Mercurial > repos > bgruening > sdf_to_tab
changeset 2:40ff81f67f5e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 09b22cceacb34dd4c6c1b42890f93232df128208"
| author | bgruening |
|---|---|
| date | Sat, 21 Mar 2020 14:03:27 -0400 |
| parents | 193389d3a5f0 |
| children | 71bc02c59d3a |
| files | sdf_to_tab.py sdf_to_tab.xml test-data/CID_3037.tab |
| diffstat | 3 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/sdf_to_tab.py Tue Mar 10 12:57:48 2020 -0400 +++ b/sdf_to_tab.py Sat Mar 21 14:03:27 2020 -0400 @@ -16,7 +16,7 @@ else: d = {prop: val for (prop, val) in d.items() if prop in vars.props.replace(' ', '').split(',')} # remove items not requested via CLI if vars.name: - d['Name'] = mols[n].GetProp('_Name') + d['SDFMoleculeName'] = mols[n].GetProp('_Name') if vars.smiles: d['SMILES'] = Chem.MolToSmiles(mols[n], isomericSmiles=False) d['Index'] = int(n)
--- a/sdf_to_tab.xml Tue Mar 10 12:57:48 2020 -0400 +++ b/sdf_to_tab.xml Sat Mar 21 14:03:27 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="sdf_to_tab" name="Extract values from an SD-file" version="@VERSION@"> +<tool id="sdf_to_tab" name="Extract values from an SD-file" version="@VERSION@.1"> <macros> <token name="@VERSION@">2019.03.1</token> </macros>
--- a/test-data/CID_3037.tab Tue Mar 10 12:57:48 2020 -0400 +++ b/test-data/CID_3037.tab Sat Mar 21 14:03:27 2020 -0400 @@ -1,2 +1,2 @@ -Index Name PUBCHEM_ATOM_DEF_STEREO_COUNT PUBCHEM_ATOM_UDEF_STEREO_COUNT PUBCHEM_BOND_DEF_STEREO_COUNT PUBCHEM_BOND_UDEF_STEREO_COUNT PUBCHEM_CACTVS_TAUTO_COUNT PUBCHEM_COMPONENT_COUNT PUBCHEM_COMPOUND_CID PUBCHEM_CONFORMER_ID PUBCHEM_CONFORMER_RMSD PUBCHEM_EFFECTIVE_ROTOR_COUNT PUBCHEM_FEATURE_SELFOVERLAP PUBCHEM_HEAVY_ATOM_COUNT PUBCHEM_ISOTOPIC_ATOM_COUNT PUBCHEM_MMFF94_ENERGY PUBCHEM_SHAPE_SELFOVERLAP PUBCHEM_SHAPE_VOLUME -0 3037 0.0 0.0 0.0 0.0 5.0 1.0 3037.0 00000BDD00000008 0.6 2.0 20.297 17.0 0.0 44.6858 722.787 193.0 +Index PUBCHEM_ATOM_DEF_STEREO_COUNT PUBCHEM_ATOM_UDEF_STEREO_COUNT PUBCHEM_BOND_DEF_STEREO_COUNT PUBCHEM_BOND_UDEF_STEREO_COUNT PUBCHEM_CACTVS_TAUTO_COUNT PUBCHEM_COMPONENT_COUNT PUBCHEM_COMPOUND_CID PUBCHEM_CONFORMER_ID PUBCHEM_CONFORMER_RMSD PUBCHEM_EFFECTIVE_ROTOR_COUNT PUBCHEM_FEATURE_SELFOVERLAP PUBCHEM_HEAVY_ATOM_COUNT PUBCHEM_ISOTOPIC_ATOM_COUNT PUBCHEM_MMFF94_ENERGY PUBCHEM_SHAPE_SELFOVERLAP PUBCHEM_SHAPE_VOLUME SDFMoleculeName +0 0.0 0.0 0.0 0.0 5.0 1.0 3037.0 00000BDD00000008 0.6 2.0 20.297 17.0 0.0 44.6858 722.787 193.0 3037