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Merge branch 'cdk-1.4.x' of git@github.com:cdk/cdk into cdk-1.4.x
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@rajarshi
rajarshi committed Nov 7, 2011
2 parents 2e76ff6 + d902312 commit fbfdd14
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Showing 22 changed files with 5,098 additions and 57 deletions.
2 changes: 1 addition & 1 deletion build.props
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@@ -1,3 +1,3 @@
# configuration file
#
version=1.4.4.git
version=1.4.5.git
72 changes: 30 additions & 42 deletions build.xml
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Expand Up @@ -940,27 +940,21 @@
<copy todir="${sourcedist.dir}/src/META-INF">
<fileset dir="src/META-INF" />
</copy>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/config/data/">
<fileset dir="${src}/main/org/openscience/cdk/config/data/"
includes="*" />
</copy>
<copy
file="${src}/main/org/openscience/cdk/dict/data/chemical.xml"
tofile="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/chemical.xml" />
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/">
<fileset dir="${src}/main/org/openscience/cdk/dict/data/" includes="*.owl"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/">
<fileset dir="${src}/main/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/">
<fileset dir="${src}/main/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/layout/templates"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/layout/templates">
<fileset dir="${src}/main/org/openscience/cdk/layout/templates" includes="*"/>
<copy todir="${sourcedist.dir}/${src}/main/">
<fileset dir="${src}/main/" includesfile="${src}/META-INF/atomtype.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/builder3d.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/core.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/dict.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/extra.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/fingerprint.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/forcefield.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/io.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/log4j.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/pdb.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/qsaratomic.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/qsar.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/qsarmolecular.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/sdg.datafiles" />
</copy>
<mkdir dir="${sourcedist.dir}/doc/" />
<copy todir="${sourcedist.dir}/doc/">
Expand Down Expand Up @@ -1004,27 +998,21 @@
<copy todir="${sourcedist.dir}/src/META-INF">
<fileset dir="src/META-INF" />
</copy>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/config/data/">
<fileset dir="${src}/main/org/openscience/cdk/config/data/"
includes="*" />
</copy>
<copy
file="${src}/main/org/openscience/cdk/dict/data/chemical.xml"
tofile="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/chemical.xml" />
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/">
<fileset dir="${src}/main/org/openscience/cdk/dict/data/" includes="*.owl"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/">
<fileset dir="${src}/main/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/">
<fileset dir="${src}/main/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/layout/templates"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/layout/templates">
<fileset dir="${src}/main/org/openscience/cdk/layout/templates" includes="*"/>
<copy todir="${sourcedist.dir}/${src}/main/">
<fileset dir="${src}/main/" includesfile="${src}/META-INF/atomtype.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/builder3d.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/core.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/dict.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/extra.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/fingerprint.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/forcefield.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/io.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/log4j.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/pdb.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/qsaratomic.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/qsar.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/qsarmolecular.datafiles" />
<fileset dir="${src}/main/" includesfile="${src}/META-INF/sdg.datafiles" />
</copy>
<mkdir dir="${sourcedist.dir}/doc/" />
<copy todir="${sourcedist.dir}/doc/">
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15 changes: 15 additions & 0 deletions doc/refs/cheminf.bibx
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Expand Up @@ -1162,4 +1162,19 @@ Method </bibtex:title>

</bibtex:entry>

<bibtex:entry id="Klekota01112008">
<bibtex:article>
<bibtex:author>Klekota, Justin and Roth, Frederick P.</bibtex:author>
<bibtex:title>Chemical substructures that enrich for biological activity</bibtex:title>
<bibtex:volume>24</bibtex:volume>
<bibtex:number>21</bibtex:number>
<bibtex:pages>2518-2525</bibtex:pages>
<bibtex:year>2008</bibtex:pages>
<bibtex:doi>10.1093/bioinformatics/btn479</bibtex:doi>
<bibtex:URL>http://bioinformatics.oxfordjournals.org/content/24/21/2518.abstract</bibtex:URL>
<bibtex:eprint>http://bioinformatics.oxfordjournals.org/content/24/21/2518.full.pdf+html</bibtex:eprint>
<bibtex:journal>Bioinformatics</bibtex:journal>
</bibtex:article>
</bibtex:entry>

</bibtex:file>
2 changes: 0 additions & 2 deletions src/META-INF/qsar.cdkdepends
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Expand Up @@ -2,5 +2,3 @@ cdk-annotation.jar
cdk-interfaces.jar
cdk-core.jar
cdk-standard.jar
cdk-valencycheck.jar
cdk-reaction.jar
1 change: 1 addition & 0 deletions src/META-INF/test-fingerprint.cdkdepends
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Expand Up @@ -16,3 +16,4 @@ cdk-formula.jar
cdk-testdata.jar
cdk-test-standard.jar
cdk-diff.jar
cdk-silent.jar
1 change: 1 addition & 0 deletions src/META-INF/test-ioformats.cdkdepends
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Expand Up @@ -9,5 +9,6 @@ cdk-smiles.jar
cdk-pdb.jar
cdk-libiocml.jar
cdk-extra.jar
cdk-data.jar
cdk-test.jar
cdk-testdata.jar
2 changes: 2 additions & 0 deletions src/META-INF/test-isomorphism.cdkdepends
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Expand Up @@ -4,3 +4,5 @@ cdk-core.jar
cdk-data.jar
cdk-test.jar
cdk-isomorphism.jar
cdk-standard.jar
cdk-nonotify.jar

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