Index

Symbols

-acolor <color> command line option -add_interactions enumsites command line option spruce command line option -add_style enumsites command line option spruce command line option -addbox <distance> [No Default] spruce4docking 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 -altloc <method> spruce 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 -assignCCP4 writedict 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 -autoMTZ aligngrid command line option flynn command line option -autoMTZ <true or false> rotfit command line option -autoThenManualSearch flynn 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 -blobsThenBox flynn command line option -blobTanimoto flynn 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 command line option -bound_ligand <ligand_file> spruce4docking 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] spruce4docking command line option -box <filename> flynn command line option -box_mol <filename> command line option, [1] -boxpad <number> flynn command line option -bu_superpose spruce command line option -build_cterm_caps spruce command line option -build_nterm_caps spruce command line option -build_sidechains spruce command line option -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 -chainid <chainid> flynn command line option -charge_radii spruce 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 -ciftype flynn command line option -clamp_at_level rscc 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 -cofactor_codes <codes> spruce command line option -collapse_nonsite_alts enumsites command line option spruce command line option -cols <number> command line option -commentEnergy omega command line option -complex <filename> szybki command line option -conflabel rocs 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 -delete_clashing_solvent spruce command line option -deleteFixHydrogens omega command line option -densityAsIs flynn 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 <value> flynn 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 -duplicate_removal enumsites command line option spruce 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 -enum_cofactors_sites enumsites command line option spruce 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 flynn 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 -excipient_codes spruce 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 -Fc <columnname> aligngrid command line option flynn command line option rotfit command line option -Fdelwt <columnname> aligngrid command line option flynn command line option rotfit 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 -fit <filename> superposition command line option -fit_lig <filename> command line option -fix_file <filename> szybki command line option -fix_serial_numbers flynn 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 -fixup_pepflips <true or false> rotfit command line option -fixup_rotamers <true or false> rotfit command line option -fixup_shapefit_residues <true or false> rotfit command line option -flatten rscc 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 flynn command line option omega command line option -flipper_maxcenters omega command line option -flipper_warts omega command line option -Fobs <columnname> aligngrid command line option flynn command line option rotfit command line option -forceExistingResidueNames writedict command line option -forcefield brood command line option -forceflip flipper command line option -forceFlip chomp command line option -format brood command line option -fragment flynn command line option -fromCT brood command line option makefraglib command line option omega command line option -Fwt <columnname> aligngrid command line option flynn command line option rotfit command line option -g <name> command line option -generate_tautomers spruce command line option -geq <number> command line option -geq_mask <number> command line option -grad_conv <c> szybki command line option -grid aligngrid 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 -het_group_nbr_dist <value> spruce command line option -hitinterval brood 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] 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], [2], [3] du2receptor command line option enumsites command line option freeform command line option makerocsdb command line option posit command line option rocs_report command line option spruce command line option spruce4docking command line option szybki command line option writedict command line option -in <molecule file> rscc command line option -in <proteinfile> rotfit 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 -includeRotors writedict 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 -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_hydrogens command line option -keepFailures szybki command line option -l <filename> command line option, [1] 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_coords command line option -lig_grids command line option -lig_point_grid command line option -ligand <filename> command line option, [1] -ligand_names command line option -ligand_names <ligand name> spruce4docking command line option -ligand_names <names> spruce command line option -ligandAsIs flynn 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 <logfile> command line option, [1] du2receptor command line option enumsites command line option spruce command line option spruce4docking command line option -log <prefix> szybki command line option -logfile <filename> command line option, [1] eon command line option rocs command line option -lookup writedict command line option -make_packing_residues spruce command line option -manualSearch <filename> flynn command line option -map <filename> command line option, [1] enumsites command line option spruce command line option spruce4docking command line option -map <mtz file> rotfit 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_bu_atoms spruce command line option -max_bu_parts spruce command line option -max_iter <m> szybki command line option -max_iterations macrocycle command line option -max_lig_atoms spruce command line option -max_lig_residues command line option spruce command line option spruce4docking command line option -max_sys_atoms spruce 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 -metadata <filename> spruce command line option -method <method> command line option -method <value> command line option -method {option} molcharge command line option -min_align_score spruce command line option -min_lig_atoms spruce 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 -minimum_rscc <number> rotfit command line option -minimum_rscc_increase <number> rotfit 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 -mmff94s flynn 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> chomp command line option 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> chomp 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 <number> command line option -mtype aligngrid command line option flynn command line option -mtype <setting> rotfit command line option -mtz <mtz file> rscc 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_preparation [Default: false] command line option spruce4docking command line option -no_table command line option -noCoulomb szybki 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> command line option, [1], [2], [3] 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 -opt_expt_protons spruce 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 aligngrid command line option 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 prefix> writedict command line option -out <filename> command line option, [1] 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 <protein> rotfit command line option -out_complex <filename> szybki command line option -out_protein <filename> szybki command line option -outer_dielectric <number> command line option -outprot aligngrid command line option -output <filename> command line option, [1] -output_all_format <format> command line option -output_grid <filename> command line option, [1] -output_mol <filename> command line option, [1] -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 -overlays flynn command line option -overwrite (-over) command line option -p <filename> command line option, [1] szybki command line option -pad_zeros command line option -padding aligngrid command line option -pagesize <size> command line option rocs_report command line option -param brood command line option chomp 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> flynn command line option rotfit 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 -pendingFile omega command line option -Phic <columnname> aligngrid command line option flynn command line option rotfit command line option -Phidelwt <columnname> aligngrid command line option flynn command line option rotfit command line option -Phiwt <columnname> aligngrid command line option flynn command line option rotfit command line option -pkanorm command line option tautomers command line option -planarAniline writedict command line option -point_grid command line option -prealigned combine_receptors command line option -precheck flynn command line option -pref_author_record spruce 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 <file prefix> flynn command line option -prefix <filename prefix> writedict 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], [2], [3] du2receptor command line option enumsites command line option eon command line option spruce command line option spruce4docking 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 -prot <filename> flynn command line option -protein aligngrid command line option -protein <filename> command line option, [1] szybki command line option -protein_elec <m> szybki command line option -protein_vdw <r> szybki command line option -protonate spruce 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> [<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 <filename> enumsites command line option, [1] spruce command line option superposition command line option -ref_lig <filename> command line option -ref_tolerance macrocycle command line option -refmol <filename> rocs_report command line option -rejected_file posit command line option -relax 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 flynn command line option rocs command line option -reportFile <filename> szybki command line option -reporthtml flynn 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 -residues flynn command line option -resname <name> flynn command line option -resolution <level> command line option -restrict_calc <level> command line option -restrict_to_refsite enumsites command line option spruce command line option -results_set <type> command line option -ringOnly (-ring) brood command line option -rms eon command line option flynn 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] -rot_coverage <value> spruce command line option -rot_library <value> spruce command line option -rotorOffsetCompress omega command line option -rows <number> command line option -rsr rscc 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 aligngrid command line option -scale <number> command line option -scatter rscc 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 <settingsfile> command line option, [1] du2receptor command line option enumsites command line option spruce command line option spruce4docking 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 <filename> enumsites command line option -site_residue <residue identifier> enumsites command line option spruce command line option spruce4docking command line option -site_size <value> enumsites command line option -site_size: <value> spruce command line option -size <size> 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 -solventCA <s> szybki command line option -solventPB szybki command line option -sort_poses [Default: false] scorepose command line option -sortAllChiral <true/false> flynn command line option -sortBy flynn 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 flynn 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 writedict command line option -strictatomtyping omega command line option -strictfrags omega command line option -strictstereo omega command line option -strip_water szybki command line option -strip_water [Default: true] du2receptor command line option spruce4docking command line option -subrocs rocs command line option -subtan rocs command line option -superpose enumsites command line option spruce command line option -superpose_method : <method> spruce command line option -superpose_method <method> enumsites command line option -suppressH flynn command line option writedict 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 -target aligngrid command line option spruce 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 -type writedict 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] -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 aligngrid command line option combine_receptors command line option command line option, [1], [2], [3], [4] eon command line option flynn command line option makefraglib command line option omega command line option rocs command line option rocs_report command line option rscc command line option szybki command line option writedict command line option -verbose (-v) command line option -verbose : Triggers copious logging output command line option enumsites command line option spruce command line option -verbose <true or false> rotfit command line option -warn_if_missing_hydrogens command line option, [1] -warts flipper command line option omega command line option pkatyper command line option tautomers command line option -water_charge <type> command line option -write_biounits spruce command line option -writeFullDict writedict command line option -writegrid eon command line option -zap_spacing <number> command line option

A

aligngrid command line option -Fc <columnname> -Fdelwt <columnname> -Fobs <columnname> -Fwt <columnname> -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -autoMTZ -grid -mtype -out -outprot -padding -protein -scale -target -verbose Analog Search 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 -mpi_hostfile <filename> -mpi_np <n> -omega -out (-o) -param -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> -bound_ligand -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 -fit_lig <filename> -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] -in, [1] -in <filename>, [1], [2], [3] -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> -inscode <letter> -int_method <value> -interval -keep_hydrogens -l <filename>, [1] -legend <bool> -leq <number> -leq_mask <number> -lig_box <filename>, [1] -lig_coords -lig_grids -lig_point_grid -ligand <filename>, [1] -ligand_names -light_background -light_bkg -like_apo <filename> -like_box <filename> -like_lig <filename> -like_std <filename> -log -log <filename>, [1] -log <logfile>, [1] -logfile <filename>, [1] -map <filename>, [1] -mask_cutoff <number>, [1] -mask_vdw -masked_point_cutoff <number> -max_lig_residues -merge <number> -method <method> -method <value> -model <type> -mol <filename> -mpi_hostfile <filename> -mpi_np <number> -nchunks N -new_value <number> -newrule -no_preparation [Default: false] -no_table -normalize -num_orientations <number>, [1] -o <filename> -o <filename>, [1], [2], [3] -op <value> -operation <value> -out, [1] -out (-o) -out <filename>, [1] -outer_dielectric <number> -output <filename>, [1] -output_all_format <format> -output_grid <filename>, [1] -output_mol <filename>, [1] -overwrite (-over) -p <filename>, [1] -pad_zeros -pagesize <size> -param -param <filename>, [1] -pkanorm -point_grid -prefix -prefix <prefix>, [1], [2], [3] -prefix <text> -progress <style>, [1] -properties <type> -protein <filename>, [1] -rankby <SD tag> -ref_lig <filename> -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 -settings <settingsfile>, [1] -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] -value_cutoff <number> -vcutoff <number> -vdw_scale <number> -verbose, [1], [2], [3], [4] -verbose (-v) -verbose : Triggers copious logging output -warn_if_missing_hydrogens, [1] -water_charge <type> -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]

du2receptor command line option -in <filename> -log <logfile> -prefix <prefix> -settings <settingsfile> -strip_water [Default: true]

E

enumsites command line option -add_interactions -add_style -collapse_nonsite_alts -duplicate_removal -enum_cofactors_sites -in <filename> -log <logfile> -map <filename> -prefix <prefix> -ref <filename>, [1] -restrict_to_refsite -settings <settingsfile> -site_residue <filename> -site_residue <residue identifier> -site_size <value> -superpose -superpose_method <method> -verbose : Triggers copious logging output 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 flynn command line option -Fc <columnname> -Fdelwt <columnname> -Fobs <columnname> -Fwt <columnname> -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -autoMTZ -autoThenManualSearch -blobTanimoto -blobsThenBox -box <filename> -boxpad <number> -chainid <chainid> -ciftype -densityAsIs -distance <value> -ewindow -fix_serial_numbers -flipper -fragment -ligandAsIs -manualSearch <filename> -mmff94s -mtype -overlays -param <parameter filename> -precheck -prefix <file prefix> -prot <filename> -reportfile <filename> -reporthtml -residues -resname <name> -rms -sortAllChiral <true/false> -sortBy -split -suppressH -verbose

fred command line option -annotate_scores [Default: false] -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] -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 -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] Philosophy and Design pkatyper command line option -count -in -max -out -param -paramfile -prefix -warts posit command line option -allowed_clashes -clashed_molecule_file <filename> -dbase <filename> -docked_molecule_file <filename> -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 -relax -report_file -score_file -score_tag -settings_file -status_file -undocked_molecule_file Preferences

Preparation Pronunciation Property Filters Property Search

Q

Query Molecule

R

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 rotfit command line option -Fc <columnname> -Fdelwt <columnname> -Fobs <columnname> -Fwt <columnname> -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -autoMTZ <true or false> -fixup_pepflips <true or false> -fixup_rotamers <true or false> -fixup_shapefit_residues <true or false> -in <proteinfile> -map <mtz file> -minimum_rscc <number> -minimum_rscc_increase <number> -mtype <setting> -out <protein> -param <parameter filename> -verbose <true or false> rscc command line option -clamp_at_level -flatten -in <molecule file> -mtz <mtz file> -rsr -scatter -verbose

S

scorepose command line option -annotate_scores [Default: false] -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 spruce command line option -add_interactions -add_style -altloc <method> -bu_superpose -build_cterm_caps -build_nterm_caps -build_sidechains -charge_radii -cofactor_codes <codes> -collapse_nonsite_alts -delete_clashing_solvent -duplicate_removal -enum_cofactors_sites -excipient_codes -generate_tautomers -het_group_nbr_dist <value> -in <filename> -ligand_names <names> -log <logfile> -make_packing_residues -map <filename> -max_bu_atoms -max_bu_parts -max_lig_atoms -max_lig_residues -max_sys_atoms -metadata <filename> -min_align_score -min_lig_atoms -opt_expt_protons -pref_author_record -prefix <prefix> -protonate -ref <filename> -restrict_to_refsite -rot_coverage <value> -rot_library <value> -settings <settingsfile> -site_residue <residue identifier> -site_size: <value> -superpose -superpose_method : <method> -target -verbose : Triggers copious logging output -write_biounits spruce4docking command line option -addbox <distance> [No Default] -bound_ligand <ligand_file> -box <box file> [No Default] -in <filename> -ligand_names <ligand name> -log <logfile> -map <filename> -max_lig_residues -no_preparation [Default: false] -prefix <prefix> -settings <settingsfile> -site_residue <residue identifier> -strip_water [Default: true]

Substructure Search superposition command line option -fit <filename> -ref <filename> 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

W

writedict command line option -assignCCP4 -forceExistingResidueNames -in <filename> -includeRotors -lookup -out <filename prefix> -planarAniline -prefix <filename prefix> -strict -suppressH -type -verbose -writeFullDict