Index

Symbols

-acolor <color> szmap_report command line option -add_interactions enumsites command line option spruce command line option -add_receptors spruce command line option -add_style enumsites command line option spruce command line option -addbox <distance> [No Default] ReceptorInDU command line option -added_date <value> loopdb_builder command line option -addfraglib omega command line option -addtorlib omega command line option -all <format> command line option -allow_filter_error spruce command line option -allow_truncate spruce command line option -allow_validation_error spruce 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 szmap command line option -apo_coords szmap command line option -apo_grids szmap command line option -apo_point_grid szmap command line option -append sitehopper_build command line option -append <bool> loopdb_builder command line option -aromstyle <style> rocs_report command line option szmap_report command line option -around <filename> szmap command line option -around_mol <filename> szmap command line option -aScale) brood command line option -assignBondiRadii checkcff command line option -assignCCP4 writedict command line option -assignColor checkcff command line option -astl <style> rocs_report command line option szmap_report command line option -at_coords <filename> command line option szmap command line option -atomcolor <color> szmap_report command line option -atomsstl <style> szmap_report command line option -atomstereostyle <style> szmap_report command line option -attachColor brood command line option -attachFrag brood command line option -attachmentCutoff (-attachcut) brood command line option -attachmentScale (-attach 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 -batchMaxRotors omega command line option -bb_clash_threshold <value> spruce command line option -bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax> szmap command line option -bcolor <color> szmap_report command line option -best_Receptor_Pose_Only posit 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> szmap_report command line option -bondOrder (-bo) brood command line option -bondsstl <style> szmap_report command line option -bondstereostyle <style> szmap_report command line option -boundary <number> szmap command line option -boundary_radius <number> szmap command line option -boundary_spacing <number> szmap command line option -bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax> szmap command line option -Box coot command line option -box <box file> [No Default] ReceptorInDU command line option -box <filename> flynn command line option -box_mol <filename> command line option szmap command line option -boxpad <number> flynn command line option -bu_superpose spruce command line option -build_cterm_caps spruce command line option -build_disulfidebridges <value> spruce command line option -build_loops spruce command line option -build_nterm_caps spruce command line option -build_sidechains spruce command line option -build_with_crystalpacking 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 -cap_delete_clashing_solvent spruce command line option -capAttach chomp command line option -ch3 tautomers command line option -chain <letter> szmap command line option -chainid <chainid> flynn command line option -charge_radii spruce command line option -charges eon command line option -Check coot 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> szmap_report command line option -commentEnergy omega command line option -complex <filename> szybki command line option -conflabel rocs command line option -coords <filename> command line option szmap command line option -count pkatyper command line option -countConfs command line option -cpddb brood command line option -cplx_grids szmap command line option -crop_length <value> loopdb_builder command line option spruce command line option -csv brood command line option -current_charges szybki command line option -cutoff <F> rocs command line option -cutoff <float> sitehopper_search command line option -cutoff <N> eon command line option -cutoff <number> command line option -database <filename> sitehopper_search command line option -db (-database) brood command line option -dbase eon command line option -dbase <filename> posit command line option rocs command line option sitehopper_build 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> szmap command line option -default <number> command line option -default_value <number> command line option -deleteFixHydrogens omega command line option -densityAsIs flynn command line option -dielectric eon command line option -dielectric_model <type> szmap command line option -dir <path> sitehopper_build 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> szmap 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 -du <filename> OptLigandInDU 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 -enhstereo flipper 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 -enum_pockets spruce command line option -enumAtoms flipper command line option -enumAtomSpecifiedStereo flipper command line option -enumBonds flipper command line option -enumBondSpecifiedStereo flipper command line option -enumBridgehead flipper command line option -enumEZ flipper command line option -enumNitrogen flipper command line option omega command line option -enumRelativeAtomStereo flipper command line option -enumRing omega command line option -enumRS flipper command line option -enumSpecifiedStereo flipper command line option -eps_in <number> szmap command line option -eps_out <number> szmap command line option -erange omega command line option -ET (-et) brood command line option -ewindow flynn command line option freeform command line option macrocycle command line option makefraglib command line option omega command line option -ewindowRing makefraglib command line option -exact_vdw szybki command line option -excipient_codes spruce command line option -exclude_reg_ss <value> loopdb_builder command line option -excludeDUligand szmap command line option -excludeDUsolvent szmap command line option -extract_custom_constraints <filename> [No Default] receptor_toolbox command line option -fail command line option -failed omega 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 [Default: ff14sb_sage] OptimizeDU command line option OptLigandInDU 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> superposition command line option -fix_bb_atoms spruce command line option -fix_bonds_to_metals spruce command line option -fix_chainID spruce command line option -fix_covalent_bond spruce command line option -fix_file <filename> szybki command line option -fix_float_res spruce command line option -fix_res_names spruce command line option -fix_res_states spruce command line option -fix_serial_numbers flynn command line option -fix_smarts <file_name> szybki command line option -fixfile omega command line option -fixmcs 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 -flexRange [Default: 2.0] OptimizeDU command line option -flextype <type> szybki command line option -flip_bias_scale spruce command line option -flipN chomp command line option -flipper chomp command line option flynn command line option omega command line option -flipper_enhstereo 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 chomp command line option -format brood command line option -fragGen makefraglib command line option -fragGenRing makefraglib command line option -fragKeep makefraglib command line option -fragKeepRing makefraglib 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 -gradTol [Default: 1.0e-6] OptimizeDU command line option OptLigandInDU 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> szmap command line option -gridBuffer eon command line option -grids <type> szmap command line option -gridSpacing eon 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> rocs command line option -i <filename> rocs_report command line option szmap_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] eon command line option 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 <directory> loopdb_builder command line option -in <filename> checkcff command line option command line option, [1] du2mmcif command line option DU2OEBReceptor command line option du2pdb command line option enumsites command line option flynn command line option freeform command line option makerocsdb command line option OEB2DUReceptor command line option OptimizeDU command line option OptLigandInDU command line option posit command line option ReceptorInDU command line option rocs_report command line option spruce 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) brooddbmerge command line option -in1 <filename> command line option -in2 (-i2) brooddbmerge command line option -in2 <filename> command line option -in3 <filename> command line option -incl_SA_term <value> spruce command line option -incl_solvation <value> spruce command line option -includeInput omega command line option -includePackingResidues du2mmcif command line option du2pdb 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> szmap command line option -innerMask eon command line option -input <filename> szmap_report 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> szmap 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 szmap_report command line option -keepFailures szybki command line option -l <filename> command line option szmap command line option szybki command line option -largest_part szybki command line option -legend <bool> szmap_report command line option -leq <number> command line option -leq_mask <number> command line option -lig_box <filename> command line option szmap command line option -lig_coords szmap command line option -lig_grids szmap command line option -lig_point_grid szmap command line option -ligand <filename> command line option szmap command line option -ligand_names <names> spruce command line option -ligandAsIs flynn command line option -ligandCharge [Default: current] OptimizeDU command line option OptLigandInDU command line option -ligands <filename> szybki command line option -light_background command line option -light_bkg command line option -like_apo <filename> szmap command line option -like_box <filename> szmap command line option -like_lig <filename> szmap command line option -like_std <filename> szmap command line option -linkOnly (-linkonly brood command line option -lipid_codes <codes> spruce command line option -loadPG <filename> szybki command line option -log brood command line option checkcff command line option command line option eon command line option makefraglib command line option omega command line option OptimizeDU command line option OptLigandInDU command line option -log <filename> command line option szmap command line option -log <logfile> du2mmcif command line option du2pdb command line option enumsites command line option loopdb_builder command line option sitehopper_build command line option sitehopper_search command line option spruce command line option superposition command line option -log <prefix> szybki command line option -logfile <filename> command line option rocs command line option szmap command line option -lookup writedict command line option -loop_clash_threshold <value> spruce command line option -loop_db_filename <filename> spruce command line option -loop_distance_buffer <value> spruce command line option -make_packing_residues spruce command line option -manualSearch <filename> flynn command line option -map <filename> enumsites command line option flynn command line option spruce command line option -map <mtz file> rotfit command line option -mask_cutoff <number> command line option szmap command line option -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_eval_loops <value> spruce command line option -max_hits <value> sitehopper_search command line option -max_iter <m> szybki command line option -max_iterations macrocycle command line option -max_length <value> loopdb_builder command line option -max_lig_atoms spruce command line option -max_lig_residues spruce command line option -max_pocket_surf_area spruce command line option -max_sys_atoms spruce command line option -maxABS) brood command line option -maxAcceptors) brood 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 -maxDonors) brood 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 -maxIter [Default: 1000] OptimizeDU command line option OptLigandInDU command line option -maxLipinski brood command line option -maxLipinskiAcc (-maxLipinskiAcceptors brood command line option -maxLipinskiDon (-maxLipinskiDonors brood command line option -maxLocalStrain brood command line option -maxlogp brood command line option -maxMartin (-maxAbbott 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 -maxTrials omega command line option -maxTrialsRange omega command line option -maxzonesize tautomers command line option -mcquery rocs command line option -mcsMinAtoms omega command line option -merge <number> command line option -metadata <filename> spruce command line option -method <method> superposition 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 -min_pocket_surf_area spruce command line option -minABS) brood command line option -minAcceptors) brood command line option -minAromFJCt brood command line option -minComplexity (-minComp) brood command line option -minDegree chomp command line option -minDistance checkcff command line option -minDonors) brood 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 brood command line option

-minLipinskiDon (-minLipinskiDonors brood command line option -minlogp brood command line option -minMartin (-minAbbott brood command line option -minMolWt (-minmolecularweight) brood command line option -minpsa (-mintpsa) brood command line option -minRotBond (-minRotatableBond) brood command line option -MMFF94s coot command line option -mmff94s flynn command line option -mod_vdw szybki command line option -model <type> szmap command line option -mol <filename> command line option -molNames checkcff command line option eon command line option flipper command line option makefraglib command line option OptimizeDU command line option OptLigandInDU command line option -molnames DU2OEBReceptor command line option macrocycle command line option OEB2DUReceptor command line option posit command line option ReceptorInDU 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 posit command line option rocs command line option szmap command line option szybki command line option -mpi_np brood command line option macrocycle command line option -mpi_np <n> chomp command line option command line option eon command line option makefraglib command line option posit command line option rocs command line option szybki command line option -mpi_np <number> szmap 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 -ncpu sitehopper_build command line option -ncpu <value> loopdb_builder command line option sitehopper_search command line option -negImageType [Default: standard] ReceptorInDU 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_prep spruce command line option -no_table command line option -noCoulomb szybki command line option -noqueryprot (-noqueryprotein) brood command line option -noqueryselection) brood command line option -noqueryselectprot (-noqueryselectionprotein brood command line option -normalize command line option -normalize_and_rescore <bool> sitehopper_search command line option -nostructs rocs command line option -nostructs [Default: false] fred command line option hybrid command line option -num_orientations <number> command line option szmap command line option -num_poses posit command line option -num_poses <num> [Default: 1] fred command line option hybrid command line option -num_top_scores eon command line option -o <filename> rocs_report command line option szmap_report command line option -o <filename> command line option, [1], [2] szmap command line option szybki command line option -oformat <extension> 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 -opt_shell <value> spruce command line option -opt_stage1_iter_multiplier <value> spruce command line option -opt_stage2_iter_multiplier <value> spruce command line option -opt_tolerance <value> 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 [Default: cartesian] OptimizeDU command line option OptLigandInDU 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 fixpa command line option flipper command line option macrocycle command line option makefraglib command line option molcharge command line option omega command line option pkatyper command line option tautomers command line option -out (-o) brooddbmerge command line option chomp command line option -out <filename prefix> writedict command line option -out <filename> command line option DU2OEBReceptor command line option flynn command line option freeform command line option OEB2DUReceptor command line option OptimizeDU command line option OptLigandInDU command line option ReceptorInDU command line option rocs_report command line option sitehopper_search command line option szybki command line option -out <oebfile> checkcff command line option -out <out> spruce 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> szmap command line option -outerMask eon command line option -outprot aligngrid command line option -output <filename> command line option szmap_report command line option -output_all_format <format> command line option -output_grid <filename> command line option, [1] -output_mol <filename> command line option szmap command line option -outputall posit command line option -outputdir combine_receptors command line option -outputdir <dirname> rocs command line option -outputquery rocs command line option -overlays flynn command line option -overwrite sitehopper_build command line option -overwrite (-over) brooddbmerge command line option -p <filename> command line option szmap command line option szybki command line option -pad_zeros command line option -padding aligngrid command line option -pagesize <size> rocs_report command line option szmap_report command line option -param brood command line option chomp command line option command line option, [1] eon command line option macrocycle command line option makefraglib command line option molcharge 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 freeform command line option szmap command line option -param <param_file> sitehopper_build 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 -param <paramfile> sitehopper_search command line option -paramfile molcharge command line option pkatyper command line option tautomers command line option -PBsolvent_dielectric <value> freeform 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 -pocket_burial_factor spruce command line option -pocketMask spruce command line option -point_grid szmap command line option -potential eon command line option -precheck flynn command line option -pref_author_record spruce command line option -prefix brood command line option checkcff command line option chomp command line option combine_receptors command line option command line option DU2OEBReceptor command line option eon command line option flipper command line option macrocycle command line option makefraglib command line option molcharge command line option OEB2DUReceptor command line option omega command line option OptimizeDU command line option OptLigandInDU command line option pkatyper command line option posit command line option ReceptorInDU 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 du2mmcif command line option du2pdb command line option enumsites command line option loopdb_builder command line option sitehopper_build command line option sitehopper_search command line option spruce command line option superposition command line option szmap 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 receptor_toolbox command line option -primaryFrag chomp command line option -priorTemperature omega command line option -progress checkcff command line option DU2OEBReceptor command line option eon command line option flipper command line option macrocycle command line option makefraglib command line option OEB2DUReceptor command line option omega command line option OptimizeDU command line option OptLigandInDU command line option ReceptorInDU command line option -progress : Shows a progress bar sitehopper_build command line option -progress <method> rocs command line option -progress <style> command line option szmap command line option -properties <type> szmap 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 szmap command line option szybki command line option -protein_elec <m> szybki command line option -protein_vdw <r> szybki command line option -proteinMask OptimizeDU command line option OptLigandInDU command line option -protonate spruce command line option -psize <size> rocs_report command line option -qconflabel rocs command line option -query eon command line option -query <filename> rocs command line option sitehopper_search command line option -queryFragment (-queryFrag) brood command line option -queryMolecule (-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> 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> superposition 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) brooddbmerge command line option -removeDups checkcff command line option -report brood command line option rocs command line option szybki command line option -report <csvfile> checkcff command line option -report <filename> 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> szybki command line option -reportfile <filename> flynn command line option rocs command line option -reporthtml flynn command line option -res <number> szmap command line option -rescored_mol_output_file <output filename> [Default: scored.oeb.gz] scorepose command line option -residue_chain <letter> szmap command line option -residue_insert <letter> szmap command line option -residue_number <number> szmap command line option -residueID [Default: None] OptimizeDU command line option -residues flynn command line option -resname <name> flynn command line option -resolution <level> szmap_report command line option -restrict_calc <level> szmap command line option -restrict_to_refsite enumsites command line option spruce command line option -results_set <type> szmap command line option -ringOnly (-ring) brood command line option -rms flynn command line option macrocycle command line option makefraglib command line option omega command line option -rms <value> freeform command line option -rmsrange omega command line option -rmsRing makefraglib command line option -rot <number> command line option szmap command line option -rot_coverage <value> spruce command line option -rot_library <value> spruce command line option -rotorOffsetCompress omega command line option -rows <number> szmap_report command line option -rsr rscc command line option -salt command line option -salt <c> szybki command line option -salt <number> szmap command line option -salt_conc <number> szmap command line option -saltConc eon command line option -sampleHydrogens 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 -sc_delete_clashing_solvent spruce command line option -scale aligngrid command line option -scale <number> command line option -scatter rscc command line option -scdbase 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 rocs command line option -searchff omega command line option -select command line option -select (-selection) brood command line option -separate szmap_report command line option -sequence_cutoff <float> sitehopper_search command line option -set_custom_constraints <filename> [No Default] receptor_toolbox command line option -settings <settingsfile> du2mmcif command line option du2pdb command line option enumsites command line option loopdb_builder command line option spruce command line option superposition 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 -site_size <value> enumsites command line option -site_size: <value> spruce command line option -size <size> szmap_report 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 -solventModel [Default: vacuum] OptimizeDU command line option OptLigandInDU 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 -source_date <value> loopdb_builder command line option -source_name <value> loopdb_builder command line option -sp3_aromatic <bool> command line option -sp3aromatic <bool> command line option -space <number> szmap command line option -split flynn command line option -split_lig szmap command line option -stabilization szmap command line option -stabilization <bool> command line option -standard_grids szmap command line option -startfact makefraglib command line option -startfactRing makefraglib command line option -stats rocs command line option -status 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 <filename> rocs command line option -stbl szmap command line option -stbl <bool> command line option -std_box <filename> command line option szmap command line option -std_coords szmap command line option -std_grids szmap command line option -stereo tautomers command line option -strict omega command line option szybki command line option writedict command line option -strict_proline_match spruce command line option -strictatomtyping omega command line option -strictfrags omega command line option -strictstereo omega command line option -strip_water szybki command line option -struc brood command line option -struct) brood 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 szmap command line option -surface <bool> szmap_report command line option -surface_points szmap command line option -szmap_mpi_hostfile <filename> command line option -szmap_mpi_np <number> command line option -t szybki command line option -t <prop> szmap_report command line option -table command line option -table <filename> szmap command line option -tableFlag command line option -tag_set <set> szmap_report command line option -tagname <prop> szmap_report command line option -tanimoto_cutoff <F> rocs command line option -target aligngrid command line option spruce command line option -target <filename> command line option szmap command line option -targetMask spruce command line option -targetMask [Default: targetComplexNoSolvent] ReceptorInDU command line option -targetPred ReceptorInDU command line option -tautomer brood command line option -thompson omega command line option -timeLimit makefraglib command line option -timeLimitRing makefraglib command line option -title brood command line option -title <text> szmap_report command line option -title <title> loopdb_builder 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 -transform_threshold <value> spruce command line option -trialsRangeIncrement omega 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> szmap command line option -use_gpu <bool> sitehopper_search command line option -useGPU omega command line option -useHydrogens checkcff command line option -userFrags chomp command line option -userUnique chomp command line option -v command line option, [1], [2] szmap command line option szmap_report command line option -value_cutoff <number> szmap command line option -vcutoff <number> szmap command line option -vdw_cutoff szybki command line option -vdw_scale <number> szmap command line option -veber (-gsk) brood command line option -verbose aligngrid command line option checkcff command line option combine_receptors command line option command line option, [1], [2] du2mmcif command line option du2pdb command line option eon command line option flynn command line option makefraglib command line option omega command line option OptimizeDU command line option OptLigandInDU command line option rocs command line option rocs_report command line option rscc command line option sitehopper_search command line option szmap command line option szmap_report command line option szybki command line option writedict command line option -verbose (-v) brooddbmerge command line option -verbose : loopdb_builder command line option -verbose : Triggers copious logging output enumsites command line option sitehopper_build command line option spruce command line option superposition command line option -verbose <true or false> rotfit command line option -warn_if_missing_hydrogens command line option szmap command line option -warts flipper command line option omega command line option pkatyper command line option spruce command line option tautomers command line option -water_charge <type> szmap command line option -write_biounits spruce command line option -writeFullDict writedict command line option -writegrid eon command line option -zap_spacing <number> szmap command line option

A

About Active ActiveConformer ActiveID ActiveKey Add AddCSVSmiles AddURLMol aligngrid command line option -autoMTZ -Fc <columnname> -Fdelwt <columnname> -Fobs <columnname> -Fwt <columnname> -grid -mtype -out -outprot -padding -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -protein -scale -target -verbose AMI Analog Search AnnotationGet AnnotationHas AnnotationSet apo protein apo proteins AppAddCallback AppComponentNameGet AppComponentNameSet AppCurrentDir AppCurrentDirSet AppDir AppDocDir Appending Data Appendix 1 Appendix 2 AppExampleDir AppGeometryGet AppGeometrySet AppGlobalFontGet AppGlobalFontSet AppInstallDir AppLastDirGet AppLastDirSet AppLastOpenDirGet AppLastOpenDirSet AppLastSaveDirGet AppLastSaveDirSet AppLayoutGet AppLayoutSet AppLayoutToIcon AppLicenseFile AppLicenseUpdate AppMainWindowGet AppMainWindowSet AppMovableWindowsGet AppMovableWindowsSet APPNAME_OE_ARCH AppOpenUrl AppPerspectiveSet AppRecordWindowEventsGet AppRecordWindowEventsSet AppRemoveCallback AppScriptSave AppShowGet AppShowMenuBarGet AppShowMenuBarSet AppShowSet AppShowStatusBarGet AppShowStatusBarSet

AppSloppyFocusGet AppSloppyFocusSet AppStatusTextSet AppUserDir AppVersion AppVersionBugFix AppVersionMajor AppVersionMinor AppWindowStyleGet AppWindowStyleSet asymmetric unit AtomAddHydrogens AtomAddHydrogensScoped AtomAtomicNumDefaultGet AtomAtomicNumDefaultSet AtomAtomicNumGet AtomAtomicNumSet AtomAtomicNumSetScoped AtomAttach AtomClearColorScoped AtomColorPaletteUpdate AtomColorReferenceScoped AtomColorResidueScoped AtomColorSetScoped AtomDarkColorsGet AtomDarkColorsSet AtomDataGet AtomDefaultColorGet AtomDefaultColorSet AtomDelete AtomDeleteHydrogens AtomDeleteHydrogensScoped AtomDeleteScoped AtomFormalChargeDefaultGet AtomFormalChargeDefaultSet AtomFormalChargeGet AtomFormalChargeModify AtomFormalChargeModifyScoped AtomFormalChargeSet AtomFormalChargeSetScoped AtomFuse AtomHaloRadiusGet AtomHaloRadiusSet AtomHybridizationGet AtomHybridizationSet AtomHybridizationSetScoped AtomHydrogenStyleGet AtomHydrogenStyleSet AtomHydrogenStyleSetScoped AtomIsotopeGet AtomIsotopeSet AtomIsotopeSetScoped AtomLabelDefaultGet AtomLabelDefaultSet AtomLabelGet AtomLabelSet AtomLabelSetScoped AtomSprout AtomSproutScoped AtomStereoDefaultGet AtomStereoDefaultSet AtomStereoSet AtomStereoSetScoped AtomStereoToggle AtomStereoToggleScoped AtomStyleGet AtomStyleGetScoped AtomStyleLargeGet AtomStyleLargeSet AtomStyleNucleicGet AtomStyleNucleicSet AtomStyleProteinGet AtomStyleProteinSet AtomStyleSet AtomStyleSetScoped AtomStyleToEnum AtomStyleToText AUC

B

B-factor biological unit BlockBegin BlockEnd BlockExemptGet BlockExemptSet BlockGet BondAngleGet BondAngleModify BondAngleSet BondBallToStickRatioGet BondBallToStickRatioSet BondClearColorScoped BondColorSetScoped BondCreate BondDelete BondDeleteScoped BondDrawAromaticGet BondDrawAromaticSet BondFuse BondHideHydrogenGet BondHideHydrogenSet BondHideNonbondedGet BondHideNonbondedSet BondLabelDefaultGet BondLabelDefaultSet BondLabelGet BondLabelSet BondLabelSetScoped BondLengthGet BondLengthModify BondLengthSet BondLengthSetScoped BondLineWidthGet BondLineWidthSet BondOrderDefaultGet BondOrderDefaultSet BondOrderGet BondOrderSet BondOrderSetScoped BondRadiusGet BondRadiusSet BondShowAromaticGet BondShowAromaticSet BondShowDipolarGet BondShowDipolarSet BondShowOrdersGet BondShowOrdersSet BondStereoDefaultGet BondStereoDefaultSet BondStereoSet BondStereoSetScoped BondStereoToggle BondStereoToggleScoped BondStyleGet BondStyleGetScoped BondStyleLargeGet BondStyleLargeSet BondStyleNucleicGet BondStyleNucleicSet BondStyleProteinGet BondStyleProteinSet BondStyleSet BondStyleSetScoped BondStyleToEnum BondStyleToText BondTorsionGet BondTorsionModify BondTorsionSet BookmarkDelete BookmarkExists BookmarkLoad BookmarkMoveDown BookmarkMoveUp BookmarkOrganizeDialog BookmarkRename Bookmarks BookmarkSave BookmarksClear BookmarksLastLoaded brood command line option -aScale) -attachColor -attachFrag -attachmentCutoff (-attachcut) -attachmentScale (-attach -bondOrder (-bo) -bumpRadius -checkBond (-checkbond) -checkGeometry -cpddb -csv -db (-database) -dots -eganEgg (-egan) -ET (-et) -fileChrg -forcefield -format -fromCT -hitinterval -hitlistProt -idea (-cluster) -info -interval -linkOnly (-linkonly -log -maxABS) -maxAcceptors) -maxAromFJCt -maxComplexity (-maxComp) -maxDonors) -maxFrag -maxFrequency (-maxFreq) -maxFsp3C -maxHit (-maxhit) -maxHvyAtom (-maxHeavyAtom) -maxLipinski -maxLipinskiAcc (-maxLipinskiAcceptors -maxLipinskiDon (-maxLipinskiDonors -maxLocalStrain -maxlogp -maxMartin (-maxAbbott -maxMolWt (-maxmolecularweight) -maxpsa (-maxtpsa) -maxRotBond (-maxRotatableBond) -minABS) -minAcceptors) -minAromFJCt -minComplexity (-minComp) -minDonors) -minFrequency (-minFreq) -minFsp3C -minHvyAtom (-minHeavyAtom) -minLipinski -minLipinskiAcc (-minLipinskiAcceptors -minLipinskiDon (-minLipinskiDonors -minlogp -minMartin (-minAbbott -minMolWt (-minmolecularweight) -minpsa (-mintpsa) -minRotBond (-minRotatableBond) -mpi_hostfile -mpi_np -neutralpH -noqueryprot (-noqueryprotein) -noqueryselection) -noqueryselectprot (-noqueryselectionprotein -param -prefix -property (-prop) -prot (-protein) -queryFragment (-queryFrag) -queryMolecule (-qMol) -quickLook (-quick) -rangeOffset -rangeSize -report -ringOnly (-ring) -sdtag -select (-selection) -shapeCutoff -struc -struct) -tautomer -title -veber (-gsk)

brooddbmerge command line option -in1 (-i1) -in2 (-i2) -out (-o) -overwrite (-over) -removeDuplicates (-duplicates) -verbose (-v) bug-fix release BuilderActiveGet BuilderActiveSet BuilderAlternateConfModeGet BuilderAlternateConfModeSet BuilderAlternateConfSet BuilderCancel BuilderEdit BuilderFinish BuilderFocusOnProperties BuilderFocusOnSketcher BuilderFragmentGet BuilderFragmentSet BuilderMinimize BuilderMinimizeScoped BuilderPropertiesGet BuilderPropertyAdd BuilderPropertyRemove BuilderPropertySetValue BuilderTorsionActivate BuilderTorsionsDeactivate BuilderUseMMFF94sGet BuilderUseMMFF94sSet

C

canonical isomeric SMILES canonical SMILES CATraceRadiusGet CATraceRadiusSet CATraceStyleGet CATraceStyleSet CATraceStyleSetScoped CenterSet CenterSetScoped checkcff command line option -assignBondiRadii -assignColor -chemff <cff_file> -in <filename> -log -minDistance -molNames -out <oebfile> -prefix -progress -removeDups -report <csvfile> -useHydrogens -verbose CheckIn ChildrenGet chiral atom chiral bond 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 CIP ClearActive ClearLocked ClearMarked ClearSelection ClearVisible ColorGet ColorSet ColorSetScoped ColorUniqueScoped combine_receptors command line option -allowedClashes -outputdir -param <filename> -prefix -receptors <filenames> -verbose command line option -all <format> -apo_box <filename> -at_coords <filename> -base <NAME> -besthits N -biggerisbetter -box_mol <filename> -by <number> -chunksize M -clean <bool> -coords <filename> -countConfs -cutoff <number> -default <number> -default_value <number> -dots -fail -filter -g <name> -geq <number> -geq_mask <number> -grid <name> -grid1 <name> -grid2 <name> -grid3 <name> -i <filename>, [1] -in, [1] -in <filename>, [1] -in1 <filename> -in2 <filename> -in3 <filename> -info -input_file1 <filename> -input_file2 <filename> -input_file3 <filename> -input_mol <filename> -int_method <value> -interval -l <filename> -leq <number> -leq_mask <number> -lig_box <filename> -ligand <filename> -light_background -light_bkg -log -log <filename> -logfile <filename> -mask_cutoff <number> -mask_vdw -masked_point_cutoff <number> -merge <number> -method <value> -mol <filename> -mpi_hostfile <filename> -mpi_np <n> -nchunks N -new_value <number> -newrule -no_table -normalize -num_orientations <number> -o <filename>, [1], [2] -op <value> -operation <value> -out -out <filename> -output <filename> -output_all_format <format> -output_grid <filename>, [1] -output_mol <filename> -p <filename> -pad_zeros -param, [1] -param <filename> -pkanorm -prefix -prefix <prefix> -prefix <text> -progress <style> -protein <filename> -rankby <SD tag> -rot <number> -salt -scale <number> -sdtag -select -slice -sp3_aromatic <bool> -sp3aromatic <bool> -stabilization <bool> -stbl <bool> -std_box <filename> -szmap_mpi_hostfile <filename> -szmap_mpi_np <number> -table -tableFlag -target <filename> -to <number> -typecheck -unique -v, [1], [2] -verbose, [1], [2] -warn_if_missing_hydrogens

conformer conformers ContextClear ContextGet ContextInsert ContextKeysSet ContextSet ContourAutoCenterGet ContourAutoCenterSet ContourAutoContourGet ContourAutoContourRadiusScaleSet ContourAutoContourSet ContourCenter ContourCloudJitterDefaultGet ContourCloudJitterGet ContourCloudJitterSet ContourColorForIndexGet ContourColorForIndexGetScoped ContourColorForIndexSet ContourColorForIndexSetScoped ContourColorSet ContourColorSetScoped ContourCountScoped ContourCreate ContourCreateSurface ContourCurrentGridGet ContourCurrentGridSet ContourDeleteAll ContourDeleteByIndex ContourDeleteByThreshold ContourDrawAsSurfaceGet ContourDrawAsSurfaceSet ContourDrawAsSurfaceSetScoped ContourDrawStyleGet ContourDrawStyleSet ContourDrawStyleSetScoped ContourEntireGridGet ContourEntireGridSet ContourExtractIsoSurface ContourFixAsSurfaceScoped ContourGetAll ContourHideIndex ContourHideIndexGet ContourHideIndexSet ContourLevelForIndexGet ContourLevelForIndexGetScoped ContourLevelForIndexSet ContourLevelForIndexSetScoped ContourLevelNudgeScoped ContourLevelSetScoped ContourLineWidthGet ContourLineWidthSet ContourMax ContourMaxScoped ContourMin ContourMinScoped ContourPickIsoSurfacesGet ContourPickIsoSurfacesSet ContourRadiusGet ContourRadiusSet ContourResolutionGet ContourResolutionSet ContourTransparencySet ContourTypedAddScoped ContourTypedCountScoped ContourTypedMaxScoped ContourTypedMinScoped ContourTypedRemoveScoped ContourTypedSetLevelForIndexScoped ContourVolume coot command line option -Box -Check -MMFF94s CopyData CopyMolecules CopyMoleculesScoped CPK CreateAngleMonitor CreateDistanceMonitor CreateSphereMonitor CreateTorsionMonitor CSV cube cubes CUDA CustomViewDocking CustomViewEON CustomViewFRED CustomViewROCS CXSMILES

D

DataAdd DataGetDB DataGetTable DatatableAddColumn DatatableCommitChanges DatatableCurrent DatatableCurrentGet DatatableCurrentSet DatatableData DatatableDeleteColumn DatatableEditableGet DatatableEditableSet DatatableFilter DatatableFromList DatatableGetColumn DatatableGetCurrentRow DatatableGetDatatables DatatableGetImageStreamAtRow DatatableGetKeys DatatableGetNumRows DatatableHeaders DatatableLingoSimSort DatatableMolNumberFunction DatatableMolStringFunction DatatableNumRows DatatableSetData DatatableSetExpression DatatableSetRowData DefaultColorLabelGet DefaultColorLabelSet DefaultColorMarkedGet DefaultColorMarkedSet DefaultColorReferenceGet DefaultColorReferenceSet DefaultColorSelectedGet DefaultColorSelectedSet DefaultColorTitleGet DefaultColorTitleSet DefaultMonitorColorGet DefaultMonitorColorSet DefaultScopeGet DefaultScopeSet Delete DeleteAll DeleteAngleMonitor DeleteDistanceMonitor DeleteScoped DeleteTorsionMonitor DeleteVisibleMonitors design unit DistanceControlsVisibilityGet DistanceControlsVisibilitySet

dock docking 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] DrawAtomsAndBondsGet DrawAtomsAndBondsSet DrawAxesGet DrawAxesSet DrawCATracesGet DrawCATracesSet DrawCATracesSetScoped DrawContoursGet DrawContoursSet DrawLabelsGet DrawLabelsSet DrawMatrixGet DrawMatrixSet DrawRibbonsGet DrawRibbonsSet DrawRibbonsSetScoped DrawSurfacesGet DrawSurfacesSet DrawSymmetryGet DrawSymmetrySet DrawTitlesGet DrawTitlesSet DrawUnitCellGet DrawUnitCellSet du2mmcif command line option -in <filename> -includePackingResidues -log <logfile> -prefix <prefix> -settings <settingsfile> -verbose DU2OEBReceptor command line option -in <filename> -molnames -out <filename> -prefix -progress du2pdb command line option -in <filename> -includePackingResidues -log <logfile> -prefix <prefix> -settings <settingsfile> -verbose

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 <N> -dbase -dielectric -fixpka_dbase -fixpka_query -gridBuffer -gridSpacing -in -innerMask -log -maxhits <N> -molNames -mpi_hostfile <filename> -mpi_np <n> -num_top_scores -outerMask -param -potential -prefix -progress -query -saltConc -scoreonly -verbose -writegrid

Error ErrorDetailsDialog Exact Search excipient ExistsAngleMonitor ExistsDistanceMonitor ExistsTorsionMonitor ExtensionsEdit

F

FASTA feature release FindByDataScoped FindByQueryScoped FindBySimilarityScoped FindBySMARTSScoped FindByTitleScoped FindInRepository FindOnDisk fingerprint fixpa command line option -in -ionize -out flipper command line option -enhstereo -enumAtoms -enumAtomSpecifiedStereo -enumBonds -enumBondSpecifiedStereo -enumBridgehead -enumEZ -enumNitrogen -enumRelativeAtomStereo -enumRS -enumSpecifiedStereo -in -maxCenters -molNames -out -prefix -progress -warts floe floes flynn command line option -autoMTZ -autoThenManualSearch -blobsThenBox -blobTanimoto -box <filename> -boxpad <number> -chainid <chainid> -ciftype -densityAsIs -distance <value> -ewindow -Fc <columnname> -Fdelwt <columnname> -fix_serial_numbers -flipper -Fobs <columnname> -fragment -Fwt <columnname> -in <filename> -ligandAsIs -manualSearch <filename> -map <filename> -mmff94s -mtype -out <filename> -overlays -param <parameter filename> -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -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] -nostructs [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 -calc <run_type> -ensemble -ewindow -ff <type> -i <filename> -in <filename> -ionic <type> -maxconfs <value> -out <filename> -param <filename> -PBsolvent_dielectric <value> -prefix <p> -report <filename> -rms <value> -solvcharges <type> -solvent <type> -track <filename>

G

GetAllContextKeys GetAtomsByScope GetAtomsScoped GetBondsByScope GetBondsScoped GetContoursByScope GetContoursScoped GetGridsByScope GetGridsScoped GetKey GetKeysByScope GetKeysForID GetKeyType GetMarkedAtoms GetMarkedAtomsScoped GetMarkedBonds GetMarkedBondsScoped GetMarkedContours GetMarkedGrids GetMarkedMolecules GetMarkedMonitors GetMarkedSurfaces GetMoleculesByScope GetMoleculesScoped GetName GetPropertyType GetScoped GetSelectedAtom GetSelectedAtoms GetSelectedBond GetSelectedBonds GetSelectedContours GetSelectedGrids GetSelectedMolecules GetSelectedMonitors GetSelectedSurfaces GetSurfacesByScope GetSurfacesScoped

GetVisibleAtoms GetVisibleBonds GetVisibleContours GetVisibleGrids GetVisibleIDs GetVisibleMolecules GetVisibleMonitors GetVisibleSurfaces GotoStylePage GRASP GridAdd GridCheckIn GridCheckOut GridClear GridCopy GridCreateElectrostaticsGrid GridCreateGaussian GridCreateGaussianProduct GridDefaultContourColorByIndexGet GridDefaultContourColorByIndexSet GridDefaultContourLevelByIndexGet GridDefaultContourLevelByIndexSet GridDefaultDrawAsSurfaceGet GridDefaultDrawAsSurfaceSet GridDefaultNumContoursGet GridDefaultNumContoursSet GridInitializeContours GridNormalize GridRegularize GridShowCornersGet GridShowCornersSet GridShowLastMaskedGrid GridToGaussianGrid GridTypeGet GridTypeGetScoped GridTypeSet GridTypeSetScoped GridWorkingGetScoped

H

HaloColorDefaultGet HaloColorDefaultSet HaloColorGet HaloColorSet HaloColorSetScoped HaloRadiusGet HaloRadiusSet HaloRadiusSetScoped HaloScaleGet HaloScaleSet HaloScaleSetScoped HasGridChildrenScoped HasSurfaceChildrenScoped HBondAddTarget HBondAddTargetsScoped HBondClearTargets HBondColorGet HBondColorSet HBondRemoveTarget HBondRemoveTargetsScoped HBondShowExternalGet HBondShowExternalSet HBondShowInternalGet HBondShowInternalSet

HideNoneScoped HideOthers HideScoped 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] -nostructs [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]

I

IconGetXPM IDGet IDTypeGet in-memory InChI InChIKey Initialize InitializeObject InterpreterClear InterpreterInteractiveGet InterpreterInteractiveSet InterpreterPopUpdateGUI InterpreterPushUpdateGUI InterpreterShowDebugTextGet InterpreterShowDebugTextSet InterpreterTimerGet

InterpreterTimerSet InterpreterUpdatesGUI Iridium IsActive IsAGrid IsAList IsAMolecule IsAReflection IsASmallMolecule IsASurface IsLicensed IsLocked IsMarked IsSelected IsTrulyVisible IsVisible

J

JournalInit

JSON

K

KeyGet KeyIDGet KeyParentIDGet

KeysGet KeySourceIDGet KeyTypeGet

L

LabelClearColorScoped LabelClearScoped LabelColorScoped LabelDefaultColorGet LabelDefaultColorSet LabelFixedSizeGet LabelFixedSizeSet LabelGet LayoutCurrentGet LayoutExists LayoutGet LayoutIcon LayoutLoad LayoutOrganizePrompt LayoutOverrideOrder LayoutRemove LayoutRename Layouts LayoutSaveCurrent LayoutSet LayoutStickyGet LayoutStickySet LINGO ListAddObject ListAddObjects ListGetNames ListGetObjectLists ListGetObjects ListMoveObject ListMoveObjects ListNew ListNewAnd ListNewMarked ListNewOr ListNewXor ListRemoveObject ListRemoveObjects ListRootList ListSubsetMarked ListSubsetQuery

ListWindowCollapseAll ListWindowCollapseCurrent ListWindowExpandAll ListWindowExpandCurrent ListWindowFirstList ListWindowFirstListItem ListWindowFocusOnOERID ListWindowGetCurrentPos ListWindowHideColumn ListWindowIsVisible ListWindowLastList ListWindowLastListItem ListWindowNavigateChildrenGet ListWindowNavigateChildrenSet ListWindowNavigateLeft ListWindowNavigateRight ListWindowNextList ListWindowNextListItem ListWindowPrevList ListWindowPrevListItem ListWindowRowColoringGet ListWindowRowColoringSet ListWindowSetCurrentPos ListWindowShowColumn Lock LockScoped loopdb_builder command line option -added_date <value> -append <bool> -crop_length <value> -exclude_reg_ss <value> -in <directory> -log <logfile> -max_length <value> -ncpu <value> -prefix <prefix> -settings <settingsfile> -source_date <value> -source_name <value> -title <title> -verbose :

M

MACCS macrocycle command line option -ewindow -in -iteration_cycle_size -max_iterations -maxconfs -molnames -mpi_hostfile -mpi_np -out -param -prefix -progress -ref_tolerance -rms MainWindowScreenshot MainWindowScreenshotPrompt makefraglib command line option -buildff -ewindow -ewindowRing -fragGen -fragGenRing -fragKeep -fragKeepRing -fromCT -in -log -molNames -mpi_hostfile <filename> -mpi_np <n> -out -param -prefix -progress -rms -rmsRing -startfact -startfactRing -timeLimit -timeLimitRing -verbose makerocsdb command line option -in <filename> -out <prefix> marching cubes Mark MarkObjectsByScope MarkScoped MarkState memory-mapped Menu Items MenuAddButton MenuAddLabel MenuAddRadioButton MenuAddSeparator MenuAddSubmenu MenuAddToggleButton MenuBeginRadioGroup MenuButtonActionSet MenuDisplayName MenuDynamicSet MenuEnableItem MenuEnableItemCommand MenuEndRadioGroup MenuExists MenuGetAllItems MenuGetAllItemsContainingName MenuHasItem MenuItemIsAMenu MenuRemoveAll MenuRemoveItem MenuUpdateItem MenuUseTearoffsGet MenuUseTearoffsSet

MimicParentVisibilityGet MimicParentVisibilitySet MimicParentVisibilitySetScoped module modules MOL molcharge command line option -in -method {option} -out -param -paramfile -prefix MoleculeAdd MoleculeAddExplicitHydrogens MoleculeAddHydrogens MoleculeAddHydrogensScoped MoleculeAltLocationShow MoleculeAltLocationVisible MoleculeAtomBondStyleSetScoped MoleculeCheckIn MoleculeCheckOut MoleculeColorByScoped MoleculeColorsResetScoped MoleculeComponentNamesGet MoleculeDarkColorsGet MoleculeDarkColorsSet MoleculeDeleteHydrogens MoleculeExamine MoleculeGenerateCoords MoleculeGenerateCoordsFixed MoleculeGenerateCoordsFixedScoped MoleculeGet MoleculeHasComponents MoleculeMaxResidueGet MoleculeMergeScoped MoleculeNew MoleculeNewSubset MoleculeNewSubsetScoped MoleculeResidueNameSetScoped MoleculeResidueSet MoleculeRotate MoleculeSetProperty MoleculeShowfAntsyGet MoleculeShowfAntsySet MoleculeSizeCutoffGet MoleculeSizeCutoffSet MoleculeStyleGet MoleculeStyleGetScoped MoleculeStyleLargeGet MoleculeStyleLargeSet MoleculeStyleNucleicGet MoleculeStyleNucleicSet MoleculeStyleProteinGet MoleculeStyleProteinSet MoleculeStyleSet MoleculeStyleSetScoped MoleculeStyleToEnum MoleculeStyleToText MoleculeUpdate MonitorAngleCreate MonitorAngleDelete MonitorAngleExists MonitorColorGet MonitorColorSet MonitorDeleteScoped MonitorDistanceCreate MonitorDistanceDelete MonitorDistanceExists MonitorSphereCreate MonitorsVisible MonitorsVisibleDelete MonitorTorsionCreate MonitorTorsionDelete MonitorTorsionExists Monte Carlo

N

NameGet

NameSet nonterminal atom

O

ObjectNameGet ObjectNameSet ObservableBool ObservableFloat ObservableInt ObservableKey ObservableOEKey ObservableString ObservableUInt ObservableUpdate ObservableVecFloat ObservableVecInt ObservableVecString ObservableVecUInt OE_ARCH, [1], [2], [3] OE_DIR OE_LICENSE OEB OEB2DUReceptor command line option -in <filename> -molnames -out <filename> -prefix -progress OEFuseKeyGroups OEGetKey OEKeyIterToVector OEKeyToID OEKeyToLabelString OEKeyToParentID OEKeyToSourceID OEPyClearActive OEPyClearLocked OEPyClearMarked OEPyClearSelected OEPyClearVisible OEPyGetActive OEPyGetIDForKey OEPyGetSelectedAtoms OEPyHide OEPyHideNone OEPyHideOthers OEPyIsActive OEPyIsLocked OEPyIsMarked OEPyIsSelected OEPyIsTrulyVisible OEPyIsVisible OEPySetActive OEPySetLocked OEPySetMarked OEPySetSelected OEPySetVisible omega command line option -addfraglib -addtorlib -batchMaxRotors -buildff -canonOrder -commentEnergy -deleteFixHydrogens -enumNitrogen -enumRing -erange -ewindow -failed -fixfile -fixmcs -fixrms -fixsmarts -flipper -flipper_enhstereo -flipper_maxcenters -flipper_warts -fromCT -includeInput -log -maxConfRange -maxconfs -maxmatch -maxrot -maxtime -maxTrials -maxTrialsRange -mcsMinAtoms -out -prefix -priorTemperature -progress -rangeIncrement -rms -rmsrange -rotorOffsetCompress -sampleHydrogens -sdEnergy -searchff -settorlib -strict -strictatomtyping -strictfrags -strictstereo -thompson -torlibtype -trialsRangeIncrement -umatch -useGPU -verbose -warts

Open OpenState OptimizeDU command line option -ff [Default: ff14sb_sage] -flexRange [Default: 2.0] -gradTol [Default: 1.0e-6] -in <filename> -ligandCharge [Default: current] -log -maxIter [Default: 1000] -molNames -optimize [Default: cartesian] -out <filename> -prefix -progress -proteinMask -residueID [Default: None] -solventModel [Default: vacuum] -verbose OptLigandInDU command line option -du <filename> -ff [Default: ff14sb_sage] -gradTol [Default: 1.0e-6] -in <filename> -ligandCharge [Default: current] -log -maxIter [Default: 1000] -molNames -optimize [Default: cartesian] -out <filename> -prefix -progress -proteinMask -solventModel [Default: vacuum] -verbose Orion back end Orion Platform

P

package packages PaneActivated PasteMolecules PATH, [1], [2], [3], [4], [5] Philosophy and Design Pick PickAgain pkatyper command line option -count -in -max -out -param -paramfile -prefix -warts popcount PopIgnoreHint PopState PopupAddButton PopupAddLabel PopupAddRadioButton PopupAddSeparator PopupAddSetupFunc PopupAddSubmenu PopupAddToggleButton PopupBeginRadioGroup PopupDisplayName PopupEnableItem PopupEnableItemCommand PopupEndRadioGroup PopupRemoveAll PopupRemoveItem posit command line option -allowed_clashes -best_Receptor_Pose_Only -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 PreferenceDump PreferenceGetBool PreferenceGetColor PreferenceGetDouble PreferenceGetFloat PreferenceGetInt PreferenceGetString PreferenceGetVBool PreferenceGetVDouble PreferenceGetVFloat PreferenceGetVInt PreferenceIsBool PreferenceIsColor PreferenceIsDouble PreferenceIsFloat

PreferenceIsInt PreferenceIsSet PreferenceIsString PreferenceIsVBool PreferenceIsVDouble PreferenceIsVFloat PreferenceIsVInt PreferenceMark PreferenceRemove PreferenceRestore Preferences PreferencesEdit PreferenceSetBool PreferenceSetColor PreferenceSetCommand PreferenceSetDouble PreferenceSetFloat PreferenceSetInt PreferenceSetString PreferenceSetVBool PreferenceSetVDouble PreferenceSetVFloat PreferenceSetVInt PreferenceValidateCommands preliminary API Preparation ProgressbarUpdate project PromptAtomicNum PromptBookmarkAnimationTime PromptColor PromptError PromptFilename PromptFilenames PromptFloat PromptFont PromptFragment PromptID PromptIDs PromptIDWriteFilters PromptInteger PromptKey PromptKeys PromptMessage PromptModeGet PromptModeSet PromptMolecule PromptMoleculeSplit PromptMulti PromptQuery PromptResponseBool PromptResponseCanceled PromptResponseColor PromptResponseFloat PromptResponseInt PromptResponseKey PromptResponseKeys PromptResponseString PromptResponseUInt PromptResponseVectInt PromptResponseVectMulti PromptResponseVectString PromptResponseVectUInt PromptSaveFilename PromptSmiles PromptString PromptStringListFromString PromptStringListToString PromptYesNo PromptYesNoSetDefault Pronunciation Property Filters Property Search PropertyTypeGet ProteinColorByBFactor ProteinColorByBFactorScoped PushIgnoreHint

Q

Query Molecule

Quit

R

raster image receptor 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_custom_constraints <filename> [No Default] -prepare_score_cache <fred -receptor <receptor file> -set_custom_constraints <filename> [No Default] -turn_inner_contour <on or off> [No Default] scorepose or hybrid> [No Default] ReceptorInDU command line option -addbox <distance> [No Default] -box <box file> [No Default] -in <filename> -molnames -negImageType [Default: standard] -out <filename> -prefix -progress -targetMask [Default: targetComplexNoSolvent] -targetPred receptors Redo RedoTo ResidueColorPaletteUpdate ResidueDarkColorsGet ResidueDarkColorsSet ResidueDefaultColorGet ResidueDefaultColorSet ResponseVectMulti Result View RibbonClearColorScoped RibbonColorSetScoped RibbonCrossResolutionGet RibbonCrossResolutionSet RibbonGapGet RibbonGapSet RibbonHeightScaleGet RibbonHeightScaleSet RibbonRadiusGet RibbonRadiusSet RibbonResolutionGet RibbonResolutionSet RibbonSplineTypeGet RibbonSplineTypeSet RibbonStyleGet RibbonStyleSet RibbonStyleSetScoped RibbonWidthScaleGet RibbonWidthScaleSet ROC curve rocs command line option -besthits <N> -chemff <cffname> -conflabel -cutoff <F> -dbase <filename> -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 rotatable bond rotfit command line option -autoMTZ <true or false> -Fc <columnname> -Fdelwt <columnname> -fixup_pepflips <true or false> -fixup_rotamers <true or false> -fixup_shapefit_residues <true or false> -Fobs <columnname> -Fwt <columnname> -in <proteinfile> -map <mtz file> -minimum_rscc <number> -minimum_rscc_increase <number> -mtype <setting> -out <protein> -param <parameter filename> -Phic <columnname> -Phidelwt <columnname> -Phiwt <columnname> -verbose <true or false> rscc command line option -clamp_at_level -flatten -in <molecule file> -mtz <mtz file> -rsr -scatter -verbose

S

Save SaveMiniState SaveState SaveStateFilter SceneDrawActiveBorderGet SceneDrawActiveBorderSet SceneMatrixModeGet SceneMatrixModeSet 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] scorepose or hybrid> [No Default] receptor_toolbox command line option ScratchClear ScratchGet ScratchInsert ScratchList ScratchSet script scripts SDataGet SDataHas SDataSet SDDataGet SDDataHas SDDataSet SDF Select SelectAllMolecules SelectByQuery SelectInvert SelectionColorBlendFactorGet SelectionColorBlendFactorSet SelectKeys SelectOERID SelectResidues SelectScoped SelectWithin SelectWithout SetProgressbar SettingsGetBool SettingsGetFloat SettingsGetInt SettingsGetString SettingsRestore SettingsSetBool SettingsSetFloat SettingsSetInt SettingsSetString SettingsSync shard ShowESGridScoped ShowSurface ShowSurfaceScoped Similarity Search sitehopper_build command line option -append -dbase <filename> -dir <path> -log <logfile> -ncpu -overwrite -param <param_file> -prefix <prefix> -progress : Shows a progress bar -verbose : Triggers copious logging output sitehopper_search command line option -cutoff <float> -database <filename> -log <logfile> -max_hits <value> -ncpu <value> -normalize_and_rescore <bool> -out <filename> -param <paramfile> -prefix <prefix> -query <filename> -sequence_cutoff <float> -use_gpu <bool> -verbose SketcherInputSet SketcherLookupFunctionSet SMARTS SMILES SMIRKS SpreadsheetAddColumn SpreadsheetColumnColorerSet SpreadsheetColumnController SpreadsheetColumnFontGet SpreadsheetColumnFontSet SpreadsheetColumnReadonly SpreadsheetColumnSigFigGet SpreadsheetColumnSigFigSet SpreadsheetCommitChanges SpreadsheetCopy SpreadsheetCreateColumnExpression SpreadsheetCreateFilter SpreadsheetCurrent SpreadsheetCurrentGet SpreadsheetCurrentSet SpreadsheetData SpreadsheetDeleteColumn SpreadsheetDisableUpdates SpreadsheetEditableGet SpreadsheetEditableSet SpreadsheetEnableUpdates SpreadsheetFilter SpreadsheetFromList SpreadsheetGetColumn SpreadsheetGetCurrentRow SpreadsheetGetIDForRow SpreadsheetGetImageStreamAtRow SpreadsheetGetKeyForRow SpreadsheetGetNumRows SpreadsheetGetRowForKey SpreadsheetGetSpreadsheets SpreadsheetHeaders SpreadsheetHideColumn SpreadsheetHideTab SpreadsheetImport SpreadsheetLingoSimSort SpreadsheetLoadFilter SpreadsheetMarkHighlighted SpreadsheetMolNumberFunction SpreadsheetMolStringFunction SpreadsheetMoveColumn SpreadsheetNumRows SpreadsheetPromptColumnExpression SpreadsheetPromptExport SpreadsheetPromptFilter SpreadsheetPromptFormat SpreadsheetPromptGraphemeOpts SpreadsheetPromptImport SpreadsheetPromptSort SpreadsheetRemoveTab SpreadsheetRowHeightGet SpreadsheetRowHeightSet SpreadsheetSetData SpreadsheetSetExpression SpreadsheetSetRowData SpreadsheetShowAllColumns SpreadsheetShowAllTabs SpreadsheetShowColumn SpreadsheetShowStats SpreadsheetShowStatsGet SpreadsheetShowStatsSet SpreadsheetShowTab SpreadsheetSort SpreadsheetUpdateContents spruce command line option -add_interactions -add_receptors -add_style -allow_filter_error -allow_truncate -allow_validation_error -altloc <method> -bb_clash_threshold <value> -bu_superpose -build_cterm_caps -build_disulfidebridges <value> -build_loops -build_nterm_caps -build_sidechains -build_with_crystalpacking -cap_delete_clashing_solvent -charge_radii -cofactor_codes <codes> -collapse_nonsite_alts -crop_length <value> -duplicate_removal -enum_cofactors_sites -enum_pockets -excipient_codes -fix_bb_atoms -fix_bonds_to_metals -fix_chainID -fix_covalent_bond -fix_float_res -fix_res_names -fix_res_states -flip_bias_scale -generate_tautomers -het_group_nbr_dist <value> -in <filename> -incl_SA_term <value> -incl_solvation <value> -ligand_names <names> -lipid_codes <codes> -log <logfile> -loop_clash_threshold <value> -loop_db_filename <filename> -loop_distance_buffer <value> -make_packing_residues -map <filename> -max_bu_atoms -max_bu_parts -max_eval_loops <value> -max_lig_atoms -max_lig_residues -max_pocket_surf_area -max_sys_atoms -metadata <filename> -min_align_score -min_lig_atoms -min_pocket_surf_area -no_prep -opt_expt_protons -opt_shell <value> -opt_stage1_iter_multiplier <value> -opt_stage2_iter_multiplier <value> -opt_tolerance <value> -out <out> -pocket_burial_factor -pocketMask -pref_author_record -prefix <prefix> -protonate -ref <filename> -restrict_to_refsite -rot_coverage <value> -rot_library <value> -sc_delete_clashing_solvent -settings <settingsfile> -site_residue <residue identifier> -site_size: <value> -strict_proline_match -superpose -superpose_method : <method> -target -targetMask -transform_threshold <value> -verbose : Triggers copious logging output -warts -write_biounits

stable API StateMark StatePop stereo atom stereo bond structural key Subset Substructure Search superposition command line option -fit <filename> -fit_lig <filename> -log <logfile> -method <method> -prefix <prefix> -ref <filename> -ref_lig <filename> -settings <settingsfile> -verbose : Triggers copious logging output SurfaceAdd SurfaceAlterTransparency SurfaceBestFloodScoped SurfaceCheckIn SurfaceCheckOut SurfaceColorBy SurfaceColorByScoped SurfaceColorGet SurfaceColorGetScoped SurfaceColorSet SurfaceColorSetScoped SurfaceCreate SurfaceCreateScoped SurfaceCropDistance SurfaceCropDistanceFrom SurfaceCropScribedScoped SurfaceCropUnscribedScoped SurfaceDelete SurfaceGenerateBox SurfaceGenerateSphere SurfaceGenerateSpline SurfaceGrowTriangle SurfaceLineWidthGet SurfaceLineWidthSet SurfacePickTriangle SurfacePotentialColorAuto SurfacePotentialColorValuesSet SurfaceProbeRadiusGet SurfaceProbeRadiusSet SurfaceResolutionGet SurfaceResolutionSet SurfaceRestoreScoped SurfaceScribeScoped SurfaceSetPotentialFromGrid SurfaceSetPotentialFromGridScoped SurfaceStyleGet SurfaceStyleGetScoped SurfaceStyleSet SurfaceStyleSetScoped SurfaceTransparencySet SurfaceTransparencySetScoped SurfaceVertexFloodScoped SurfaceVolume SVG SymmetryColorModeGet SymmetryColorModeSet SymmetryNumOperators SymmetryOperatorEnabledGet SymmetryOperatorEnabledSet SymmetryRadiusGet SymmetryRadiusSet SymmetryRealize szmap command line option -apo_box <filename> -apo_coords -apo_grids -apo_point_grid -around <filename> -around_mol <filename> -at_coords <filename> -bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax> -boundary <number> -boundary_radius <number> -boundary_spacing <number> -bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax> -box_mol <filename> -chain <letter> -coords <filename> -cplx_grids -dcutoff <number> -dielectric_model <type> -distance_cutoff <number> -eps_in <number> -eps_out <number> -excludeDUligand -excludeDUsolvent -grid_spacing <number> -grids <type> -inner_dielectric <number> -inscode <letter> -l <filename> -lig_box <filename> -lig_coords -lig_grids -lig_point_grid -ligand <filename> -like_apo <filename> -like_box <filename> -like_lig <filename> -like_std <filename> -log <filename> -logfile <filename> -mask_cutoff <number> -model <type> -mpi_hostfile <filename> -mpi_np <number> -num_orientations <number> -o <filename> -outer_dielectric <number> -output_mol <filename> -p <filename> -param <filename> -point_grid -prefix <prefix> -progress <style> -properties <type> -protein <filename> -res <number> -residue_chain <letter> -residue_insert <letter> -residue_number <number> -restrict_calc <level> -results_set <type> -rot <number> -salt <number> -salt_conc <number> -space <number> -split_lig -stabilization -standard_grids -stbl -std_box <filename> -std_coords -std_grids -surf -surface_points -table <filename> -target <filename> -use_apo_from <filename> -v -value_cutoff <number> -vcutoff <number> -vdw_scale <number> -verbose -warn_if_missing_hydrogens -water_charge <type> -zap_spacing <number> szmap_report command line option -acolor <color> -aromstyle <style> -astl <style> -atomcolor <color> -atomsstl <style> -atomstereostyle <style> -bcolor <color> -bondcolor <color> -bondsstl <style> -bondstereostyle <style> -cols <number> -i <filename> -input <filename> -keep_hydrogens -legend <bool> -o <filename> -output <filename> -pagesize <size> -resolution <level> -rows <number> -separate -size <size> -surface <bool> -t <prop> -tag_set <set> -tagname <prop> -title <text> -v -verbose 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 -optdof -optGeometry <dof> -optMethod <type> -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

Tanimoto Tautomers tautomers command line option -ch3 -in -maxgenerated -maxtautomericatoms -maxtime -maxtoreturn -maxzonesize -out -param -paramfile -pkanorm -prefix -rank -stereo -warts Technical Details TitleDefaultColorGet TitleDefaultColorSet TitlesDrawAboveGet

TitlesDrawAboveSet ToolbarAddSeparator ToolbarAddToggle ToolbarBeginRadio ToolbarButtonEnableGet ToolbarButtonEnableSet ToolbarCreate ToolbarEnabledGet ToolbarEnabledSet ToolbarEndRadio ToolbarGetAll ToolbarItemCheckedGet ToolbarItemCheckedSet ToolbarItemUpdate ToolbarItemVisibleGet ToolbarItemVisibleSet ToolbarRemove ToolbarUpdate ToolbarVisibleGet ToolbarVisibleSet TransparencySet TransparencySetScoped

U

Undo UndoHint UndoMark

UndoTo UpdateRedo UpdateStyleWidget UpdateUndo

V

vector image VFCopyFile VFGetMol VFSleep ViewerActiveAnnotation ViewerActiveAnnotationBackgroundColorGet ViewerActiveAnnotationBackgroundColorSet ViewerActiveAnnotationClose ViewerActiveAnnotationFontGet ViewerActiveAnnotationFontSet ViewerActiveAnnotationForegroundColorGet ViewerActiveAnnotationForegroundColorSet ViewerActiveAnnotationVisible ViewerActiveDataFontSizeGet ViewerActiveDataFontSizeSet ViewerActiveDataHide ViewerActiveDataShow ViewerActiveDataVisible ViewerAmbientLightGet ViewerAmbientLightSet ViewerAmbientMaterialGet ViewerAmbientMaterialSet ViewerAnimate ViewerAnimateTo ViewerAntialiasGet ViewerAntialiasSet ViewerAutoCenterGet ViewerAutoCenterPanesGet ViewerAutoCenterPanesSet ViewerAutoCenterSet ViewerAutoFitGet ViewerAutoFitSet ViewerBackgroundColorGet ViewerBackgroundColorSet ViewerBookmarkLoad ViewerBookmarksGetAnimated ViewerBookmarksGetAnimationTime ViewerBookmarksSetAnimated ViewerBookmarksSetAnimationTime ViewerBookmarkWidget ViewerBookmarkWidgetFontSizeGet ViewerBookmarkWidgetFontSizeSet ViewerBookmarkWidgetHide ViewerBookmarkWidgetShow ViewerButtonImage ViewerCenterAndRadiusGet ViewerCenterAndRadiusSet ViewerCenterGet ViewerCenterSet ViewerCenterSetScoped ViewerClick ViewerCursorSet ViewerDepict ViewerDepictionAntiAliasGet ViewerDepictionAntiAliasSet ViewerDepictionHeightGet ViewerDepictionLineWidthGet ViewerDepictionLineWidthSet ViewerDepictionSizeSet ViewerDepictionWidthGet ViewerDepthcueEndGet ViewerDepthcueEndSet ViewerDepthCueFollowsSlab ViewerDepthcueGet ViewerDepthcueSet ViewerDepthcueStartGet ViewerDepthcueStartSet ViewerDiffuseLightGet ViewerDiffuseLightSet ViewerDiffuseMaterialGet ViewerDiffuseMaterialSet ViewerDrawDepictionsGet ViewerDrawDepictionsSet ViewerExportPOVRAY ViewerFit ViewerFontSizeGet ViewerFontSizeSet ViewerForwardGet ViewerGetShowObjectToolbar ViewerLabel ViewerLabelDialog ViewerLightPositionGet ViewerLightPositionSet ViewerLODGet ViewerLODSet ViewerLookAt ViewerMirrorSlabsGet

ViewerMirrorSlabsSet ViewerMouseClick ViewerMouseDoubleClick ViewerMouseFunctionGet ViewerMouseFunctionNameGet ViewerMouseFunctionSet ViewerMouseMap ViewerMouseMove ViewerMouseOutsideAwareGet ViewerMouseOutsideAwareSet ViewerMouseReset ViewerMouseSensitivityGet ViewerMouseSensitivitySet ViewerMouseWheel ViewerMove ViewerNiceFontsGet ViewerNiceFontsSet ViewerOrientationGet ViewerOrientationSet ViewerPickSurfaceTrianglesGet ViewerPickSurfaceTrianglesSet ViewerProgress ViewerProjectorModeGet ViewerProjectorModeSet ViewerRadiusGet ViewerRadiusSet ViewerRecenter ViewerRemoveWidget ViewerReprobeStereo ViewerRotate ViewerScaleGet ViewerScaleSet ViewerScreenshot ViewerSetShowObjectToolbar ViewerShininessMaterialGet ViewerShininessMaterialSet ViewerShowActiveBorderGet ViewerShowActiveBorderSet ViewerShowGridGet ViewerShowGridSet ViewerShowTrackballGuideSet ViewerSlabEnableGet ViewerSlabEnableSet ViewerSlabFarGet ViewerSlabFarSet ViewerSlabNearGet ViewerSlabNearSet ViewerSlabWidthGet ViewerSlabWidthSet ViewerSpecularMaterialGet ViewerSpecularMaterialSet ViewerStereoAngleGet ViewerStereoAngleSet ViewerStereoCrossEyedGet ViewerStereoCrossEyedSet ViewerStereoEnableGet ViewerStereoEnableSet ViewerStereoSeparationGet ViewerStereoSeparationSet ViewerStereoStyleGet ViewerStereoStyleSet ViewerStyleControlVisibleGet ViewerStyleControlVisibleSet ViewerSupportsHWStereo ViewerTextBox ViewerTextFontGet ViewerTextFontSet ViewerTextScaleGet ViewerTextScaleSet ViewerToggleRenderFeatures ViewerTranslateX ViewerTranslateY ViewerTranslateZ ViewerUpGet ViewerUseDisplayListGet ViewerUseDisplayListSet ViewerUseInertiaGet ViewerUseInertiaSet ViewerUseKeyMapGet ViewerUseKeyMapSet ViewerUseSystemFontsGet ViewerUseSystemFontsSet ViewerWheel ViewerWidgetUpdate Visible VisibleScoped VisualizeCommandScopeGet VisualizeCommandScopeSet

W

WaitBegin WaitEnd WindowEnabledGet WindowEnabledSet WindowMenuUpdate WindowRegisterHotkey WindowVisibleGet WindowVisibleSet writedict command line option -assignCCP4 -forceExistingResidueNames -in <filename> -includeRotors -lookup -out <filename prefix> -planarAniline -prefix <filename prefix> -strict -suppressH -type -verbose -writeFullDict

WriteHistory

X

XRayAutoMapCalculationPrefsSet XRayCalculateMap XRayCalculatePhases XRayGetCell XRayGetSpaceGroup

XRayMTZColumnNamesCurrentDefaultsGet XRayMTZColumnNamesGet XRayMTZColumnNamesSet XRayMTZColumnNamesStandardDefaultsGet XRaySetCrystalParams XRayValidMaptypes

Z

zwitterion

zwitterionic