# HG changeset patch # User bgruening # Date 1495523375 14400 # Node ID 41e31a198b34e089ae953e27689ebf6d17d38fcd # Parent b2cad51889eaf0a6c53e5ae5fe0c46a9a452877a planemo upload for repository https://github.com/CS76/NP-Likeness commit 63130752ef267b8239e39562b6d0d7bcf4d6d80a diff -r b2cad51889ea -r 41e31a198b34 natural_product_likeness_calculator.xml --- a/natural_product_likeness_calculator.xml Thu Aug 15 03:38:29 2013 -0400 +++ b/natural_product_likeness_calculator.xml Tue May 23 03:09:35 2017 -0400 @@ -1,70 +1,56 @@ - - likeness calculator - - - np-likeness-scorer - - - ## NPLC is really picky with file extensions. We need to specify every datatype as file extension - ## A workaround is to create a symlink with a proper file-extension. - #import tempfile - #set $temp_file = tempfile.NamedTemporaryFile() - #set $temp_link = "%s.%s" % ($temp_file.name, $infile.ext) - $temp_file.close() - ln -s $infile $temp_link; - - java -jar \$NPLS_JAR_PATH/NP-Likeness-2.0.jar - -in "${temp_link}" - -out "${outfile}" - #if $reconstruct_fragments: - -reconstructFragments true - -outFragments $outfragments - #end if - ; - rm $temp_link - - - - - - - - - - - - - reconstruct_fragments is True - - - - - - - -.. class:: infomark - -**What this tool does** - -The `Natural-Product-Likeness Scorer`_ calculates the Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. The more positive the score, the higher is the NP-likeness and vice versa. - -.. _Natural-Product-Likeness Scorer: http://sourceforge.net/projects/np-likeness/ - -.. image:: $PATH_TO_IMAGES/score_distribution.png - - ------ - -.. class:: infomark - -**Cite** - -| KV Jayaseelan, C Steinbeck, P Moreno, A Truszkowski, P Ertl - `Natural product-likeness score revisited: an open-source, open-data implementation`_ -| -| P Ertl, S Roggo, and A Schuffenhauer - `Natural product-likeness score and its application for prioritization of compound libraries`_ - -.. _`Natural product-likeness score revisited: an open-source, open-data implementation`: http://www.biomedcentral.com/1471-2105/13/106/abstract -.. _`Natural product-likeness score and its application for prioritization of compound libraries`: http://www.ncbi.nlm.nih.gov/pubmed/18034468 - - - + + likeness calculator + + np-likeness-scorer + + + + + + + + + + + + reconstruct_fragments is True + + + + + + + + + + + + + 10.1186/1471-2105-13-106 + 10.1021/ci700286x + + diff -r b2cad51889ea -r 41e31a198b34 repository_dependencies.xml --- a/repository_dependencies.xml Thu Aug 15 03:38:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r b2cad51889ea -r 41e31a198b34 test-data/CID_3037.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CID_3037.sdf Tue May 23 03:09:35 2017 -0400 @@ -0,0 +1,220 @@ +3037 + -OEChem-08231108593D + + 27 28 0 0 0 0 0 0 0999 V2000 + -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 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+341.858.381.91.10.020-1.151.94-0.010-0.39-4.150.010 + +> +722.787 + +> +193 + +> +25255 + +> +-00.1511 + +> +eb878dfc-1074-456a-ab86-c7fc4f84bf2a + +$$$$ diff -r b2cad51889ea -r 41e31a198b34 tool_dependencies.xml --- a/tool_dependencies.xml Thu Aug 15 03:38:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ - - - - - http://downloads.sourceforge.net/project/np-likeness/Natural_Product_Likeness_calculator_2.0.zip - - Natural_Product_Likeness_calculator_2.0/NP-Likeness-2.0.jar - $INSTALL_DIR - - - $INSTALL_DIR - - - - Opsin requires a JAVA (1.5+) runtime evironment. - -