Subsections
4.2 Command line options
4.2.1 Basic
-in- file containing input molecules
-out- file containing output molecules
-firstonly- Convert first molecule only and exit.
-helpformats- List supported formats.
-n- Convert first n-molecules (0, the default, means all).
-skip- Skip first n-molecules.
-v- verbose
-vv- very verbose
4.2.2 Advanced
-ifmt- input format specification. Not normally needed, since formats are implied by filename extensions. Specify by extension (e.g., "mol2", "sdf", "smi", etc.).
-ofmt- output format specification. Not normally needed, since formats are implied by filename extensions. Specify by extension (e.g., "mol2", "sdf", "smi", etc.). Useful with
-chunk.
-add2d- Generate 2D coordinates and include in the output. This functionality is disabled in the absence of a valid Ogham (oedepict) license.
-add2d is incompatible with output formats which cannot represent 2D.
-chunk- Split, a.k.a. "chunk", the output into several files. See also -chunk_prefix, -chunk_molcount, and -chunk_filecount. The default output file prefix is the input file directory and basename, and the specified output format. Output format should be specified by -ofmt and -ogz.
-chunk_filecount- number of chunk output files
-chunk_molcount- molecules per chunk output file
-chunk_prefix- file prefix for output chunk files (default is
INPATH/INBASE_XX)
-hydrogens- Hydrogen handling: allowed values are "add", "delete" and "same" (meaning same as input).
-igz- Ungzip input. Not normally needed, since file extension can imply gzipped.
-input_params- read execution parameters from file.
-mc- Treat the file as multi-conformer. Not needed for OEB which is multi-conformer by default.
-mc2sc- One output scmol for each input mcmol.
-mc_isomer- Treat the file as multi-conformer (isomeric).
-mc_titles- Multi-conformer perception title-sensitive.
-mdlstereocorrect- Correct non-compliant MDL stereo if
possible.
-molcount- Write molecule count to stdout.
-nowarn- Supress warnings.
-ogz- Gzip output. Not normally needed, since file extension can imply gzipped. Useful with
-chunk.
-output_names- Write molecule names (titles) 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 input and output as single-conformer molecules. This is the default for all input formats except OEBinary v1 and v2 (.bin and .oeb).
-sd2title- Copy specified SD data to title.
-stereofrom3d- perceive stereo from input 3D
4.2.3 Format flavors
If no format flavor flags are invoked, Babel will use the default flavors for the specified input and output
formats. These defaults are also available by using a flavor which combines the individual flavors; for example,
-mdloDefault. To see what these defaults are, view the detailed help for the specific default
flavor (e.g., babel -help -mdloDefault). If any input flavors are specified, the user must take
full control over all input flavors. Likewise for output flavors. So, to add one flavor to the defaults,
that flavor should be used in combination with the default flavor (e.g., babel -mdloDefault -mdloMV30).
Combining flavors involves a bitwise OR-ing of an integer datatype which represents a binary array for these
purposes. Babel reports flavors used as hex integers.
-iAroMask-
-iFlavorNone- Raw, no standardizations.
-iGenericMask-
-iOEAroModelDaylight- Daylight aromaticity model.
-iOEAroModelMDL- MDL aromaticity model.
-iOEAroModelMMFF- MMFF aromaticity model.
-iOEAroModelOpenEye- OpenEye aromaticity model.
-iOEAroModelTripos- Tripos aromaticity model.
-iRings- Perceive rings.
-oAroMask-
-oFlavorNone- Raw, no standardizations.
-oGenericMask-
-oOEAroModelDaylight- Daylight aromaticity model.
-oOEAroModelMDL- MDL aromaticity model.
-oOEAroModelMMFF- MMFF aromaticity model.
-oOEAroModelOpenEye- OpenEye aromaticity model.
-oOEAroModelTripos- Tripos aromaticity model.
-oRings-
-mmodiDefault- default flavors
-mmodiFormalCrg-
-mol2iDefault- default flavors
-mol2iM2H-
-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-
-smiiCanon- skips Kekulization test
-smiiDefault- default flavors
-smiiStrict- disallow format extensions
-xyziBondOrder-
-xyziConnect-
-xyziDefault- default flavors
-xyziExtraMask-
-xyziFormalCrg-
-xyziImplicitH-
-xyziRings-
-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-
-mfoDefault- default flavors
-mfoTitle- include title
-mmodoAtomTypes-
-mmodoDefault- default flavors
-mol2oAtomNames-
-mol2oAtomTypeNames-
-mol2oBondTypeNames-
-mol2oDefault- default flavors
-mol2oHydrogens-
-mol2oNameMask-
-mol2oOrderAtoms-
-mol2oSubstructure-
-mopacoCHARGES- write charges
-mopacoDefault- default flavors
-mopacoXYZ- cartesian coords (default is internal coords/z-matrix)
-pdboBONDS- write CONECT records (all single without -pdboORDERS)
-pdboBOTH- write bi-directional CONECT records
-pdboCHARGE- write partial charges to b-factor field
-pdboCurrentResidues-
-pdboDELPHI- combines -pdboCHARGE and -pdboRADIUS
-pdboDefault- default flavors
-pdboELEMENT- writes the chemical symbol in columns 77-78 of the output
-pdboFormalCrg- writes non-zero formal charges in columns 79-80 (and implies -pdboELEMENT)
-pdboHETBONDS- all bonds between (and to/from) hetero atoms are written to the output PDB file
-pdboNoResidues-
-pdboOEResidues-
-pdboORDERS- include bond orders in CONECT records
-pdboOrderAtoms-
-pdboRADIUS- write atomic radii to occupancy field
-pdboTER- terminate with TER rather than END
-smioAtomMaps-
-smioAtomStereo-
-smioBondStereo-
-smioCanonical-
-smioDefault- default flavors
-smioExtBonds-
-smioHydrogens-
-smioImpHCount-
-smioIsotopes-
-smioKekule-
-smioRGroups-
-smioSmiMask-
-smioSuperAtoms-
