Mercurial > repos > bgruening > openbabel
changeset 11:77b82f259298
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Mon, 27 May 2013 16:52:53 +0200 |
| parents | cc63a42fd22e |
| children | dace1bc1168b |
| files | filter/ob_grep.xml repository_dependencies.xml search/ob_spectrophore_search.py tool_dependencies.xml |
| diffstat | 4 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/filter/ob_grep.xml Sat May 25 12:54:40 2013 -0400 +++ b/filter/ob_grep.xml Mon May 27 16:52:53 2013 +0200 @@ -33,7 +33,7 @@ </inputs> <options sanitize="False"/> <outputs> - <data name="outfile" format_source="infile" /> + <data name="outfile" format_source="infile" label="${tool.name} on ${on_string}"/> </outputs> <tests> <test>
--- a/repository_dependencies.xml Sat May 25 12:54:40 2013 -0400 +++ b/repository_dependencies.xml Mon May 27 16:52:53 2013 +0200 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version='1.0' encoding='utf-8'?> <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository changeset_revision="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> -</repositories> + <repository changeset_revision="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> +</repositories> \ No newline at end of file
--- a/search/ob_spectrophore_search.py Sat May 25 12:54:40 2013 -0400 +++ b/search/ob_spectrophore_search.py Mon May 27 16:52:53 2013 +0200 @@ -43,7 +43,7 @@ outfile = open(args.output, 'w') for mol in open(args.library, 'r'): try: - distance = ((np.asarray( target_spectrophore ) - np.asarray( mol.split('\t')[ args.column - 1 ].strip().split(', ') ))**2).sum() + distance = ( ( np.asarray( target_spectrophore, dtype=float ) - np.asarray( mol.split('\t')[ args.column - 1 ].strip().split(', '), dtype=float) )**2).sum() except ValueError: distance = 0 outfile.write( '%s\t%f\n' % (mol.strip(), distance ) )
--- a/tool_dependencies.xml Sat May 25 12:54:40 2013 -0400 +++ b/tool_dependencies.xml Mon May 27 16:52:53 2013 +0200 @@ -1,10 +1,10 @@ -<?xml version="1.0"?> +<?xml version='1.0' encoding='utf-8'?> <tool_dependency> <package name="openbabel" version="2.3.2"> - <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="numpy" version="1.7.1"> - <repository changeset_revision="7283651b62fe" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1aa6410e151b" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> <package name="cheminfolib" version="0.1"> <install version="1.0"> @@ -21,4 +21,4 @@ </install> <readme>cheminfolib is just a small helper library for the chemicaltoolbox project and has no further dependencies.</readme> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file