Mercurial > repos > bgruening > molecule_datatypes
changeset 10:e6493849afd3
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Fri, 19 Jul 2013 16:27:33 +0200 |
| parents | a1474892287e |
| children | 18ff2d6e1dca |
| files | force_pre-commit_hook_temp_file sdf_to_smi_converter.xml |
| diffstat | 1 files changed, 0 insertions(+), 21 deletions(-) [+] |
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--- a/sdf_to_smi_converter.xml Mon May 27 16:58:40 2013 +0200 +++ b/sdf_to_smi_converter.xml Fri Jul 19 16:27:33 2013 +0200 @@ -6,33 +6,12 @@ </requirements> <command > obabel -isdf "${input}" - #if $can: -ocan - #else: - -osmi - #end if -O "${output}" -e - $remove_h - #if $iso_chi or $can or $exp_h: - -x$iso_chi$exp_h$can - #end if - #if $dative_bonds: - -b - #end if - #if int($ph) >= 0: - -p $ph - #end if - 2>&1 </command> <inputs> <param name="input" type="data" format="sdf" label="Molecules in SDF-format"/> - <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" /> - <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" /> - <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" /> - <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" /> - <param name="ph" size="3" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/> - <param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" /> </inputs> <outputs> <data name="output" format="smi"/>