# HG changeset patch
# User bgruening
# Date 1376552245 14400
# Node ID cda22c799d0aec68842868bff70b0324bef3390b
Uploaded
diff -r 000000000000 -r cda22c799d0a opsin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/opsin.xml Thu Aug 15 03:37:25 2013 -0400
@@ -0,0 +1,62 @@
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+ converter (OPSIN)
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+ opsin
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+ java -jar \$JAVA_JAR_PATH/opsin-1.4.0-jar-with-dependencies.jar "${radicals}" "${wildcards}" -o$oformat < "${infile}" > "${outfile}"
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+.. class:: infomark
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+**What this tool does**
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+OPSIN_ is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature.
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+.. _OPSIN: https://bitbucket.org/dan2097/opsin/overview
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+-----
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+.. class:: infomark
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+**Cite**
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+Daniel M Lowe, Peter T Corbett, Peter Murray-Rust, Robert C Glen - `Chemical Name to Structure: OPSIN, an Open Source Solution`_
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+.. _`Chemical Name to Structure: OPSIN, an Open Source Solution`: http://dx.doi.org/10.1021/ci100384d
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diff -r 000000000000 -r cda22c799d0a repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Thu Aug 15 03:37:25 2013 -0400
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diff -r 000000000000 -r cda22c799d0a test-data/iupac_names.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/iupac_names.txt Thu Aug 15 03:37:25 2013 -0400
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+acetonitrile
+bla
+foo
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diff -r 000000000000 -r cda22c799d0a test-data/opsin_results.smi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/opsin_results.smi Thu Aug 15 03:37:25 2013 -0400
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+C(C)#N
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diff -r 000000000000 -r cda22c799d0a tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Aug 15 03:37:25 2013 -0400
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+ https://bitbucket.org/dan2097/opsin/downloads/opsin-1.4.0-jar-with-dependencies.jar
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+ opsin-1.4.0-jar-with-dependencies.jar
+ $INSTALL_DIR/jars
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+ $INSTALL_DIR/jars
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+ Opsin requires a JAVA (1.5+) runtime evironment.
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