Mercurial > repos > bgruening > natural_product_likeness
changeset 1:41e31a198b34 draft
planemo upload for repository https://github.com/CS76/NP-Likeness commit 63130752ef267b8239e39562b6d0d7bcf4d6d80a
| author | bgruening |
|---|---|
| date | Tue, 23 May 2017 03:09:35 -0400 |
| parents | b2cad51889ea |
| children | 40d181cc8c19 |
| files | natural_product_likeness_calculator.xml repository_dependencies.xml test-data/CID_3037.sdf test-data/Score.sdf tool_dependencies.xml |
| diffstat | 5 files changed, 415 insertions(+), 91 deletions(-) [+] |
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--- 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 @@ -<tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.2.1"> - <description>likeness calculator</description> - <!--<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,outfragments"></parallelism>--> - <requirements> - <requirement type="package" version="2.0">np-likeness-scorer</requirement> - </requirements> - <command> - ## 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 - </command> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <inputs> - <param format="smi,sdf" name="infile" type="data" label="Molecule file" help="Dataset missing? See TIP below"/> - <param name='reconstruct_fragments' type='boolean' label='Fragments-scores are written out in SMILES format' truevalue='' falsevalue='' /> - </inputs> - <outputs> - <data format_source="infile" name="outfile" /> - <data format="tabular" name="outfragments"> - <filter>reconstruct_fragments is True</filter> - </data> - </outputs> - <tests> - </tests> - <help> - - -.. 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:: $PATH_TO_IMAGES/score_distribution.png - - ------ - -.. class:: infomark - -**Cite** - -| KV Jayaseelan, C Steinbeck, P Moreno, A Truszkowski, P Ertl - `Natural product-likeness score revisited: an open-source, open-data implementation`_ -| -| P Ertl, S Roggo, and A Schuffenhauer - `Natural product-likeness score and its application for prioritization of compound libraries`_ - -.. _`Natural product-likeness score revisited: an open-source, open-data implementation`: http://www.biomedcentral.com/1471-2105/13/106/abstract -.. _`Natural product-likeness score and its application for prioritization of compound libraries`: http://www.ncbi.nlm.nih.gov/pubmed/18034468 - - </help> -</tool> +<tool id="ctb_np-likeness-calculator" name="Natural Product" version="2.1"> + <description>likeness calculator</description> + <requirements> + <requirement type="package" version="2.1">np-likeness-scorer</requirement> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + np-likeness + -in '$infile' + -intype $infile.ext + -out '$outfile' + -outtype $infile.ext + #if $reconstruct_fragments: + -reconstructFragments true + -outFragments $outfragments + #end if + ]]> + </command> + <inputs> + <param format="smi,sdf" name="infile" type="data" + label="Molecule file" help="Dataset missing? See TIP below"/> + <param name='reconstruct_fragments' type='boolean' + truevalue='' falsevalue='' + label='Fragments and scores are written out in SMILES format' /> + </inputs> + <outputs> + <data format_source="infile" name="outfile" /> + <data format="tabular" name="outfragments"> + <filter>reconstruct_fragments is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="infile" value="CID_3037.sdf"/> + <output name="outfile" file="Score.sdf" ftype="sdf" lines_diff="4"/> + </test> + </tests> + <help> +<![CDATA[ + +**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 + +]]> + </help> + <citations> + <citation type="doi">10.1186/1471-2105-13-106</citation> + <citation type="doi">10.1021/ci700286x</citation> + </citations> +</tool>
--- 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 @@ -<?xml version="1.0"?> -<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> -</repositories>
--- /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 + 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 14 1 0 0 0 0 + 2 15 1 0 0 0 0 + 3 8 1 0 0 0 0 + 3 26 1 0 0 0 0 + 4 9 1 0 0 0 0 + 4 27 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 1 0 0 0 0 + 5 18 1 0 0 0 0 + 5 19 1 0 0 0 0 + 6 8 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 9 2 0 0 0 0 + 7 11 1 0 0 0 0 + 8 12 1 0 0 0 0 + 9 13 1 0 0 0 0 + 10 14 2 0 0 0 0 + 10 20 1 0 0 0 0 + 11 15 2 0 0 0 0 + 11 21 1 0 0 0 0 + 12 16 2 0 0 0 0 + 12 22 1 0 0 0 0 + 13 17 2 0 0 0 0 + 13 23 1 0 0 0 0 + 14 16 1 0 0 0 0 + 15 17 1 0 0 0 0 + 16 24 1 0 0 0 0 + 17 25 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3037 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +8 +10 +12 +1 +7 +5 +11 +3 +6 +9 +4 +2 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +25 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 -0.15 +17 -0.15 +2 -0.18 +20 0.15 +21 0.15 +22 0.15 +23 0.15 +24 0.15 +25 0.15 +26 0.45 +27 0.45 +3 -0.53 +4 -0.53 +5 0.29 +6 -0.14 +7 -0.14 +8 0.08 +9 0.08 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +2 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +4 +1 3 donor +1 4 donor +6 6 8 10 12 14 16 rings +6 7 9 11 13 15 17 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +17 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +5 + +> <PUBCHEM_CONFORMER_ID> +00000BDD00000008 + +> <PUBCHEM_MMFF94_ENERGY> +44.6858 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +20.297 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10062212 137 18261117369936506423 +104564 63 17986963035811110412 +11458722 120 18339359768245870841 +11471102 22 5472872458301843344 +11578080 2 18190204380446433792 +116883 192 18265608969609498196 +12236239 1 18410856576819659107 +12592029 89 18338223951597366363 +13549 16 18410575084668353682 +13693222 15 6555421915516066822 +13764800 53 14189033175566991199 +14115302 16 18186237320680093898 +14341114 328 10087642619424135543 +14787075 74 9511159855286719151 +14993402 34 18410855451538227223 +15099037 51 18340768233908588503 +15207287 21 15719111361650760302 +15375358 24 15647053767618106914 +15775835 57 18272650117329930317 +16945 1 17906452130063974618 +17834072 14 15936410035134206066 +18186145 218 17132117918276567720 +19422 9 18271525295227750719 +20279233 1 15719389529571237654 +20645476 183 18339080393619327415 +23402539 116 18186809105365620101 +23402655 69 18342736308283284156 +23559900 14 17603590712323212176 +25 1 17561083592297532664 +26918003 58 6266902359448424189 +296302 2 15213020427345972082 +3082319 5 18338798905472319583 +34934 24 18341891845236497020 +633830 44 17703790310130762689 +74978 22 18266740181857992718 +7832392 63 18340206284835898173 +81228 2 15720767252053392762 +9981440 41 17403743242177431832 + +> <PUBCHEM_SHAPE_MULTIPOLES> +341.85 +8.38 +1.9 +1.1 +0.02 +0 +-1.15 +1.94 +-0.01 +0 +-0.39 +-4.15 +0.01 +0 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +722.787 + +> <PUBCHEM_SHAPE_VOLUME> +193 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Score.sdf Tue May 23 03:09:35 2017 -0400 @@ -0,0 +1,139 @@ +3037 + CDK 0523170409 + + 27 28 0 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 + 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 14 1 0 0 0 0 + 2 15 1 0 0 0 0 + 3 8 1 0 0 0 0 + 3 26 1 0 0 0 0 + 4 9 1 0 0 0 0 + 4 27 1 0 0 0 0 + 5 6 1 0 0 0 0 + 5 7 1 0 0 0 0 + 5 18 1 0 0 0 0 + 5 19 1 0 0 0 0 + 6 8 2 0 0 0 0 + 6 10 1 0 0 0 0 + 7 9 2 0 0 0 0 + 7 11 1 0 0 0 0 + 8 12 1 0 0 0 0 + 9 13 1 0 0 0 0 + 10 14 2 0 0 0 0 + 10 20 1 0 0 0 0 + 11 15 2 0 0 0 0 + 11 21 1 0 0 0 0 + 12 16 2 0 0 0 0 + 12 22 1 0 0 0 0 + 13 17 2 0 0 0 0 + 13 23 1 0 0 0 0 + 14 16 1 0 0 0 0 + 15 17 1 0 0 0 0 + 16 24 1 0 0 0 0 + 17 25 1 0 0 0 0 +M END +> <cdk:Title> +3037 + +> <cdk:Remark> +null + +> <PUBCHEM_COMPOUND_CID> +3037 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +810121751136942 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +251 -0.1810 -0.1511 -0.1512 -0.1513 -0.1514 0.1815 0.1816 -0.1517 -0.152 -0.1820 0.1521 0.1522 0.1523 0.1524 0.1525 0.1526 0.4527 0.453 -0.534 -0.535 0.296 -0.147 -0.148 0.089 0.08 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +2 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +41 3 donor1 4 donor6 6 8 10 12 14 16 rings6 7 9 11 13 15 17 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +17 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +5 + +> <PUBCHEM_CONFORMER_ID> +00000BDD00000008 + +> <PUBCHEM_MMFF94_ENERGY> +44.6858 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +20.297 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10062212 137 18261117369936506423104564 63 1798696303581111041211458722 120 1833935976824587084111471102 22 547287245830184334411578080 2 18190204380446433792116883 192 1826560896960949819612236239 1 1841085657681965910712592029 89 1833822395159736636313549 16 1841057508466835368213693222 15 655542191551606682213764800 53 1418903317556699119914115302 16 1818623732068009389814341114 328 1008764261942413554314787075 74 951115985528671915114993402 34 1841085545153822722315099037 51 1834076823390858850315207287 21 1571911136165076030215375358 24 1564705376761810691415775835 57 1827265011732993031716945 1 1790645213006397461817834072 14 1593641003513420606618186145 218 1713211791827656772019422 9 1827152529522775071920279233 1 1571938952957123765420645476 183 1833908039361932741523402539 116 1818680910536562010123402655 69 1834273630828328415623559900 14 1760359071232321217625 1 1756108359229753266426918003 58 6266902359448424189296302 2 152130204273459720823082319 5 1833879890547231958334934 24 18341891845236497020633830 44 1770379031013076268974978 22 182667401818579927187832392 63 1834020628483589817381228 2 157207672520533927629981440 41 17403743242177431832 + +> <PUBCHEM_SHAPE_MULTIPOLES> +341.858.381.91.10.020-1.151.94-0.010-0.39-4.150.010 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +722.787 + +> <PUBCHEM_SHAPE_VOLUME> +193 + +> <PUBCHEM_COORDINATE_TYPE> +25255 + +> <NATURAL_PRODUCT_LIKENESS_SCORE> +-00.1511 + +> <UNIQUE_MOLECULE_ID> +eb878dfc-1074-456a-ab86-c7fc4f84bf2a + +$$$$
--- 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 @@ -<tool_dependency> - <package name="np-likeness-scorer" version="2.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/np-likeness/Natural_Product_Likeness_calculator_2.0.zip</action> - <action type="move_file"> - <source>Natural_Product_Likeness_calculator_2.0/NP-Likeness-2.0.jar</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="set_environment"> - <environment_variable name="NPLS_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme>Opsin requires a JAVA (1.5+) runtime evironment.</readme> - </package> -</tool_dependency>