2.3 Flavors

For each supported format there may be input and output flavors. Some flavors are generic and applicable to multiple formats. If none are specified the default flavor will be used. Babel is intended to expose all the format flavors defined in the official OEChem API. To list the available flavors, run "babel -help all":
prompt> babel --help all

          :jGf:
        :jGDDDDf:
      ,fDDDGjLDDDf,         ______       _          _
    ,fDDLt:   :iLDDL;       | ___ \     | |        | |
  ;fDLt:         :tfDG;     | |_/ / __ _| |__   ___| |
,jft:   ,ijfffji,   :iff    | ___ \/ _` | '_ \ / _ \ |
     .jGDDDDDDDDDGt.        | |_/ / (_| | |_) |  __/ |
    ;GDDGt:''':tDDDG,       \____/ \__,_|_.__/ \___|_|
   .DDDG:       :GDDG.
   ;DDDj         tDDDi      babel - molecular structure file conversion
   ,DDDf         fDDD,      version: 3.3
    LDDDt.     .fDDDj
    .tDDDDfjtjfDDDGt        copyright (c) 2005,2006,2007
      :ifGDDDDDGfi.         OpenEye Scientific Software, Inc.
          .:::.             OEChem version: 1.4.3
  ......................    platform: osx-10.4-g++3.3-G4
  DDDDDDDDDDDDDDDDDDDDDD    built: 20070401
  DDDDDDDDDDDDDDDDDDDDDD

        licensee: OpenEye
            site: Albuquerque

Complete parameter list
    basic : file i/o and other top level options
      -in : input file
      -out : output file
      -firstonly : convert first molecule
      -helpformats : list supported formats
      -n : convert only N molecules (0 means all)
      -skip : skip first N molecules
      -v : verbose
      -vv : very verbose

    advanced
      -ifmt : input format
      -ofmt : output format
      -add2d : add 2D coordinates
      -chunk : split the output into several files
      -chunk_filecount : number of chunk output files
      -chunk_molcount : molecules per chunk output file
      -chunk_prefix : file prefix for output chunk files (default is
                      <inbase>_XX)
      -hydrogens : hydrogen handling
      -igz : ungzip input
      -input_params : read execution parameters from file
      -mc : treat the file as multi-conformer
      -mc2sc : one output scmol for each input mcmol
      -mc_isomer : treat the file as multi-conformer (isomeric)
      -mc_titles : mc perception title-sensitive
      -mdlstereocorrect : correct non-compliant MDL stereo if possible
      -molcount : write molcount to stdout
      -nowarn : supress warnings
      -ogz : gzip output
      -output_names : write molecule names to file
      -output_params : write execution parameters to file
      -parts2mols : split out connected components
      -perceive_residues : perceive macromolecular residues
      -perceive_residues_preserve_All
      -perceive_residues_preserve_AlternateLocation
      -perceive_residues_preserve_ChainID
      -perceive_residues_preserve_HetAtom
      -perceive_residues_preserve_InsertCode
      -perceive_residues_preserve_ResidueName
      -perceive_residues_preserve_ResidueNumber
      -perceive_residues_preserve_SerialNumber
      -quiet : minimal verbosity, no banner
      -sc : handle as single-conformer molecules
      -sd2title : copy specified SD data to title
      -stereofrom3d : perceive stereo from input 3D

    flavors, input generic : generic (format non-specific) input flavors
      -iAroMask
      -iFlavorNone : raw, no standardizations
      -iGenericMask
      -iOEAroModelDaylight
      -iOEAroModelMDL
      -iOEAroModelMMFF
      -iOEAroModelOpenEye
      -iOEAroModelTripos
      -iRings

    flavors, output generic : generic (format non-specific) output flavors
      -oAroMask
      -oFlavorNone : raw, no standardizations
      -oGenericMask
      -oOEAroModelDaylight
      -oOEAroModelMDL
      -oOEAroModelMMFF
      -oOEAroModelOpenEye
      -oOEAroModelTripos
      -oRings

    flavors, input format specific : format specific input flavors
      flavors, mmod specific
        -mmodiDefault : default flavors
        -mmodiFormalCrg

      flavors, mol2 specific
        -mol2iDefault : default flavors
        -mol2iM2H

      flavors, pdb specific
        -pdbiALL : read all atoms including alternate locations, dummy atoms,
                   etc.
        -pdbiAllMask
        -pdbiBasicMask
        -pdbiBondOrder
        -pdbiCHARGE : read partial charges from b-factor field
        -pdbiConnect
        -pdbiDATA : preserve header data as generic data
        -pdbiDELPHI : combines -pdbiCHARGE and -pdbiRADIUS
        -pdbiDefault : default flavors
        -pdbiEND : read END as separator
        -pdbiENDM : read ENDM as separator
        -pdbiExtraMask
        -pdbiFormalCrg
        -pdbiImplicitH
        -pdbiRADIUS : read atomic radius from occupancy field
        -pdbiRings
        -pdbiTER : read TER as separator
        -pdbiTerMask

      flavors, smiles specific
        -smiiCanon
        -smiiDefault : default flavors
        -smiiStrict

      flavors, xyz specific
        -xyziBondOrder
        -xyziConnect
        -xyziDefault : default flavors
        -xyziExtraMask
        -xyziFormalCrg
        -xyziImplicitH
        -xyziRings


    flavors, output format specific : format specific output flavors
      flavors, mdl specific
        -mdloCurrentParity : write internal parity
        -mdloDefault : default flavors
        -mdloMCHG : write MCHG and MRAD fields for charged/radical atoms
        -mdloMDLParity : write MDL parity
        -mdloMISO : write ISO field for isotopes
        -mdloMMask
        -mdloMRGP : write RGP field for each R-group atom
        -mdloMV30 : MDL V3000 format
        -mdloNoParity : write no parity
        -mdloPMask

      flavors, mf specific
        -mfoDefault : default flavors
        -mfoTitle

      flavors, mmod specific
        -mmodoAtomTypes
        -mmodoDefault : default flavors

      flavors, mol2 specific
        -mol2oAtomNames
        -mol2oAtomTypeNames
        -mol2oBondTypeNames
        -mol2oDefault : default flavors
        -mol2oHydrogens
        -mol2oNameMask
        -mol2oOrderAtoms
        -mol2oSubstructure

      flavors, mopac specific
        -mopacoCHARGES : write charges
        -mopacoDefault : default flavors
        -mopacoXYZ : cartesian coords (default is internal coords/z-matrix)

      flavors, pdb specific
        -pdboBONDS : write CONECT records (all single without -pdboORDERS)
        -pdboBOTH : bi-directional CONECT records
        -pdboCHARGE : write partial charges to b-factor field
        -pdboCurrentResidues
        -pdboDELPHI : combines -pdboCHARGE and -pdboRADIUS
        -pdboDefault : default flavors
        -pdboELEMENT
        -pdboFormalCrg
        -pdboHETBONDS
        -pdboNoResidues
        -pdboOEResidues
        -pdboORDERS : include bond orders in CONECT records
        -pdboOrderAtoms
        -pdboRADIUS : write atomic radii to occupancy field
        -pdboTER : terminate with TER rather than END

      flavors, smiles specific
        -smioAtomMaps
        -smioAtomStereo
        -smioBondStereo
        -smioCanonical
        -smioDefault : default flavors
        -smioExtBonds
        -smioHydrogens
        -smioImpHCount
        -smioIsotopes
        -smioKekule
        -smioRGroups
        -smioSmiMask
        -smioSuperAtoms