mirror of
https://github.com/openbabel/openbabel.git
synced 2026-08-27 05:37:38 -05:00
Daniel Leidert
1deca607f1
doc/obfit.1, doc/obgen.1, doc/obgrep.1, doc/obminimize.1, doc/obprobe.1, doc/obprop.1, doc/obrotamer.1, doc/obrotate.1, doc/roundtrip.1: Prevent hyphenation of URLs. Fixed an mdoc issue.
368 lines
8.9 KiB
Groff
368 lines
8.9 KiB
Groff
.Dd July 4, 2008
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.Os "Open Babel" 2.2
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.Dt babel 1 URM
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.Sh NAME
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.Nm babel
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.Nd "a converter for chemistry and molecular modeling data files"
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.Sh SYNOPSIS
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.Nm
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.Op Fl H Ar help-options
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.Nm
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.Op Ar OPTIONS
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.Op Fl i Ar input-type
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.Ar infile
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.Op Fl o Ar output-type
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.Ar outfile
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.Sh DESCRIPTION
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.Re
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Babel is a cross-platform program designed to interconvert
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between many file formats used in molecular modeling and computational
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chemistry and related areas.
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.Pp
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Open Babel is also a complete programmers toolkit for developing
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chemistry software. For more information, se the Open Babel web pages
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\%<\fBhttp://openbabel.org/\fR>.
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.Sh OPTIONS
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.Re
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If only input and ouput files are given, Open Babel will guess the
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file type from the filename extension.
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.Bl -tag -width flag
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.It Fl a Ar options
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Format-specific input options. See
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.Fl H Ar format-ID
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for options allowed by a particular format
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.It Fl -addtotitle
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Append text to the current molecule title
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.It Fl -addformula
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Append the molecular formula after the current molecule title
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.It Fl b
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Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O
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.It Fl c
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Center atomic coordinates at (0,0,0)
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.It Fl C
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Combine molecules in first file with others having the same name
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.It Fl e
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Continue after errors
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.It Fl d
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Delete Hydrogens
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.It Fl --errorlevel Ar 2
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Filter the level of errors and warnings displayed:
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.br
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1 = critical errors only
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2 = include warnings too (default)
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3 = include informational messages too
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4 = include "audit log" messages of changes to data
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5 = include debugging messages too
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.It Fl f Ar #
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For multiple entry input, start import with molecule # as the first entry
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.It Fl F
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Output the available fingerprint types
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.It Fl h
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Add hydrogens
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.It Fl H
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Output usage information
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.It Fl H Ar format-ID
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Output formatting information and options for format specified
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.It Fl Hall
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Output formatting information and options for all formats
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.It Fl i<format-ID>
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Specifies input format, see below for the available formats
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.It Fl j
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.It Fl -join
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Join all input molecules into a single output molecule entry
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.It Fl k
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Translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian)
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.It Fl m
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Produce multiple output files, to allow:
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.Bl -dash -offset indent -compact
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.It
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Splitting one input file - put each molecule into consecutively
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numbered output files
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.It
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Batch conversion - convert each of multiple input files into a
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specified output format
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.El
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.It Fl l Ar #
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For multiple entry input, stop import with molecule # as the last entry
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.It Fl o Ar format-ID
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Specifies output format, see below for the available formats
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.It Fl p
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Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
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.It Fl -property
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Add or replace a property (e.g., in an MDL SD file)
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.It Fl s Ar SMARTS
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Convert only molecules matching the SMARTS pattern specified
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.It Fl -separate
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Separate disconnected fragments into individual molecular records
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.It Fl t
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All input files describe a single molecule
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.It Fl -title Ar title
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Add or replace molecular title
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.It Fl x Ar options
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Format-specific output options. See
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.Fl H Ar format-ID
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for options allowed by a particular format
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.It Fl v Ar SMARTS
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Convert only molecules \fBNOT\fP matching SMARTS pattern specified
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.It Fl V
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Output version number and exit
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.It Fl z
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Compress the output with gzip
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.El
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.Sh "FILE FORMATS"
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.Re
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The following formats are currently supported by Open Babel:
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.Bl -item -offset indent -compact
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.It
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acr -- Carine ASCI Crystal
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.It
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alc -- Alchemy format
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.It
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arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
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.It
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bgf -- MSI BGF format
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.It
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box -- Dock 3.5 Box format
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.It
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bs -- Ball and Stick format
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.It
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c3d1 -- Chem3D Cartesian 1 format
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.It
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c3d2 -- Chem3D Cartesian 2 format
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.It
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caccrt -- Cacao Cartesian format
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.It
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cache -- CAChe MolStruct format [Write-only]
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.It
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cacint -- Cacao Internal format [Write-only]
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.It
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can -- Canonical SMILES format
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.It
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car -- Accelrys/MSI Biosym/Insight II CAR format [Read-only]
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.It
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ccc -- CCC format [Read-only]
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.It
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cdx -- ChemDraw binary format [Read-only]
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.It
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cdxml -- ChemDraw CDXML format
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.It
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cht -- Chemtool format [Write-only]
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.It
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cif -- Crystallographic Information File
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.It
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cml -- Chemical Markup Language
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.It
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cmlr -- CML Reaction format
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.It
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com -- Gaussian 98/03 Cartesian Input [Write-only]
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.It
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copy -- Copies raw text [Write-only]
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.It
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crk2d -- Chemical Resource Kit 2D diagram format
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.It
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crk3d -- Chemical Resource Kit 3D format
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.It
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csr -- Accelrys/MSI Quanta CSR format [Write-only]
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.It
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cssr -- CSD CSSR format [Write-only]
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.It
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ct -- ChemDraw Connection Table format
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.It
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dmol -- DMol3 coordinates format
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.It
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ent -- Protein Data Bank format
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.It
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fa -- FASTA format [Write-only]
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.It
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fasta -- FASTA format [Write-only]
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.It
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fch -- Gaussian formatted checkpoint file format [Read-only]
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.It
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fchk -- Gaussian formatted checkpoint file format [Read-only]
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.It
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fck -- Gaussian formatted checkpoint file format [Read-only]
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.It
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feat -- Feature format
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.It
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fh -- Fenske-Hall Z-Matrix format [Write-only]
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.It
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fix -- SMILES FIX format [Write-only]
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.It
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fpt -- Fingerprint format [Write-only]
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.It
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fract -- Free Form Fractional format
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.It
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fs -- Open Babel FastSearching database
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.It
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fsa -- FASTA format [Write-only]
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.It
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g03 -- Gaussian 98/03 Output [Read-only]
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.It
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g98 -- Gaussian 98/03 Output [Read-only]
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.It
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gam -- GAMESS Output [Read-only]
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.It
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gamin -- GAMESS Input [Write-only]
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.It
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gamout -- GAMESS Output [Read-only]
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.It
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gau -- Gaussian 98/03 Cartesian Input [Write-only]
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.It
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gjc -- Gaussian 98/03 Cartesian Input [Write-only]
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.It
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gjf -- Gaussian 98/03 Cartesian Input [Write-only]
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.It
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gpr -- Ghemical format
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.It
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gr96 -- GROMOS96 format [Write-only]
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.It
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hin -- HyperChem HIN format
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.It
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inchi -- IUPAC InChI [Write-only]
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.It
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inp -- GAMESS Input [Write-only]
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.It
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ins -- ShelX format [Read-only]
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.It
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jin -- Jaguar input format [Write-only]
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.It
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jout -- Jaguar output format [Read-only]
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.It
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mdl -- MDL MOL format
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.It
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mmd -- MacroModel format
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.It
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mmod -- MacroModel format
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.It
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mol -- MDL MOL format
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.It
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mol2 -- Sybyl Mol2 format
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.It
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molreport -- Open Babel molecule report [Write-only]
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.It
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moo -- MOPAC Output format [Read-only]
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.It
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mop -- MOPAC Cartesian format
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.It
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mopcrt -- MOPAC Cartesian format
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.It
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mopin -- MOPAC Internal
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.It
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mopout -- MOPAC Output format [Read-only]
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.It
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mpc -- MOPAC Cartesian format
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.It
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mpd -- Sybyl descriptor format [Write-only]
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.It
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mpqc -- MPQC output format [Read-only]
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.It
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mpqcin -- MPQC simplified input format [Write-only]
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.It
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nw -- NWChem input format [Write-only]
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.It
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nwo -- NWChem output format [Read-only]
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.It
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pc -- PubChem format [Read-only]
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.It
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pcm -- PCModel format
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.It
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pdb -- Protein Data Bank format
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.It
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pov -- POV-Ray input format [Write-only]
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.It
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pqs -- Parallel Quantum Solutions format
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.It
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prep -- Amber Prep format [Read-only]
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.It
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qcin -- Q-Chem input format [Write-only]
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.It
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qcout -- Q-Chem output format [Read-only]
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.It
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report -- Open Babel report format [Write-only]
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.It
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res -- ShelX format [Read-only]
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.It
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rxn -- MDL RXN format
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.It
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sd -- MDL MOL format
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.It
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sdf -- MDL MOL format
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.It
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smi -- SMILES format
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.It
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sy2 -- Sybyl Mol2 format
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.It
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tdd -- Thermo format
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.It
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test -- Test format [Write-only]
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.It
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therm -- Thermo format
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.It
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tmol -- TurboMole Coordinate format
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.It
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txyz -- Tinker MM2 format [Write-only]
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.It
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unixyz -- UniChem XYZ format
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.It
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vmol -- ViewMol format
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.It
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xed -- XED format [Write-only]
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.It
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xml -- General XML format [Read-only]
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.It
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xyz -- XYZ cartesian coordinates format
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.It
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yob -- YASARA.org YOB format
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.It
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zin -- ZINDO input format [Write-only]
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.El
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.Sh "FORMAT OPTIONS"
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Individual file formats may have additional formatting options.
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.Pp
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Input format options are preceded by 'a', e.g. -as
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.Pp
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Output format options are preceded by 'x', e.g. -xn
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.Pp
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For further specific information and options, use -H<format-type>
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.br
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e.g., -Hcml
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.Sh EXAMPLES
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Standard conversion:
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.Dl "babel -ixyz ethanol.xyz -opdb ethanol.pdb"
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Conversion from a SMI file in STDIN to a Mol2 file written to STDOUT:
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.Dl "babel -ismi -omol2"
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Split a multi-molecule file into new1.smi, new2.smi, etc.:
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.Dl "babel infile.mol new.smi -m"
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.Sh SEE ALSO
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.Xr obenergy 1 ,
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.Xr obfit 1 ,
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.Xr obgrep 1 ,
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.Xr obminimize 1 ,
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.Xr obprop 1 ,
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.Xr obrotate 1 ,
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.Xr obrotamer 1 .
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The web pages for Open Babel can be found at:
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\%<\fBhttp://openbabel.org/\fR>
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.Sh AUTHORS
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.An -nosplit
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A cast of many, including the currrent maintainers
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.An Geoff Hutchison ,
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.An Chris Morley ,
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.An Michael Banck ,
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and innumerable others who have contributed fixes and additions.
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For more contributors to Open Babel, see
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\%<\fBhttp://openbabel.org/wiki/THANKS\fR>
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.Sh COPYRIGHT
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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.br
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Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison
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.Pp
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation version 2 of the License.
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.Pp
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This program is distributed in the hope that it will be useful, but
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WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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General Public License for more details.
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