!read lang/help.phtml.$modu_lang $special_parm
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
-L <category> Lists plugin classes of this category, e.g. <formats>
Use just
-L
for a
list of plugin categories
. Use -L <ID> e.g. -L sdf for details of a format or other plugin.
-m Produces multiple output files, to allow:
Splitting: e.g. obabel infile.mol -O new.smi -m
puts
each molecule into new1
.smi new2
.smi etc
Batch conversion: e.g. obabel *.mol -osmi -m
For conversions of molecules
Additional options :
-d Delete hydrogens (make implicit)
-h Add hydrogens (make explicit)
-p <pH> Add hydrogens appropriate for this pH
-b Convert dative bonds e.g.[N+]([O-])=O to N(=O)=O
-r Remove all but the largest contiguous fragment
-c Center Coordinates
-C Combine mols in first
file with others having same name
--filter <filterstring> Filter: convert only when tests are true:
--add <list> Add properties from descriptors
--delete
<list
> Delete properties in
list --append
<list
> Append properties or descriptors in
list to title
: -s
"smarts" Convert only
if match SMARTS or mols in
file: -v
"smarts" Convert only
if NO match to SMARTS or mols in
file(not displayed in GUI
) --join Join all input molecules into a single output molecule
--separate Output disconnected fragments separately
--property <attrib> <value> add or replace a property (SDF)
--title <title> Add or replace molecule title
--addtotitle <text> Append text to title
--writeconformers Output multiple conformers separately
--addoutindex Append output index to title
--0xout
<file.xxx
> Additional
file output
--AddInIndex Append input index to title
--AddPolarH Adds hydrogen to polar atoms only
--canonical Canonicalize the atom order
--fillUC <param> Fill the unit cell (strict or keepconnect)
--gen2D Generate 2D coordinates
--gen3D Generate 3D coordinates
--partialcharge <method> Calculate partial charges by specified method
--readconformer Adjacent conformers combined into a single molecule
--sort <desc
> Sort by descriptor
(~desc
for reverse
) --unique [param] remove duplicates by descriptor;default inchi