Subversion Repositories wimsdev

!read lang/help.phtml.$modu_lang $special_parm

!exit

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

      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 <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