> command line option

A

Analog Search apopdb2receptor command line option -pdb <filename> -receptor <filename> [Default: receptor.oeb.gz] -site_residue <residue identifier> -solvent_residues <name> [<name> ...] [Default: HOH] Appending Data

Appendix 1 Appendix 2 APPNAME_OE_ARCH

B

brood command line option -ET (-et) -attachColor -attachFrag -attachmentCutoff (-attachcut) -attachmentScale (-attach, -aScale) -bondOrder (-bo) -bumpRadius -checkBond (-checkbond) -checkGeometry -cpddb -csv -db (-database) -dots -eganEgg (-egan) -fileChrg -forcefield -format -fromCT -hitinterval -hitlistProt -idea (-cluster) -info -interval -linkOnly (-linkonly, -struc, -struct) -log -maxAromFJCt -maxComplexity (-maxComp) -maxFrag -maxFrequency (-maxFreq) -maxFsp3C -maxHit (-maxhit) -maxHvyAtom (-maxHeavyAtom) -maxLipinski -maxLipinskiAcc (-maxLipinskiAcceptors, -maxAcceptors) -maxLipinskiDon (-maxLipinskiDonors, -maxDonors) -maxLocalStrain -maxMartin (-maxAbbott, -maxABS) -maxMolWt (-maxmolecularweight) -maxRotBond (-maxRotatableBond) -maxlogp -maxpsa (-maxtpsa) -minAromFJCt -minComplexity (-minComp) -minFrequency (-minFreq) -minFsp3C -minHvyAtom (-minHeavyAtom) -minLipinski -minLipinskiAcc (-minLipinskiAcceptors, -minAcceptors) -minLipinskiDon (-minLipinskiDonors, -minDonors) -minMartin (-minAbbott, -minABS) -minMolWt (-minmolecularweight) -minRotBond (-minRotatableBond) -minlogp -minpsa (-mintpsa) -mpi_hostfile -mpi_np -neutralpH -noqueryprot (-noqueryprotein) -noqueryselectprot (-noqueryselectionprotein, -noqueryselection) -param -prefix -property (-prop) -prot (-protein) -queryFragment (-queryFrag) -queryMol (-qMol) -quickLook (-quick) -rangeOffset -rangeSize -report -ringOnly (-ring) -sdtag -select (-selection) -shapeCutoff -tautomer -title -veber (-gsk)

C

checkcff command line option -chemff <cff_file> -in <filename> -out <oebfile> -report <filename> chomp command line option -capAttach -dots -filter -flipN -flipper -forceFlip -in (-i) -maxChiral -maxDegree -maxHvy -maxMolWt -minDegree -minFrequency -minHvy -omega -out (-o) -prefix -primaryFrag -readConfs -smarts -userFrags -userUnique

combine_receptors command line option -allowedClashes -outputdir -param <filename> -prealigned -prefix -receptors <filenames> -verbose command line option -acolor <color> -all <format> -apo_box <filename>, [1] -apo_coords -apo_grids -apo_point_grid -aromstyle <style> -around <filename> -around_mol <filename> -astl <style> -at_coords <filename>, [1] -atomcolor <color> -atomsstl <style> -atomstereostyle <style> -base <NAME> -bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax> -bcolor <color> -besthits N -biggerisbetter -bondcolor <color> -bondsstl <style> -bondstereostyle <style> -boundary <number> -boundary_radius <number> -boundary_spacing <number> -bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax> -box_mol <filename>, [1] -by <number> -chain <letter> -chunksize M -clean <bool> -cols <number> -coords <filename>, [1] -countConfs -cplx_grids -cutoff <number> -dcutoff <number> -default <number> -default_value <number> -dielectric_model <type> -distance_cutoff <number> -dots -eps_in <number> -eps_out <number> -fail -filter -fix_elements -g <name> -geq <number> -geq_mask <number> -grid <name> -grid1 <name> -grid2 <name> -grid3 <name> -grid_spacing <number> -grids <type> -i <filename> -i <filename>, [1], [2], [3], [4] -in, [1] -in <filename>, [1] -in1 (-i1) -in1 <filename> -in2 (-i2) -in2 <filename> -in3 <filename> -info -inner_dielectric <number> -input <filename> -input_file1 <filename> -input_file2 <filename> -input_file3 <filename> -input_mol <filename>, [1], [2], [3] -inscode <letter> -int_method <value> -interval -keep_alts -keep_hydrogens -keep_numbers -l <filename>, [1], [2] -legend <bool> -leq <number> -leq_mask <number> -lig_box <filename>, [1] -lig_ch <char> -lig_coords -lig_end <int> -lig_grids -lig_ins <char> -lig_model <int> -lig_num <int> -lig_point_grid -lig_res <RES> -ligand <filename>, [1] -ligand_chain <char> -ligand_inscode <char> -ligand_model <int> -ligand_res <RES> -ligand_resnum <int> -ligand_resnum_end <int> -light_background -light_bkg -like_apo <filename> -like_box <filename> -like_lig <filename> -like_std <filename> -log -log <filename>, [1] -logfile <filename>, [1] -mask_cutoff <number>, [1] -mask_vdw -masked_point_cutoff <number> -merge <number> -method <value> -model <type> -mol <filename> -mpi_hostfile <filename> -mpi_np <number> -nchunks N -new_value <number> -newrule -no_fixup -no_pka_adjustment -no_table -noadj -nonsym -nonsymmetrized_charges -normalize -num_orientations <number>, [1] -o <filename> -o <filename.txt> -o <filename>, [1], [2], [3], [4] -op <value> -operation <value> -out, [1] -out (-o) -out <filename> -outer_dielectric <number> -output <filename>, [1] -output_all_format <format> -output_grid <filename>, [1] -output_lig <filename> -output_mol <filename>, [1], [2] -output_prot <filename> -output_txt <filename.txt> -output_waters <filename> -overwrite (-over) -p <filename>, [1], [2] -pad_zeros -pagesize <size> -param -param <filename>, [1] -pkanorm -point_grid -prefix -prefix <prefix>, [1] -prefix <text> -progress <style>, [1] -properties <type> -protein <filename>, [1] -rankby <SD tag> -removeDuplicates (-duplicates) -res <number> -residue_chain <letter> -residue_insert <letter> -residue_number <number> -resolution <level> -restrict_calc <level> -results_set <type> -rot <number>, [1] -rows <number> -salt -salt <number> -salt_conc <number> -scale <number> -sdtag -select -separate -size <size> -slice -sp3_aromatic <bool> -sp3aromatic <bool> -space <number> -split_lig -stabilization -stabilization <bool> -standard_grids -stbl -stbl <bool> -std_box <filename>, [1] -std_coords -std_grids -surf -surface <bool> -surface_points -szmap_mpi_hostfile <filename> -szmap_mpi_np <number> -t <prop> -table -table <filename> -tableFlag -tag_set <set> -tagname <prop> -title <text> -to <number> -typecheck -unique -use_apo_from <filename> -v, [1], [2], [3], [4], [5], [6], [7] -value_cutoff <number> -vcutoff <number> -vdw_scale <number> -verbose, [1], [2], [3], [4], [5], [6], [7] -verbose (-v) -warn_if_missing_hydrogens, [1] -water_charge <type> -waters <filename> -zap_spacing <number>

D

docking_report command line option -docked_poses <filename> -names <molecule name> [<molecule name> ...] [No Default] -receptor <filename> [<filename> ...] -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_DIR OE_LICENSE PATH, [1], [2], [3], [4], [5] eon command line option -besthits <N> -charges -cutoff <score> -dbase <filename> -ewindow -fixpka_dbase -fixpka_query -hitsfile <filename> -logfile <filename> -maxhits <N> -mpi_hostfile <filename> -mpi_np <n> -oformat <extension> -outputquery -param -prefix <prefix> -progress -query <filename> -rankby <score> -reportfile <filename> -rms -salt -sampleHydrogens -scdbase -scoreonly -sdTags -spacing -statusfile -verbose -writegrid

Exact Search

F

fixpa command line option -in -ionize -out flipper command line option -enumNitrogen -forceflip -in -maxcenters -out -warts

fred command line option -annotate_scores [Default: false] -conftest <test type> [Default: isomeric] -dbase <input filename1> [<input filename2> ... ] -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> -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] freeform command line option -PBsolvent_dielectric <value> -calc <run_type> -ensemble -ewindow -ff <type> -i <filename> -in <filename> -ionic <type> -maxconfs <value> -out <filename> -param <filename> -prefix <p> -report <filename> -rms <value> -solvcharges <type> -solvent <type> -track <filename>

H

hybrid command line option -annotate_scores [Default: false] -conftest <test type> [Default: isomeric] -dbase <input filename1> [<input filename2> ...] -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> ...] -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]

M

macrocycle command line option -dielectric_constant -ewindow -in -iteration_cycle_size -max_iterations -maxconfs -mpi_hostfile -mpi_np -out -param -prefix -ref_tolerance -rms -rmsd_deduplicate makefraglib command line option -buildff -ewindow -fromCT -in -log -mpi_hostfile <filename> -mpi_np <n> -out -param -prefix -progress -rms -skip -startfact -verbose makerocsdb command line option -in <filename> -out <prefix>

Menu Items molcharge command line option -in -method {option} -out -param -paramfile -prefix

O

OE_ARCH, [1], [2], [3] OE_DIR

OE_LICENSE omega command line option -addfraglib -addtorlib -buildff -canonOrder -commentEnergy -deleteFixHydrogens -dielectric -enumNitrogen -enumRing -erange -ewindow -exponent -fixfile -fixrms -fixsmarts -flipper -flipper_maxcenters -flipper_warts -fromCT -includeInput -log -maxConfRange -maxconfs -maxmatch -maxrot -maxtime -mpi_hostfile <filename> -mpi_np <n> -param -pendingFile -prefix -progress -rangeIncrement -rms -rmsrange -rotorOffsetCompress -sampleHydrogens -sdEnergy -searchff -setfraglib -settorlib -status -strict -strictatomtyping -strictfrags -strictstereo -torlibtype -umatch -verbose -warts

P

PATH, [1], [2], [3], [4], [5] pdb2receptor command line option -ligand_residue <residue identifier> -pdb <filename> -receptor <filename> [Default: receptor.oeb.gz] -solvent_residues <name> [<name> ...] [Default: HOH] Philosophy and Design pkatyper command line option -count -in -max -out -param -paramfile -prefix posit command line option -allowed_clashes -clashed_molecule_file <filename> -conftest <test type> [Default: isomeric] -dbase <filename> -docked_molecule_file <filename> -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

Preferences Preparation Pronunciation Property Filters Property Search

Q

Query Molecule

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> -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> -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] Result View

rocs command line option -besthits <N> -chemff <cffname> -conflabel -cutoff <F> -dbase <filename> -eon_input -eon_input_file <filename> -eon_input_size <N> -eon_maxconfs <N> -hitsfile <filename> -logfile <filename> -maxconfs <N> -maxhits <N> -mcquery -mpi_hostfile <filename> -mpi_np <n> -nostructs -oformat <extension> -opt -optchem -outputdir <dirname> -outputquery -param -prefix <name> -progress <method> -qconflabel -query <filename> -randomstarts <N> -rankby <score> -report -reportfile <filename> -scdbase -scoreonly -sdTags -shapeonly -stats -status -statusfile <filename> -subrocs -subtan -tanimoto_cutoff <F> -verbose rocs_report command line option -aromstyle <style> -astl <style> -i <filename> -in <filename> -maxpages -o <filename> -out <filename> -pagesize <size> -psize <size> -refmol <filename> -verbose

S

scorepose command line option -annotate_scores [Default: false] -conftest <test type> [Default: isomeric] -dbase <input filename1> [<input filename2> ...] -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> -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] Similarity Search

Substructure Search szybki command line option -am1bcc -complex <filename> -current_charges -entropy <type> -exact_vdw -ff -fix_file <filename> -fix_smarts <file_name> -flex_file <filename> -flexdist <d> -flexlist <fn> -flextype <type> -grad_conv <c> -harm_constr1 <k> -harm_constr2 <d> -harm_smarts <file.txt> -heavy_rms -i <filename> -in <filename> -inner_dielectric <d> -keepFailures -l <filename> -largest_part -ligands <filename> -loadPG <filename> -log <prefix> -max_iter <m> -mod_vdw -mpi_hostfile <filename> -mpi_np <n> -neglect_frozen -noCoulomb -o <filename> -optDOF -optGeometry <dof> -optMethod <type> -optdof -out <filename> -out_complex <filename> -out_protein <filename> -p <filename> -param -prefix <pn> -protein <filename> -protein_elec <m> -protein_vdw <r> -radii <type> -report -reportFile <filename> -salt <c> -savePG <filename> -sdtag <string> -shefA <a> -shefB <b> -sheffield -silent -solv_dielectric <d> -solventCA <s> -solventPB -strict -strip_water -t -tor_constr <fn> -vdw_cutoff -verbose

T

Tautomers tautomers command line option -ch3 -in -maxgenerated -maxtautomericatoms -maxtime -maxtoreturn -maxzonesize -out -param -paramfile -pkanorm -prefix -rank -stereo -warts

Technical Details