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Add or replace molecule title<br>
--addtotitle <text> Append to title<br>
--addformula Append formula to title</p>
<p>However the wiki page gives further details (eg -a) and in alphabetical order, would it be worth updating?</p>
<p>-a options<br>
Format-specific input options. See -H format-ID for options allowed by a particular format<br>
--addtotitle<br>
Append text after the current molecule title<br>
--addformula<br>
Append the molecular formula after the current molecule title<br>
-b<br>
Convert dative bonds (e.g., <a class="" href="[O-]">N+</a>=O to N(=O)=O<br>
-c<br>
Center atomic coordinates at (0,0,0)<br>
-C<br>
Combine molecules in first file with others having the same name<br>
-d<br>
Delete Hydrogens<br>
-e<br>
Continue to convert molecules after errors<br>
---errorlevel 2<br>
Filter the level of errors and warnings displayed:<br>
1 = critical errors only<br>
2 = include warnings too (default)<br>
3 = include informational messages too<br>
4 = include "audit log" messages of changes to data<br>
5 = include debugging messages too<br>
-f #<br>
For multiple entry input, start import with molecule # as the first entry<br>
-F<br>
Output the available fingerprint types<br>
-h<br>
Add hydrogens<br>
-H<br>
Output usage information<br>
-H format-ID<br>
Output formatting information and options for format specified<br>
-Hall<br>
Output formatting information and options for all formats<br>
-i<format-ID><br>
Specifies input format, see below for the available formats<br>
-j<br>
--join<br>
Join all input molecules into a single output molecule entry<br>
-k<br>
Translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian)<br>
-m<br>
Produce multiple output files, to allow:<br>
Splitting one input file - put each molecule into consecutively numbered output files<br>
Batch conversion - convert each of multiple input files into a specified output format<br>
-l #<br>
For multiple entry input, stop import with molecule # as the last entry<br>
-o format-ID<br>
Specifies output format, see below for the available formats<br>
-p<br>
Add Hydrogens appropriate for pH (use transforms in phmodel.txt)<br>
--property<br>
Add or replace a property (e.g., in an MDL SD file)<br>
-s SMARTS<br>
Convert only molecules matching the SMARTS pattern specified<br>
--separate<br>
Separate disconnected fragments into individual molecular records<br>
-t<br>
All input files describe a single molecule<br>
--title title<br>
Add or replace molecular title<br>
-x options<br>
Format-specific output options. See -H format-ID for options allowed by a particular format<br>
-v SMARTS<br>
Convert only molecules NOT matching SMARTS pattern specified<br>
-V<br>
Output version number and exit<br>
-z<br>
Compress the output with gzip</p>
<p>Chris</p>
#115 Need to update help
If you type babel -H
you get
Open Babel converts chemical structures from one file format to another
Usage: babel <input spec=""> <output spec=""> [Options]
Each spec can be a file whose extension decides the format.
Optionally the format can be specified by preceding the file by
-i<format-type> e.g. -icml, for input and -o<format-type> for output
See below for available format-types, which are the same as the
file extensions and are case independent.
If no input or output file is given stdin or stdout are used instead.
More than one input file can be specified and their names can contain
wildcard chars (* and ?).The molecules are aggregated in the output file.
Conversion options
-f <#> Start import at molecule # specified
-l <#> End import at molecule # specified
-e Continue with next object after error, if possible
-z Compress the output with gzip
-k Attempt to translate keywords
-H Outputs this help text
-Hxxx (xxx is file format ID e.g. -Hcml) gives format info
-Hall Outputs details of all formats
-V Outputs version number
-F Outputs the available fingerprint types
-m Produces multiple output files, to allow:
Splitting: e.g. babel infile.mol new.smi -m
puts each molecule into new1.smi new2.smi etc
Batch conversion: e.g. babel *.mol -osmi -m
converts each input file to a .smi file
For conversions of molecules
Additional options :
-d Delete hydrogens (make implicit)
-h Add hydrogens (make explicit)
-p Add Hydrogens appropriate for pH model
-b Convert dative bonds e.g.N+=O to N(=O)=O
-c Center Coordinates
--join Join all input molecules into a single output molecule
--separate Output disconnected fragments separately
-C Combine mols in first file with others having same name
-s"smarts" Convert only molecules matching SMARTS:
-v"smarts" Convert only molecules NOT matching SMARTS:
--property <attrib> <value> add or replace a property (SDF)
--title
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There's too much info already. I'd like to see something like the help system of svn:
svn help
svn help commit
Which equates to:
babel --help (or -H)
babel --help formats (or babel -H formats)
babel --help SMI
babel --help convert
babel --help filter
and so on, the more the merrier. The only manual users read is probably babel --help, so if it's not in there, it doesn't exist.
Noel
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I'm converting this to a feature request. I think Noel's comment is useful, but this is going to take some work.