Index

Symbols | A | B | C | D | E | F | H | M | O | P | Q | R | S | T

Symbols

-acolor <color>
command line option
-addbox <distance> [No Default]
receptor_setup command line option
-addfraglib
omega command line option
-addtorlib
omega command line option
-all <format>
command line option
-allowed_clashes
posit command line option
-allowedClashes
combine_receptors command line option
-am1bcc
szybki command line option
-annotate_scores [Default: false]
fred command line option
hybrid command line option
scorepose command line option
-apo_box <filename>
command line option, [1]
-apo_coords
command line option
-apo_grids
command line option
-apo_point_grid
command line option
-aromstyle <style>
command line option
rocs_report command line option
-around <filename>
command line option
-around_mol <filename>
command line option
-astl <style>
command line option
rocs_report command line option
-at_coords <filename>
command line option, [1]
-atomcolor <color>
command line option
-atomsstl <style>
command line option
-atomstereostyle <style>
command line option
-attachColor
brood command line option
-attachFrag
brood command line option
-attachmentCutoff (-attachcut)
brood command line option
-attachmentScale (-attach, -aScale)
brood command line option
-base <NAME>
command line option
-bbox <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
command line option
-bcolor <color>
command line option
-besthits <N>
eon command line option
rocs command line option
-besthits N
command line option
-biggerisbetter
command line option
-bondcolor <color>
command line option
-bondOrder (-bo)
brood command line option
-bondsstl <style>
command line option
-bondstereostyle <style>
command line option
-bound_ligand <bound ligand file> [No Default]
receptor_setup command line option
-boundary <number>
command line option
-boundary_radius <number>
command line option
-boundary_spacing <number>
command line option
-bounding_box <xmin> <ymin> <zmin> <xmax> <ymax> <zmax>
command line option
-box <box file> [No Default]
receptor_setup command line option
-box_mol <filename>
command line option, [1]
-buildff
makefraglib command line option
omega command line option
-bumpRadius
brood command line option
-by <number>
command line option
-calc <run_type>
freeform command line option
-canonOrder
omega command line option
-capAttach
chomp command line option
-ch3
tautomers command line option
-chain <letter>
command line option
-charges
eon command line option
-checkBond (-checkbond)
brood command line option
-checkGeometry
brood command line option
-chemff <cff_file>
checkcff command line option
-chemff <cffname>
rocs command line option
-chunksize M
command line option
-clashed_molecule_file <filename>
posit command line option
-clean <bool>
command line option
-clear_score_cache [Default: false]
receptor_toolbox command line option
-cols <number>
command line option
-commentEnergy
omega command line option
-complex <filename>
szybki command line option
-conflabel
rocs command line option
-conftest <test type> [Default: isomeric]
fred command line option
hybrid command line option
posit command line option
scorepose command line option
-coords <filename>
command line option, [1]
-count
pkatyper command line option
-countConfs
command line option
-cpddb
brood command line option
-cplx_grids
command line option
-csv
brood command line option
-current_charges
szybki command line option
-cutoff <F>
rocs command line option
-cutoff <number>
command line option
-cutoff <score>
eon command line option
-db (-database)
brood command line option
-dbase <filename>
eon command line option
posit command line option
rocs command line option
-dbase <input filename1> [<input filename2> ... ]
fred command line option
-dbase <input filename1> [<input filename2> ...]
hybrid command line option
scorepose command line option
-dcutoff <number>
command line option
-default <number>
command line option
-default_value <number>
command line option
-deleteFixHydrogens
omega command line option
-dielectric
omega command line option
-dielectric_constant
macrocycle command line option
-dielectric_model <type>
command line option
-disable_all_custom_constraints [Default: false]
receptor_toolbox command line option
-disable_all_protein_constraints [Default: false]
receptor_toolbox command line option
-disable_custom_constraint <constraint> [<constraint> ...] [No Default]
receptor_toolbox command line option
-disable_protein_constraint <name> [<name> ...] [No Default]
receptor_toolbox command line option
-distance_cutoff <number>
command line option
-dock_resolution <setting> [Default: Standard]
fred command line option
hybrid command line option
-docked_molecule_file <filename>
posit command line option
-docked_molecule_file <filename> [Default: docked.oeb.gz]
hybrid command line option
-docked_molecule_file <filename> [Default: docked.oeb.gz]
fred command line option
-docked_poses <filename>
docking_report command line option
-dots
brood command line option
chomp command line option
command line option
-eganEgg (-egan)
brood command line option
-enable_all_custom_constraints [Default: false]
receptor_toolbox command line option
-enable_all_protein_constraints [Default: false]
receptor_toolbox command line option
-enable_custom_constraint <constraint> [<constraint> ...] [No Default]
receptor_toolbox command line option
-enable_protein_constraint <name> [<name> ...] [No Default]
receptor_toolbox command line option
-ensemble
freeform command line option
-entropy <type>
szybki command line option
-enumNitrogen
flipper command line option
omega command line option
-enumRing
omega command line option
-eon_input
rocs command line option
-eon_input_file <filename>
rocs command line option
-eon_input_size <N>
rocs command line option
-eon_maxconfs <N>
rocs command line option
-eps_in <number>
command line option
-eps_out <number>
command line option
-erange
omega command line option
-ET (-et)
brood command line option
-ewindow
eon command line option
freeform command line option
macrocycle command line option
makefraglib command line option
omega command line option
-exact_vdw
szybki command line option
-exponent
omega command line option
-extract_bound_ligand <filename> [No Default]
receptor_toolbox command line option
-extract_custom_constraints <filename> [No Default]
receptor_toolbox command line option
-extract_extra_molecules <filename> [No Default]
receptor_toolbox command line option
-extract_protein <filename> [No Default]
receptor_toolbox command line option
-fail
command line option
-ff
szybki command line option
-ff <type>
freeform command line option
-fileChrg
brood command line option
-filter
chomp command line option
command line option
-fix_elements
command line option
-fix_file <filename>
szybki command line option
-fix_smarts <file_name>
szybki command line option
-fixfile
omega command line option
-fixpka_dbase
eon command line option
-fixpka_query
eon command line option
-fixrms
omega command line option
-fixsmarts
omega command line option
-flex_file <filename>
szybki command line option
-flexdist <d>
szybki command line option
-flexlist <fn>
szybki command line option
-flextype <type>
szybki command line option
-flipN
chomp command line option
-flipper
chomp command line option
omega command line option
-flipper_maxcenters
omega command line option
-flipper_warts
omega command line option
-forcefield
brood command line option
-forceflip
flipper command line option
-forceFlip
chomp command line option
-format
brood command line option
-fromCT
brood command line option
makefraglib command line option
omega command line option
-g <name>
command line option
-geq <number>
command line option
-geq_mask <number>
command line option
-grad_conv <c>
szybki command line option
-grid <name>
command line option
-grid1 <name>
command line option
-grid2 <name>
command line option
-grid3 <name>
command line option
-grid_spacing <number>
command line option
-grids <type>
command line option
-harm_constr1 <k>
szybki command line option
-harm_constr2 <d>
szybki command line option
-harm_smarts <file.txt>
szybki command line option
-heavy_rms
szybki command line option
-hitinterval
brood command line option
-hitlist_size
posit command line option
-hitlist_size <num> [Default: 500]
scorepose command line option
-hitlist_size <num> [Default: 500]
fred command line option
hybrid command line option
-hitlistProt
brood command line option
-hitsfile <filename>
eon command line option
rocs command line option
-i <filename>
command line option
rocs_report command line option
-i <filename>
command line option, [1], [2], [3], [4]
freeform command line option
szybki command line option
-idea (-cluster)
brood command line option
-ignore_nitrogen_stereo
posit command line option
-in
command line option, [1]
fixpa command line option
flipper command line option
macrocycle command line option
makefraglib command line option
molcharge command line option
pkatyper command line option
tautomers command line option
-in (-i)
chomp command line option
-in <filename>
checkcff command line option
command line option, [1]
freeform command line option
makerocsdb command line option
posit command line option
rocs_report command line option
szybki command line option
-in1 (-i1)
command line option
-in1 <filename>
command line option
-in2 (-i2)
command line option
-in2 <filename>
command line option
-in3 <filename>
command line option
-includeInput
omega command line option
-info
brood command line option
command line option
-inner_dielectric <d>
szybki command line option
-inner_dielectric <number>
command line option
-input <filename>
command line option
-input_file1 <filename>
command line option
-input_file2 <filename>
command line option
-input_file3 <filename>
command line option
-input_mol <filename>
command line option, [1], [2], [3]
-inscode <letter>
command line option
-int_method <value>
command line option
-interval
brood command line option
command line option
-ionic <type>
freeform command line option
-ionize
fixpa command line option
-iteration_cycle_size
macrocycle command line option
-keep_alts
command line option
-keep_hydrogens
command line option
-keep_numbers
command line option
-keepFailures
szybki command line option
-l <filename>
command line option, [1], [2]
szybki command line option
-largest_part
szybki command line option
-legend <bool>
command line option
-leq <number>
command line option
-leq_mask <number>
command line option
-lig_box <filename>
command line option, [1]
-lig_ch <char>
command line option
-lig_coords
command line option
-lig_end <int>
command line option
-lig_grids
command line option
-lig_ins <char>
command line option
-lig_model <int>
command line option
-lig_num <int>
command line option
-lig_point_grid
command line option
-lig_res <RES>
command line option
-ligand <filename>
command line option, [1]
-ligand_chain <char>
command line option
-ligand_inscode <char>
command line option
-ligand_model <int>
command line option
-ligand_res <RES>
command line option
-ligand_residue <residue identifier>
pdb2receptor command line option
-ligand_resnum <int>
command line option
-ligand_resnum_end <int>
command line option
-ligands <filename>
szybki command line option
-light_background
command line option
-light_bkg
command line option
-like_apo <filename>
command line option
-like_box <filename>
command line option
-like_lig <filename>
command line option
-like_std <filename>
command line option
-linkOnly (-linkonly, -struc, -struct)
brood command line option
-loadPG <filename>
szybki command line option
-log
brood command line option
command line option
makefraglib command line option
omega command line option
-log <filename>
command line option, [1]
-log <prefix>
szybki command line option
-logfile <filename>
command line option, [1]
eon command line option
rocs command line option
-mask_cutoff <number>
command line option, [1]
-mask_vdw
command line option
-masked_point_cutoff <number>
command line option
-max
pkatyper command line option
-max_iter <m>
szybki command line option
-max_iterations
macrocycle command line option
-maxAromFJCt
brood command line option
-maxcenters
flipper command line option
-maxChiral
chomp command line option
-maxComplexity (-maxComp)
brood command line option
-maxConfRange
omega command line option
-maxconfs
macrocycle command line option
omega command line option
-maxconfs <N>
rocs command line option
-maxconfs <value>
freeform command line option
-maxDegree
chomp command line option
-maxFrag
brood command line option
-maxFrequency (-maxFreq)
brood command line option
-maxFsp3C
brood command line option
-maxgenerated
tautomers command line option
-maxHit (-maxhit)
brood command line option
-maxhits <N>
eon command line option
rocs command line option
-maxHvy
chomp command line option
-maxHvyAtom (-maxHeavyAtom)
brood command line option
-maxLipinski
brood command line option
-maxLipinskiAcc (-maxLipinskiAcceptors, -maxAcceptors)
brood command line option
-maxLipinskiDon (-maxLipinskiDonors, -maxDonors)
brood command line option
-maxLocalStrain
brood command line option
-maxlogp
brood command line option
-maxMartin (-maxAbbott, -maxABS)
brood command line option
-maxmatch
omega command line option
-maxMolWt
chomp command line option
-maxMolWt (-maxmolecularweight)
brood command line option
-maxpages
rocs_report command line option
-maxpsa (-maxtpsa)
brood command line option
-maxrot
omega command line option
-maxRotBond (-maxRotatableBond)
brood command line option
-maxtautomericatoms
tautomers command line option
-maxtime
omega command line option
tautomers command line option
-maxtoreturn
tautomers command line option
-maxzonesize
tautomers command line option
-mcquery
rocs command line option
-merge <number>
command line option
-method <value>
command line option
-method {option}
molcharge command line option
-minAromFJCt
brood command line option
-minComplexity (-minComp)
brood command line option
-minDegree
chomp command line option
-minFrequency
chomp command line option
-minFrequency (-minFreq)
brood command line option
-minFsp3C
brood command line option
-minHvy
chomp command line option
-minHvyAtom (-minHeavyAtom)
brood command line option
-minimum_probability
posit command line option
-minLipinski
brood command line option
-minLipinskiAcc (-minLipinskiAcceptors, -minAcceptors)
brood command line option
-minLipinskiDon (-minLipinskiDonors, -minDonors)
brood command line option
-minlogp
brood command line option
-minMartin (-minAbbott, -minABS)
brood command line option
-minMolWt (-minmolecularweight)
brood command line option
-minpsa (-mintpsa)
brood command line option
-minRotBond (-minRotatableBond)
brood command line option
-mod_vdw
szybki command line option
-model <type>
command line option
-mol <filename>
command line option
-molnames
posit command line option
-molnames <input filename> [No Default]
fred command line option
hybrid command line option
scorepose command line option
-mpi_hostfile
brood command line option
macrocycle command line option
-mpi_hostfile <filename>
command line option
eon command line option
makefraglib command line option
omega command line option
posit command line option
rocs command line option
szybki command line option
-mpi_np
brood command line option
macrocycle command line option
-mpi_np <n>
eon command line option
makefraglib command line option
omega command line option
posit command line option
rocs command line option
szybki command line option
-mpi_np <number>
command line option
-names <molecule name> [<molecule name> ...] [No Default]
docking_report command line option
-nchunks N
command line option
-neglect_frozen
szybki command line option
-neutralpH
brood command line option
-new_value <number>
command line option
-newrule
command line option
-no_dots
posit command line option
-no_dots [Default: false]
fred command line option
hybrid command line option
scorepose command line option
-no_extra_output_files
posit command line option
-no_extra_output_files [Default: false]
hybrid command line option
scorepose command line option
-no_extra_output_files [Default: false]
fred command line option
-no_fixup
command line option
-no_pka_adjustment
command line option
-no_strip_water [Default: false]
receptor_setup command line option
-no_table
command line option
-noadj
command line option
-noCoulomb
szybki command line option
-nonsym
command line option
-nonsymmetrized_charges
command line option
-noqueryprot (-noqueryprotein)
brood command line option
-noqueryselectprot (-noqueryselectionprotein, -noqueryselection)
brood command line option
-normalize
command line option
-nostructs
rocs command line option
-num_orientations <number>
command line option, [1]
-num_poses
posit command line option
-num_poses <num> [Default: 1]
fred command line option
hybrid command line option
-o <filename>
command line option
rocs_report command line option
-o <filename.txt>
command line option
-o <filename>
command line option, [1], [2], [3], [4]
szybki command line option
-oformat <extension>
eon command line option
rocs command line option
-omega
chomp command line option
-op <value>
command line option
-operation <value>
command line option
-opt
rocs command line option
-optchem
rocs command line option
-optdof
szybki command line option
-optDOF
szybki command line option
-optGeometry <dof>
szybki command line option
-optimize <level> [No Default]
scorepose command line option
-optMethod <type>
szybki command line option
-out
command line option, [1]
fixpa command line option
flipper command line option
macrocycle command line option
makefraglib command line option
molcharge command line option
pkatyper command line option
tautomers command line option
-out (-o)
chomp command line option
command line option
-out <filename>
command line option
freeform command line option
rocs_report command line option
szybki command line option
-out <oebfile>
checkcff command line option
-out <prefix>
makerocsdb command line option
-out_complex <filename>
szybki command line option
-out_protein <filename>
szybki command line option
-outer_dielectric <number>
command line option
-output <filename>
command line option, [1]
-output_all_format <format>
command line option
-output_grid <filename>
command line option, [1]
-output_lig <filename>
command line option
-output_mol <filename>
command line option, [1], [2]
-output_prot <filename>
command line option
-output_txt <filename.txt>
command line option
-output_waters <filename>
command line option
-outputall
posit command line option
-outputdir
combine_receptors command line option
-outputdir <dirname>
rocs command line option
-outputquery
eon command line option
rocs command line option
-overwrite (-over)
command line option
-p <filename>
command line option, [1], [2]
szybki command line option
-pad_zeros
command line option
-pagesize <size>
command line option
rocs_report command line option
-param
brood command line option
command line option
eon command line option
macrocycle command line option
makefraglib command line option
molcharge command line option
omega command line option
pkatyper command line option
posit command line option
rocs command line option
szybki command line option
tautomers command line option
-param <filename>
combine_receptors command line option
command line option, [1]
freeform command line option
-param <parameter filename> [No Default]
fred command line option
hybrid command line option
scorepose command line option
-paramfile
molcharge command line option
pkatyper command line option
tautomers command line option
-PBsolvent_dielectric <value>
freeform command line option
-pdb <filename>
apopdb2receptor command line option
pdb2receptor command line option
-pendingFile
omega command line option
-pkanorm
command line option
tautomers command line option
-point_grid
command line option
-prealigned
combine_receptors command line option
-prefix
brood command line option
chomp command line option
combine_receptors command line option
command line option
macrocycle command line option
makefraglib command line option
molcharge command line option
omega command line option
pkatyper command line option
posit command line option
tautomers command line option
-prefix <name>
rocs command line option
-prefix <p>
freeform command line option
-prefix <pn>
szybki command line option
-prefix <prefix>
command line option, [1]
eon command line option
-prefix <text>
command line option
-prefix <value> [Default: hybrid]
hybrid command line option
-prefix <value> [Default: fred]
fred command line option
-prefix <value> [Default: rescore]
scorepose command line option
-prepare_score_cache <fred, scorepose or hybrid> [No Default]
receptor_toolbox command line option
-primaryFrag
chomp command line option
-progress
eon command line option
makefraglib command line option
omega command line option
-progress <method>
rocs command line option
-progress <style>
command line option, [1]
-properties <type>
command line option
-property (-prop)
brood command line option
-prot (-protein)
brood command line option
-protein <filename>
command line option, [1]
szybki command line option
-protein <input filename>
receptor_setup command line option
-protein_elec <m>
szybki command line option
-protein_vdw <r>
szybki command line option
-psize <size>
rocs_report command line option
-qconflabel
rocs command line option
-query <filename>
eon command line option
rocs command line option
-queryFragment (-queryFrag)
brood command line option
-queryMol (-qMol)
brood command line option
-quickLook (-quick)
brood command line option
-radii <type>
szybki command line option
-randomstarts <N>
rocs command line option
-rangeIncrement
omega command line option
-rangeOffset
brood command line option
-rangeSize
brood command line option
-rank
tautomers command line option
-rankby <score>
eon command line option
rocs command line option
-rankby <SD tag>
command line option
-readConfs
chomp command line option
-receptor <filename> [Default: receptor.oeb.gz]
pdb2receptor command line option
receptor_setup command line option
-receptor <filename> [Default: receptor.oeb.gz]
apopdb2receptor command line option
-receptor <filename> [<filename> ...]
docking_report command line option
-receptor <filenames>
posit command line option
-receptor <receptor file1> [<receptor file2> ...]
hybrid command line option
-receptor <receptor file>
fred command line option
receptor_toolbox command line option
scorepose command line option
-receptors <filenames>
combine_receptors command line option
-ref_tolerance
macrocycle command line option
-refmol <filename>
rocs_report command line option
-rejected_file
posit command line option
-removeDuplicates (-duplicates)
command line option
-report
brood command line option
rocs command line option
szybki command line option
-report <filename>
checkcff command line option
freeform command line option
-report_file
posit command line option
-report_file <filename> [Default: docking_report.pdf]
docking_report command line option
-report_file <filename> [Default: report.txt]
fred command line option
hybrid command line option
scorepose command line option
-reportfile <filename>
eon command line option
rocs command line option
-reportFile <filename>
szybki command line option
-res <number>
command line option
-rescored_mol_output_file <output filename> [Default: scored.oeb.gz]
scorepose command line option
-residue_chain <letter>
command line option
-residue_insert <letter>
command line option
-residue_number <number>
command line option
-resolution <level>
command line option
-restrict_calc <level>
command line option
-results_set <type>
command line option
-ringOnly (-ring)
brood command line option
-rms
eon command line option
macrocycle command line option
makefraglib command line option
omega command line option
-rms <value>
freeform command line option
-rmsd_deduplicate
macrocycle command line option
-rmsrange
omega command line option
-rot <number>
command line option, [1]
-rotorOffsetCompress
omega command line option
-rows <number>
command line option
-salt
command line option
eon command line option
-salt <c>
szybki command line option
-salt <number>
command line option
-salt_conc <number>
command line option
-sampleHydrogens
eon command line option
omega command line option
-save_component_scores [Default: false]
fred command line option
hybrid command line option
scorepose command line option
-savePG <filename>
szybki command line option
-scale <number>
command line option
-scdbase
eon command line option
rocs command line option
-score_file
posit command line option
-score_file <filename> [Default: score.txt]
fred command line option
hybrid command line option
scorepose command line option
-score_tag
posit command line option
-score_tag <score tag> [No Default]
fred command line option
-score_tag <tag> [No Default]
scorepose command line option
-score_tag <tag> [No Default]
hybrid command line option
-scoreonly
eon command line option
rocs command line option
-sd_tags <Tag> [<Tag> ...] [No Default]
docking_report command line option
-sdEnergy
omega command line option
-sdtag
brood command line option
command line option
-sdtag <string>
szybki command line option
-sdTags
eon command line option
rocs command line option
-searchff
omega command line option
-select
command line option
-select (-selection)
brood command line option
-separate
command line option
-set_bound_ligand_title <title> [No Default]
receptor_toolbox command line option
-set_custom_constraints <filename> [No Default]
receptor_toolbox command line option
-set_receptor_title <title> [No Default]
receptor_toolbox command line option
-setfraglib
omega command line option
-settings_file
posit command line option
-settings_file <filename> [Default: settings.param]
fred command line option
hybrid command line option
scorepose command line option
-settorlib
omega command line option
-shapeCutoff
brood command line option
-shapeonly
rocs command line option
-shefA <a>
szybki command line option
-shefB <b>
szybki command line option
-sheffield
szybki command line option
-silent
szybki command line option
-site_residue <residue identifier>
apopdb2receptor command line option
-size <size>
command line option
-skip
makefraglib command line option
-slice
command line option
-smarts
chomp command line option
-smiles_file <filename> [No Default]
docking_report command line option
-solv_dielectric <d>
szybki command line option
-solvcharges <type>
freeform command line option
-solvent <type>
freeform command line option
-solvent_residues <name> [<name> ...] [Default: HOH]
apopdb2receptor command line option
-solvent_residues <name> [<name> ...] [Default: HOH]
pdb2receptor command line option
-solventCA <s>
szybki command line option
-solventPB
szybki command line option
-sort_poses [Default: false]
scorepose command line option
-sortby
posit command line option
-sp3_aromatic <bool>
command line option
-sp3aromatic <bool>
command line option
-space <number>
command line option
-spacing
eon command line option
-split_lig
command line option
-stabilization
command line option
-stabilization <bool>
command line option
-standard_grids
command line option
-startfact
makefraglib command line option
-stats
rocs command line option
-status
omega command line option
rocs command line option
-status_file
posit command line option
-status_file <filename> [Default: status.txt]
fred command line option
hybrid command line option
scorepose command line option
-statusfile
eon command line option
-statusfile <filename>
rocs command line option
-stbl
command line option
-stbl <bool>
command line option
-std_box <filename>
command line option, [1]
-std_coords
command line option
-std_grids
command line option
-stereo
tautomers command line option
-strict
omega command line option
szybki command line option
-strictatomtyping
omega command line option
-strictfrags
omega command line option
-strictstereo
omega command line option
-strip_water
szybki command line option
-subrocs
rocs command line option
-subtan
rocs command line option
-surf
command line option
-surface <bool>
command line option
-surface_points
command line option
-szmap_mpi_hostfile <filename>
command line option
-szmap_mpi_np <number>
command line option
-t
szybki command line option
-t <prop>
command line option
-table
command line option
-table <filename>
command line option
-tableFlag
command line option
-tag_set <set>
command line option
-tagname <prop>
command line option
-tanimoto_cutoff <F>
rocs command line option
-tautomer
brood command line option
-title
brood command line option
-title <text>
command line option
-to <number>
command line option
-tor_constr <fn>
szybki command line option
-torlibtype
omega command line option
-track <filename>
freeform command line option
-turn_inner_contour <on or off> [No Default]
receptor_toolbox command line option
-typecheck
command line option
-umatch
omega command line option
-undocked_molecule_file
posit command line option
-undocked_molecule_file <filename> [Default: undocked.oeb.gz]
fred command line option
hybrid command line option
-unique
command line option
-use_apo_from <filename>
command line option
-userFrags
chomp command line option
-userUnique
chomp command line option
-v
command line option, [1], [2], [3], [4], [5], [6], [7]
-value_cutoff <number>
command line option
-vcutoff <number>
command line option
-vdw_cutoff
szybki command line option
-vdw_scale <number>
command line option
-veber (-gsk)
brood command line option
-verbose
combine_receptors command line option
command line option, [1], [2], [3], [4], [5], [6], [7]
eon command line option
makefraglib command line option
omega command line option
rocs command line option
rocs_report command line option
szybki command line option
-verbose (-v)
command line option
-warn_if_missing_hydrogens
command line option, [1]
-warts
flipper command line option
omega command line option
tautomers command line option
-water_charge <type>
command line option
-waters <filename>
command line option
-writegrid
eon command line option
-zap_spacing <number>
command line option

A

Analog Search
apopdb2receptor command line option
-pdb <filename>
-receptor <filename> [Default: receptor.oeb.gz]
-site_residue <residue identifier>
-solvent_residues <name> [<name> ...] [Default: HOH]
Appending Data
Appendix 1
Appendix 2
APPNAME_OE_ARCH

B

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

C

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

D

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

E

environment variable
APPNAME_OE_ARCH
OE_ARCH, [1], [2], [3]
OE_DIR
OE_LICENSE
PATH, [1], [2], [3], [4], [5]
eon command line option
-besthits <N>
-charges
-cutoff <score>
-dbase <filename>
-ewindow
-fixpka_dbase
-fixpka_query
-hitsfile <filename>
-logfile <filename>
-maxhits <N>
-mpi_hostfile <filename>
-mpi_np <n>
-oformat <extension>
-outputquery
-param
-prefix <prefix>
-progress
-query <filename>
-rankby <score>
-reportfile <filename>
-rms
-salt
-sampleHydrogens
-scdbase
-scoreonly
-sdTags
-spacing
-statusfile
-verbose
-writegrid
Exact Search

F

fixpa command line option
-in
-ionize
-out
flipper command line option
-enumNitrogen
-forceflip
-in
-maxcenters
-out
-warts
fred command line option
-annotate_scores [Default: false]
-conftest <test type> [Default: isomeric]
-dbase <input filename1> [<input filename2> ... ]
-dock_resolution <setting> [Default: Standard]
-docked_molecule_file <filename> [Default: docked.oeb.gz]
-hitlist_size <num> [Default: 500]
-molnames <input filename> [No Default]
-no_dots [Default: false]
-no_extra_output_files [Default: false]
-num_poses <num> [Default: 1]
-param <parameter filename> [No Default]
-prefix <value> [Default: fred]
-receptor <receptor file>
-report_file <filename> [Default: report.txt]
-save_component_scores [Default: false]
-score_file <filename> [Default: score.txt]
-score_tag <score tag> [No Default]
-settings_file <filename> [Default: settings.param]
-status_file <filename> [Default: status.txt]
-undocked_molecule_file <filename> [Default: undocked.oeb.gz]
freeform command line option
-PBsolvent_dielectric <value>
-calc <run_type>
-ensemble
-ewindow
-ff <type>
-i <filename>
-in <filename>
-ionic <type>
-maxconfs <value>
-out <filename>
-param <filename>
-prefix <p>
-report <filename>
-rms <value>
-solvcharges <type>
-solvent <type>
-track <filename>

H

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

M

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

O

OE_ARCH, [1], [2], [3]
OE_DIR
OE_LICENSE
omega command line option
-addfraglib
-addtorlib
-buildff
-canonOrder
-commentEnergy
-deleteFixHydrogens
-dielectric
-enumNitrogen
-enumRing
-erange
-ewindow
-exponent
-fixfile
-fixrms
-fixsmarts
-flipper
-flipper_maxcenters
-flipper_warts
-fromCT
-includeInput
-log
-maxConfRange
-maxconfs
-maxmatch
-maxrot
-maxtime
-mpi_hostfile <filename>
-mpi_np <n>
-param
-pendingFile
-prefix
-progress
-rangeIncrement
-rms
-rmsrange
-rotorOffsetCompress
-sampleHydrogens
-sdEnergy
-searchff
-setfraglib
-settorlib
-status
-strict
-strictatomtyping
-strictfrags
-strictstereo
-torlibtype
-umatch
-verbose
-warts

P

PATH, [1], [2], [3], [4], [5]
pdb2receptor command line option
-ligand_residue <residue identifier>
-pdb <filename>
-receptor <filename> [Default: receptor.oeb.gz]
-solvent_residues <name> [<name> ...] [Default: HOH]
Philosophy and Design
pkatyper command line option
-count
-in
-max
-out
-param
-paramfile
-prefix
posit command line option
-allowed_clashes
-clashed_molecule_file <filename>
-conftest <test type> [Default: isomeric]
-dbase <filename>
-docked_molecule_file <filename>
-hitlist_size
-ignore_nitrogen_stereo
-in <filename>
-minimum_probability
-molnames
-mpi_hostfile <filename>
-mpi_np <n>
-no_dots
-no_extra_output_files
-num_poses
-outputall
-param
-prefix
-receptor <filenames>
-rejected_file
-report_file
-score_file
-score_tag
-settings_file
-sortby
-status_file
-undocked_molecule_file
Preferences
Preparation
Pronunciation
Property Filters
Property Search

Q

Query Molecule

R

receptor_setup command line option
-addbox <distance> [No Default]
-bound_ligand <bound ligand file> [No Default]
-box <box file> [No Default]
-no_strip_water [Default: false]
-protein <input filename>
-receptor <filename> [Default: receptor.oeb.gz]
receptor_toolbox command line option
-clear_score_cache [Default: false]
-disable_all_custom_constraints [Default: false]
-disable_all_protein_constraints [Default: false]
-disable_custom_constraint <constraint> [<constraint> ...] [No Default]
-disable_protein_constraint <name> [<name> ...] [No Default]
-enable_all_custom_constraints [Default: false]
-enable_all_protein_constraints [Default: false]
-enable_custom_constraint <constraint> [<constraint> ...] [No Default]
-enable_protein_constraint <name> [<name> ...] [No Default]
-extract_bound_ligand <filename> [No Default]
-extract_custom_constraints <filename> [No Default]
-extract_extra_molecules <filename> [No Default]
-extract_protein <filename> [No Default]
-prepare_score_cache <fred, scorepose or hybrid> [No Default]
-receptor <receptor file>
-set_bound_ligand_title <title> [No Default]
-set_custom_constraints <filename> [No Default]
-set_receptor_title <title> [No Default]
-turn_inner_contour <on or off> [No Default]
Result View
rocs command line option
-besthits <N>
-chemff <cffname>
-conflabel
-cutoff <F>
-dbase <filename>
-eon_input
-eon_input_file <filename>
-eon_input_size <N>
-eon_maxconfs <N>
-hitsfile <filename>
-logfile <filename>
-maxconfs <N>
-maxhits <N>
-mcquery
-mpi_hostfile <filename>
-mpi_np <n>
-nostructs
-oformat <extension>
-opt
-optchem
-outputdir <dirname>
-outputquery
-param
-prefix <name>
-progress <method>
-qconflabel
-query <filename>
-randomstarts <N>
-rankby <score>
-report
-reportfile <filename>
-scdbase
-scoreonly
-sdTags
-shapeonly
-stats
-status
-statusfile <filename>
-subrocs
-subtan
-tanimoto_cutoff <F>
-verbose
rocs_report command line option
-aromstyle <style>
-astl <style>
-i <filename>
-in <filename>
-maxpages
-o <filename>
-out <filename>
-pagesize <size>
-psize <size>
-refmol <filename>
-verbose

S

scorepose command line option
-annotate_scores [Default: false]
-conftest <test type> [Default: isomeric]
-dbase <input filename1> [<input filename2> ...]
-hitlist_size <num> [Default: 500]
-molnames <input filename> [No Default]
-no_dots [Default: false]
-no_extra_output_files [Default: false]
-optimize <level> [No Default]
-param <parameter filename> [No Default]
-prefix <value> [Default: rescore]
-receptor <receptor file>
-report_file <filename> [Default: report.txt]
-rescored_mol_output_file <output filename> [Default: scored.oeb.gz]
-save_component_scores [Default: false]
-score_file <filename> [Default: score.txt]
-score_tag <tag> [No Default]
-settings_file <filename> [Default: settings.param]
-sort_poses [Default: false]
-status_file <filename> [Default: status.txt]
Similarity Search
Substructure Search
szybki command line option
-am1bcc
-complex <filename>
-current_charges
-entropy <type>
-exact_vdw
-ff
-fix_file <filename>
-fix_smarts <file_name>
-flex_file <filename>
-flexdist <d>
-flexlist <fn>
-flextype <type>
-grad_conv <c>
-harm_constr1 <k>
-harm_constr2 <d>
-harm_smarts <file.txt>
-heavy_rms
-i <filename>
-in <filename>
-inner_dielectric <d>
-keepFailures
-l <filename>
-largest_part
-ligands <filename>
-loadPG <filename>
-log <prefix>
-max_iter <m>
-mod_vdw
-mpi_hostfile <filename>
-mpi_np <n>
-neglect_frozen
-noCoulomb
-o <filename>
-optDOF
-optGeometry <dof>
-optMethod <type>
-optdof
-out <filename>
-out_complex <filename>
-out_protein <filename>
-p <filename>
-param
-prefix <pn>
-protein <filename>
-protein_elec <m>
-protein_vdw <r>
-radii <type>
-report
-reportFile <filename>
-salt <c>
-savePG <filename>
-sdtag <string>
-shefA <a>
-shefB <b>
-sheffield
-silent
-solv_dielectric <d>
-solventCA <s>
-solventPB
-strict
-strip_water
-t
-tor_constr <fn>
-vdw_cutoff
-verbose

T

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