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  • 10 commits
  • 327 files changed
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  • 1 contributor
Showing with 1,152 additions and 3,733 deletions.
  1. 0  ...ence/cdk/config → base/atomtype/src/main/resources/org/openscience/cdk/dict}/data/conversion_table.xml
  2. 0  ...tein → descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic}/.gitattributes
  3. 0  ...olecular → descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond}/.gitattributes
  4. 0  ...bond → descriptor/qsarionpot/src/main/java/org/openscience/cdk/qsar/descriptors/atomic}/.gitattributes
  5. 0  ...ompair → descriptor/qsarionpot/src/main/java/org/openscience/cdk/qsar/descriptors/bond}/.gitattributes
  6. 0  ...c → descriptor/qsarionpot/src/main/java/org/openscience/cdk/qsar/descriptors/molecular}/.gitattributes
  7. +1 −0  descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/atompair/.gitattributes
  8. +1 −0  descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/.gitattributes
  9. +1 −0  descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/.gitattributes
  10. +1 −0  descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/protein/.gitattributes
  11. +327 −327 {src/main/org/openscience/cdk → doc}/dict/data/react/bibtexml2xhtml.xsl
  12. +272 −272 {src/main/org/openscience/cdk → doc}/dict/data/react/dictReactxhtml.xsl
  13. +174 −174 {src/main/org/openscience/cdk → doc}/dict/data/react/reaction-types-metadata.xml
  14. +375 −375 {src/main/org/openscience/cdk → doc}/dict/data/react/reaction-types.xml
  15. 0  {src/main/org/openscience/cdk/config/data → doc/dict/xsl}/html.xsl
  16. 0  ...cience/cdk/iupac/parser → misc/extra/src/main/resources/org/openscience/cdk/iupac.parser}/package.html
  17. 0  ...nscience/cdk/iupac → misc/test-extra/src/test/resources/org/openscience/cdk/iupac/parser}/package.html
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  276. +0 −6 src/META-INF/test-sdg.libdepends
  277. +0 −15 src/META-INF/test-signature.cdkdepends
  278. +0 −3  src/META-INF/test-signature.devellibdepends
  279. +0 −5 src/META-INF/test-signature.libdepends
  280. +0 −8 src/META-INF/test-silent.cdkdepends
  281. +0 −3  src/META-INF/test-silent.devellibdepends
  282. +0 −3  src/META-INF/test-silent.libdepends
  283. +0 −14 src/META-INF/test-smarts.cdkdepends
  284. +0 −3  src/META-INF/test-smarts.devellibdepends
  285. +0 −6 src/META-INF/test-smarts.libdepends
  286. +0 −18 src/META-INF/test-smiles.cdkdepends
  287. +0 −3  src/META-INF/test-smiles.devellibdepends
  288. +0 −8 src/META-INF/test-smiles.libdepends
  289. +0 −14 src/META-INF/test-smsd.cdkdepends
  290. +0 −2  src/META-INF/test-smsd.devellibdepends
  291. +0 −8 src/META-INF/test-smsd.libdepends
  292. +0 −17 src/META-INF/test-standard.cdkdepends
  293. +0 −3  src/META-INF/test-standard.devellibdepends
  294. +0 −9 src/META-INF/test-standard.libdepends
  295. +0 −16 src/META-INF/test-structgen.cdkdepends
  296. +0 −2  src/META-INF/test-structgen.devellibdepends
  297. +0 −5 src/META-INF/test-structgen.libdepends
  298. +0 −14 src/META-INF/test-tautomer.cdkdepends
  299. +0 −2  src/META-INF/test-tautomer.devellibdepends
  300. +0 −7 src/META-INF/test-tautomer.libdepends
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654 ...ce/cdk/dict/data/react/bibtexml2xhtml.xsl → doc/dict/data/react/bibtexml2xhtml.xsl
@@ -1,327 +1,327 @@
-<?xml version="1.0"?>
-
-<!-- this XSL is taken from http://www.cs.duke.edu/~sprenkle/bibtex2html/ and
- copyright (c) 2003 licensed with GPL by Sara E. Sprenkle -->
-
-<!--
- File : $Id: bibtexml2xhtml.xsl 104 2005-02-17 15:34:07Z egonw $
- Abstract: Transform bibteXML file into a publication list HTML page
- -->
-
-<!--
- Modified by SES 2003.01.15
-
- &#160; = &nbsp;
-
- -->
-
-<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
- xmlns:bibxml="http://bibtexml.sf.net/"
- xmlns="http://www.w3.org/1999/xhtml"
- version="1.0">
-
-<!--
- - bibtex entry types
- - follows bibtex specs mostly
- -->
-
-
-<xsl:template match="bibxml:article">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:apply-templates select="bibxml:journal"/>
-
- <xsl:choose>
- <xsl:when test="bibxml:volume != '' and (not(bibxml:number) or bibxml:number = '')">
- <xsl:apply-templates select="bibxml:volume"/>
- </xsl:when>
- <xsl:when test="bibxml:volume != '' and bibxml:number != '' ">
- <xsl:value-of select="bibxml:volume"/>
- (<xsl:value-of select="bibxml:number"/>).
- </xsl:when>
- <!-- only a number, no volume -->
- <xsl:when test="bibxml:number != ''">
- no. <xsl:apply-templates select="bibxml:number"/>.
- </xsl:when>
- </xsl:choose>
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
- <xsl:apply-templates select="bibxml:pages"/>
- <xsl:apply-templates select="bibxml:doi"/>
-</xsl:template>
-
-<xsl:template match="bibxml:inproceedings | bibxml:conference">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:apply-templates select="bibxml:booktitle"/>
- <xsl:if test="bibxml:organization != ''">
- <xsl:value-of select="bibxml:organization"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:address"/>
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
- <xsl:apply-templates select="bibxml:pages"/>
- <xsl:apply-templates select="bibxml:url"/>
-</xsl:template>
-
-<xsl:template match="bibxml:techreport">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:apply-templates select="bibxml:booktitle"/>
- <xsl:value-of select="bibxml:institution"/>.
- <xsl:if test="bibxml:number != ''">
- <xsl:value-of select="bibxml:number"/>.
- </xsl:if>
- <xsl:if test="bibxml:type != ''">
- <xsl:value-of select="bibxml:type"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
- <xsl:apply-templates select="bibxml:url"/>
-</xsl:template>
-
-<xsl:template match="bibxml:book">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:if test="bibxml:editor != ''">
- <xsl:value-of select="bibxml:editor"/>.
- </xsl:if>
- <xsl:if test="bibxml:publisher != ''">
- <xsl:value-of select="bibxml:publisher"/>.
- </xsl:if>
- <xsl:if test="bibxml:series != ''">
- <xsl:value-of select="bibxml:series"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:volume"/>
- <xsl:apply-templates select="bibxml:edition"/>
- <xsl:apply-templates select="bibxml:address"/>
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
-</xsl:template>
-
-<xsl:template match="bibxml:phdthesis | bibxml:masterthesis">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:if test="bibxml:school != ''">
- <xsl:value-of select="bibxml:school"/>.
- </xsl:if>
- <xsl:if test="bibxml:number != ''">
- <xsl:value-of select="bibxml:number"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:year"/>
-</xsl:template>
-
-<xsl:template match="bibxml:misc">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:if test="bibxml:title != ''">
- <xsl:apply-templates select="bibxml:title"/>
- </xsl:if>
- <xsl:if test="bibxml:howpublished != ''">
- <xsl:value-of select="bibxml:howpublished"/>.
- </xsl:if>
- <xsl:if test="bibxml:url != ''">
- <xsl:apply-templates select="bibxml:url"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
-</xsl:template>
-
-<xsl:template match="bibxml:unpublished">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:apply-templates select="bibxml:note"/>
-</xsl:template>
-
-<xsl:template match="bibxml:manual">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:if test="bibxml:organization != ''">
- <xsl:value-of select="bibxml:organization"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:edition"/>
- <xsl:apply-templates select="bibxml:address"/>
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
- <xsl:apply-templates select="bibxml:note"/>
-</xsl:template>
-
-<xsl:template match="bibxml:proceedings">
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:if test="bibxml:editor != ''">
- <xsl:value-of select="bibxml:editor"/>.
- </xsl:if>
- <xsl:if test="bibxml:publisher != ''">
- <xsl:value-of select="bibxml:publisher"/>.
- </xsl:if>
- <xsl:if test="bibxml:organization != ''">
- <xsl:value-of select="bibxml:organization"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:address"/>
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
- <xsl:apply-templates select="bibxml:note"/>
-</xsl:template>
-
-<xsl:template match="bibxml:booklet">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:if test="bibxml:howpublished != ''">
- <xsl:value-of select="bibxml:howpublished"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:address"/>
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
- <xsl:apply-templates select="bibxml:note"/>
-</xsl:template>
-
-
-<xsl:template match="bibxml:inbook">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:if test="bibxml:chapter != ''">
- <xsl:value-of select="bibxml:chapter"/>.
- </xsl:if>
- <xsl:if test="bibxml:editor != ''">
- Editted by <xsl:value-of select="bibxml:editor"/>.
- </xsl:if>
- <xsl:if test="bibxml:howpublished != ''">
- <xsl:value-of select="bibxml:howpublished"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:address"/>
-
- <xsl:if test="bibxml:publisher != ''">
- <xsl:value-of select="bibxml:publisher"/>.
- </xsl:if>
- <xsl:if test="bibxml:series != ''">
- <xsl:value-of select="bibxml:series"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:volume"/>
- <xsl:apply-templates select="bibxml:edition"/>
-
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
- <xsl:apply-templates select="bibxml:pages"/>
-</xsl:template>
-
-
-<xsl:template match="bibxml:incollection">
- <xsl:apply-templates select="bibxml:author"/>
- <xsl:apply-templates select="bibxml:title"/>
- <xsl:apply-templates select="bibxml:booktitle"/>
- <xsl:if test="bibxml:editor != ''">
- Editted by <xsl:value-of select="bibxml:editor"/>.
- </xsl:if>
- <xsl:apply-templates select="bibxml:address"/>
-
- <xsl:if test="bibxml:publisher != ''">
- <xsl:value-of select="bibxml:publisher"/>.
- </xsl:if>
-
- <xsl:apply-templates select="bibxml:month"/>
- <xsl:apply-templates select="bibxml:year"/>
- <xsl:apply-templates select="bibxml:pages"/>
-</xsl:template>
-
-<!-- fields -->
-
-
-<xsl:template match="bibxml:pages">
- <xsl:if test=". != ''">
- pp. <xsl:value-of select="."/>.
- </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:month">
- <xsl:if test=". != ''">
- <xsl:value-of select="."/> </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:volume">
- <xsl:if test=". != ''">
- vol. <xsl:value-of select="."/>.
- </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:edition">
- <xsl:if test=". != ''">
- ed. <xsl:value-of select="."/>.
- </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:title">
- <xsl:if test=". != ''">
- <i><xsl:value-of select="."/></i>,
- </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:note">
- <xsl:if test=". != ''">
- <i>Note: </i>
- <xsl:value-of select="."/>.
- </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:address">
- <xsl:if test=". != ''">
- <xsl:value-of select="."/>.
- </xsl:if>
-</xsl:template>
-
-
-<xsl:template match="bibxml:booktitle | bibxml:journal">
- <xsl:if test=". != ''">
- <i><xsl:value-of select="."/></i>
- </xsl:if>
- <xsl:if test="position() + 1 != last()">. </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:year">
- <xsl:if test=". != ''">
- <b><xsl:value-of select="."/></b>,
- </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:author">
- <xsl:value-of select="."/>
- <xsl:choose>
- <xsl:when test="position() = count(../bibxml:author)">. </xsl:when>
- <xsl:when test="count(../bibxml:author) = 2 and position() = 1"> and </xsl:when>
- <xsl:when test="position() + 1 != count(../bibxml:author)">, </xsl:when>
- <xsl:when test="position() + 1 = count(../bibxml:author)">, and </xsl:when>
- </xsl:choose>
-</xsl:template>
-
-<xsl:template match="bibxml:editor |
- bibxml:number | bibxml:series | bibxml:institution |
- bibxml:organization |
- bibxml:publisher | bibxml:school |
- bibxml:type | bibxml:bookshelf |
- bibxml:annotate | bibxml:crossref |
- bibxml:issn | bibxml:isbn | bibxml:uri |
- bibxml:urn">
- <xsl:value-of select="."/>
- <xsl:if test="position() + 1 != last()">, </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:url">
- <xsl:if test=". != ''">
- <a href="{.}">
- <xsl:value-of select="."/>
- </a>
- </xsl:if>
-</xsl:template>
-
-<xsl:template match="bibxml:doi">
- <xsl:if test=". != ''">
- <a href="http://dx.doi.org/{.}">
- <xsl:value-of select="."/>
- </a>
- </xsl:if>
-</xsl:template>
-
-<!--
- - Do not print the following entries
- -->
-<xsl:template match="bibxml:category | bibxml:key |
- bibxml:keywords"/>
-</xsl:stylesheet>
+<?xml version="1.0"?>
+
+<!-- this XSL is taken from http://www.cs.duke.edu/~sprenkle/bibtex2html/ and
+ copyright (c) 2003 licensed with GPL by Sara E. Sprenkle -->
+
+<!--
+ File : $Id: bibtexml2xhtml.xsl 104 2005-02-17 15:34:07Z egonw $
+ Abstract: Transform bibteXML file into a publication list HTML page
+ -->
+
+<!--
+ Modified by SES 2003.01.15
+
+ &#160; = &nbsp;
+
+ -->
+
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+ xmlns:bibxml="http://bibtexml.sf.net/"
+ xmlns="http://www.w3.org/1999/xhtml"
+ version="1.0">
+
+<!--
+ - bibtex entry types
+ - follows bibtex specs mostly
+ -->
+
+
+<xsl:template match="bibxml:article">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:apply-templates select="bibxml:journal"/>
+
+ <xsl:choose>
+ <xsl:when test="bibxml:volume != '' and (not(bibxml:number) or bibxml:number = '')">
+ <xsl:apply-templates select="bibxml:volume"/>
+ </xsl:when>
+ <xsl:when test="bibxml:volume != '' and bibxml:number != '' ">
+ <xsl:value-of select="bibxml:volume"/>
+ (<xsl:value-of select="bibxml:number"/>).
+ </xsl:when>
+ <!-- only a number, no volume -->
+ <xsl:when test="bibxml:number != ''">
+ no. <xsl:apply-templates select="bibxml:number"/>.
+ </xsl:when>
+ </xsl:choose>
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+ <xsl:apply-templates select="bibxml:pages"/>
+ <xsl:apply-templates select="bibxml:doi"/>
+</xsl:template>
+
+<xsl:template match="bibxml:inproceedings | bibxml:conference">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:apply-templates select="bibxml:booktitle"/>
+ <xsl:if test="bibxml:organization != ''">
+ <xsl:value-of select="bibxml:organization"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:address"/>
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+ <xsl:apply-templates select="bibxml:pages"/>
+ <xsl:apply-templates select="bibxml:url"/>
+</xsl:template>
+
+<xsl:template match="bibxml:techreport">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:apply-templates select="bibxml:booktitle"/>
+ <xsl:value-of select="bibxml:institution"/>.
+ <xsl:if test="bibxml:number != ''">
+ <xsl:value-of select="bibxml:number"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:type != ''">
+ <xsl:value-of select="bibxml:type"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+ <xsl:apply-templates select="bibxml:url"/>
+</xsl:template>
+
+<xsl:template match="bibxml:book">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:if test="bibxml:editor != ''">
+ <xsl:value-of select="bibxml:editor"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:publisher != ''">
+ <xsl:value-of select="bibxml:publisher"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:series != ''">
+ <xsl:value-of select="bibxml:series"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:volume"/>
+ <xsl:apply-templates select="bibxml:edition"/>
+ <xsl:apply-templates select="bibxml:address"/>
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+</xsl:template>
+
+<xsl:template match="bibxml:phdthesis | bibxml:masterthesis">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:if test="bibxml:school != ''">
+ <xsl:value-of select="bibxml:school"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:number != ''">
+ <xsl:value-of select="bibxml:number"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:year"/>
+</xsl:template>
+
+<xsl:template match="bibxml:misc">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:if test="bibxml:title != ''">
+ <xsl:apply-templates select="bibxml:title"/>
+ </xsl:if>
+ <xsl:if test="bibxml:howpublished != ''">
+ <xsl:value-of select="bibxml:howpublished"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:url != ''">
+ <xsl:apply-templates select="bibxml:url"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+</xsl:template>
+
+<xsl:template match="bibxml:unpublished">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:apply-templates select="bibxml:note"/>
+</xsl:template>
+
+<xsl:template match="bibxml:manual">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:if test="bibxml:organization != ''">
+ <xsl:value-of select="bibxml:organization"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:edition"/>
+ <xsl:apply-templates select="bibxml:address"/>
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+ <xsl:apply-templates select="bibxml:note"/>
+</xsl:template>
+
+<xsl:template match="bibxml:proceedings">
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:if test="bibxml:editor != ''">
+ <xsl:value-of select="bibxml:editor"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:publisher != ''">
+ <xsl:value-of select="bibxml:publisher"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:organization != ''">
+ <xsl:value-of select="bibxml:organization"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:address"/>
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+ <xsl:apply-templates select="bibxml:note"/>
+</xsl:template>
+
+<xsl:template match="bibxml:booklet">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:if test="bibxml:howpublished != ''">
+ <xsl:value-of select="bibxml:howpublished"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:address"/>
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+ <xsl:apply-templates select="bibxml:note"/>
+</xsl:template>
+
+
+<xsl:template match="bibxml:inbook">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:if test="bibxml:chapter != ''">
+ <xsl:value-of select="bibxml:chapter"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:editor != ''">
+ Editted by <xsl:value-of select="bibxml:editor"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:howpublished != ''">
+ <xsl:value-of select="bibxml:howpublished"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:address"/>
+
+ <xsl:if test="bibxml:publisher != ''">
+ <xsl:value-of select="bibxml:publisher"/>.
+ </xsl:if>
+ <xsl:if test="bibxml:series != ''">
+ <xsl:value-of select="bibxml:series"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:volume"/>
+ <xsl:apply-templates select="bibxml:edition"/>
+
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+ <xsl:apply-templates select="bibxml:pages"/>
+</xsl:template>
+
+
+<xsl:template match="bibxml:incollection">
+ <xsl:apply-templates select="bibxml:author"/>
+ <xsl:apply-templates select="bibxml:title"/>
+ <xsl:apply-templates select="bibxml:booktitle"/>
+ <xsl:if test="bibxml:editor != ''">
+ Editted by <xsl:value-of select="bibxml:editor"/>.
+ </xsl:if>
+ <xsl:apply-templates select="bibxml:address"/>
+
+ <xsl:if test="bibxml:publisher != ''">
+ <xsl:value-of select="bibxml:publisher"/>.
+ </xsl:if>
+
+ <xsl:apply-templates select="bibxml:month"/>
+ <xsl:apply-templates select="bibxml:year"/>
+ <xsl:apply-templates select="bibxml:pages"/>
+</xsl:template>
+
+<!-- fields -->
+
+
+<xsl:template match="bibxml:pages">
+ <xsl:if test=". != ''">
+ pp. <xsl:value-of select="."/>.
+ </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:month">
+ <xsl:if test=". != ''">
+ <xsl:value-of select="."/> </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:volume">
+ <xsl:if test=". != ''">
+ vol. <xsl:value-of select="."/>.
+ </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:edition">
+ <xsl:if test=". != ''">
+ ed. <xsl:value-of select="."/>.
+ </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:title">
+ <xsl:if test=". != ''">
+ <i><xsl:value-of select="."/></i>,
+ </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:note">
+ <xsl:if test=". != ''">
+ <i>Note: </i>
+ <xsl:value-of select="."/>.
+ </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:address">
+ <xsl:if test=". != ''">
+ <xsl:value-of select="."/>.
+ </xsl:if>
+</xsl:template>
+
+
+<xsl:template match="bibxml:booktitle | bibxml:journal">
+ <xsl:if test=". != ''">
+ <i><xsl:value-of select="."/></i>
+ </xsl:if>
+ <xsl:if test="position() + 1 != last()">. </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:year">
+ <xsl:if test=". != ''">
+ <b><xsl:value-of select="."/></b>,
+ </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:author">
+ <xsl:value-of select="."/>
+ <xsl:choose>
+ <xsl:when test="position() = count(../bibxml:author)">. </xsl:when>
+ <xsl:when test="count(../bibxml:author) = 2 and position() = 1"> and </xsl:when>
+ <xsl:when test="position() + 1 != count(../bibxml:author)">, </xsl:when>
+ <xsl:when test="position() + 1 = count(../bibxml:author)">, and </xsl:when>
+ </xsl:choose>
+</xsl:template>
+
+<xsl:template match="bibxml:editor |
+ bibxml:number | bibxml:series | bibxml:institution |
+ bibxml:organization |
+ bibxml:publisher | bibxml:school |
+ bibxml:type | bibxml:bookshelf |
+ bibxml:annotate | bibxml:crossref |
+ bibxml:issn | bibxml:isbn | bibxml:uri |
+ bibxml:urn">
+ <xsl:value-of select="."/>
+ <xsl:if test="position() + 1 != last()">, </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:url">
+ <xsl:if test=". != ''">
+ <a href="{.}">
+ <xsl:value-of select="."/>
+ </a>
+ </xsl:if>
+</xsl:template>
+
+<xsl:template match="bibxml:doi">
+ <xsl:if test=". != ''">
+ <a href="http://dx.doi.org/{.}">
+ <xsl:value-of select="."/>
+ </a>
+ </xsl:if>
+</xsl:template>
+
+<!--
+ - Do not print the following entries
+ -->
+<xsl:template match="bibxml:category | bibxml:key |
+ bibxml:keywords"/>
+</xsl:stylesheet>
View
544 ...ce/cdk/dict/data/react/dictReactxhtml.xsl → doc/dict/data/react/dictReactxhtml.xsl
@@ -1,273 +1,273 @@
-<?xml version="1.0"?>
-<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
- xmlns="http://www.w3.org/1999/xhtml"
- version="1.0">
-
- <!-- $Author: mrc $
- $Date: 2006/05/08 17:00:44 $
- $Revision: 0.1 $ -->
-
- <xsl:output method="xml" indent="yes"
- omit-xml-declaration="no" encoding="utf-8"
- doctype-public="-//W3C//DTD XHTML 1.1 plus MathML 2.0 plus SVG 1.1//EN"
- doctype-system="http://www.w3.org/2002/04/xhtml-math-svg/xhtml-math-svg.dtd"/>
-
- <xsl:variable name="metadataDoc" select="document('reaction-types-metadata.xml')"/>
-
- <xsl:key name="entryKey" match="*" use="@id"/>
-
- <xsl:include href="bibtexml2xhtml.xsl"/>
-
- <xsl:template match="*">
- <xsl:apply-templates/>
- </xsl:template>
-
- <xsl:template match="*[namespace-uri(.)='http://www.w3.org/1998/Math/MathML']">
- <xsl:element name="{name(.)}">
- <xsl:apply-templates select="text()|*"/>
- </xsl:element>
- </xsl:template>
-
- <xsl:template match="*[name(.)='mrow']">
- <xsl:element name="math">
- <xsl:element name="mrow">
- <xsl:apply-templates select="*"/>
- </xsl:element>
- </xsl:element>
- </xsl:template>
-
- <xsl:template match="text()">
- <xsl:value-of select="."/>
- </xsl:template>
-
- <xsl:template match="/">
-<html xml:lang="en">
-<head>
-<title><xsl:value-of select=".//*[name(.)='dictionary']/@title"/>
-[<xsl:value-of select=".//*[name(.)='dictionary']/@id"/>]</title>
-<style type="text/css">
-p.small {font-size: 70%}
-a:hover {background-color: #000000; color: white; text-decoration: none}
-div.toc { margin-left: 2em; }
-h1 {background-color: #CCCCCC}
-h2 {background-color: #DDDDDD}
-h3 {background-color: #EEEEEE}
-</style>
-</head>
-<body>
-<h1><xsl:value-of select=".//*[name(.)='dictionary']/@title"/></h1>
-<p>
- <xsl:for-each select=".//*[name(.)='contributor']">
- <xsl:if test="position()=last() and last()!=1"><xsl:text> and </xsl:text></xsl:if>
- <i><xsl:value-of select="."/></i>
- <xsl:if test="position() &lt; (last()-1)"><xsl:text>, </xsl:text></xsl:if>
- </xsl:for-each>
-</p>
-<p>
- <xsl:apply-templates select=".//*[name(.)='dictionary']/*[name(.)='description']"/>
-</p>
-<p>
- <!-- table of content -->
- [<a href="#Entries">Entries</a>]
- [<a href="#Bibliography">Bibliography</a>]
- [<a href="#FinalNotes">Final Notes</a>]
-</p>
-<xsl:if test="/*[name(.)='dictionary']/@id='reaction-types'">
-<h2><a name="TOC">Table of Contents</a></h2>
-<p>
- <!-- entries index -->
- <xsl:variable name="self" select="/"/>
- <xsl:for-each select="$metadataDoc//*[name(.)='entry']//*[name(.)='relatedEntry' and @type='reaction-types-metadata:instanceOf' and (@href='reactionType' or @href='reactionClass')]">
- <xsl:sort select="./@href"/>
- <xsl:variable name="className" select="../@id"/>
- <b><xsl:value-of select="../@term"/>s</b>
- <xsl:for-each select="$self//*[name(.)='metadata' and @content=concat('reaction-types-metadata:', $className)]">
- <div class="toc">
- <xsl:element name="a">
- <xsl:attribute name="href">#<xsl:value-of select="../../@id"/></xsl:attribute>
- <xsl:value-of select="../../@id"/>
- </xsl:element>
- </div>
- </xsl:for-each><br/>
- </xsl:for-each>
-</p>
-</xsl:if>
-<h2><a name="Entries">Entries</a></h2>
-<xsl:for-each select=".//*[name(.)='entry']">
- <xsl:sort select="./@term" order="ascending"/>
- <xsl:apply-templates select="."/>
-</xsl:for-each>
-<h2><a name="Bibliography">Bibliography</a></h2>
-<p>
-<xsl:for-each select=".//*[name(.)='bibtex:entry']">
- <xsl:sort select="./@id" order="ascending"/>
- <xsl:apply-templates select="."/>
-</xsl:for-each>
-</p>
-<h2><a name="FinalNotes">Final Notes</a></h2>
-<p>
- This dictionary
- [<xsl:value-of select=".//*[name(.)='metadata' and ./@name='cvs:revision']/@content"/>]
- was last modified by
- [<xsl:value-of select=".//*[name(.)='metadata' and ./@name='cvs:last-change-by']/@content"/>]
- on
- [<xsl:value-of select=".//*[name(.)='metadata' and ./@name='cvs:date']/@content"/>].
-</p>
-<p>
- <a href="http://validator.w3.org/check?uri=referer"><img
- src="http://www.w3.org/Icons/valid-xhtml10"
- alt="Valid XHTML 1.0!" height="31" width="88" /></a>
-</p>
-</body>
-</html>
- </xsl:template>
-
- <xsl:template match="*[name(.)='entry']">
-<h3><xsl:element name="a">
- <xsl:attribute name="id"><xsl:value-of select="./@id"/></xsl:attribute>
- <xsl:value-of select="./@term"/> (<xsl:value-of select="./@id"/>)
- </xsl:element>
-</h3>
-<ul>
-<li><p>
- <xsl:if test="./*[name(.)='definition']">
- <b>Definition</b><br/>
- <xsl:apply-templates select="./*[name(.)='definition']"/>
- </xsl:if>
-</p>
-<p>
- <xsl:if test="./*[name(.)='description']">
- <b>Description</b><br/>
- <xsl:apply-templates select="./*[name(.)='description']"/> Examples
- with JChemPaint Viewer <xsl:element name="a">
- <xsl:attribute name="href">http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/examples/"./@id"/>&amp;ie=UTF-8&amp;oe=UTF-8</xsl:attribute>
- here
- </xsl:element>
-
- </xsl:if>
-</p>
-<p>
- <xsl:if test="./*[name(.)='relatedEntry']">
- <b>Relations</b><br />
- <xsl:for-each select="./*[name(.)='relatedEntry']">
- <xsl:apply-templates select="."/><br />
- </xsl:for-each>
- </xsl:if>
- <xsl:if test="./*[name(.)='metadataList']">
- <b>Classification</b><br />
- <xsl:apply-templates select="./*[name(.)='metadataList']"/>
- </xsl:if>
-</p>
-
-<!--<p>
- <xsl:if test="./*[name(.)='exemplesReaction']">
- <b>Exemple</b>
- <xsl:apply-templates select="./*[name(.)='exemplesReaction']"/>
- with JChemPaint Viewer <xsl:element name="a">
- <xsl:attribute name="href">http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/examples/"./@id"/>&amp;ie=UTF-8&amp;oe=UTF-8</xsl:attribute>
- here
- </xsl:element>
- </xsl:if>
-</p>-->
-
- <!-- the Google.com search link -->
-<p>
- <b>Implementations</b><br />
- <xsl:text>Search implementations on </xsl:text>
- <xsl:element name="a">
- <!-- <xsl:attribute name="href">http://www.google.com/search?q=http%3A//qsar.sf.net/dicts/qsar-descriptors/%23<xsl:value-of select="./@id"/>&amp;ie=UTF-8&amp;oe=UTF-8</xsl:attribute> -->
- <xsl:attribute name="href">http://www.google.com/search?<xsl:value-of select="./@term"/>&amp;ie=UTF-8&amp;oe=UTF-8</xsl:attribute>
- Google.com
- </xsl:element>
-</p>
-
-</li>
-</ul>
-<p class="small"><i>
-Contributed by:
-<xsl:for-each select="./*[name(.)='annotation']/*[name(.)='documentation']/*[name(.)='metadata' and @name='dc:contributor']">
- <xsl:variable name="contributorID" select="./@content"/>
- <xsl:value-of select="key('entryKey',$contributorID)/."/>
- <xsl:if test="position()!=last()"><xsl:text>, </xsl:text></xsl:if>
-</xsl:for-each><xsl:text>.</xsl:text>
-Created on: <xsl:value-of select="./*[name(.)='annotation']/*[name(.)='documentation']/*[name(.)='metadata' and @name='dc:date']/@content"/>.
-</i></p>
- </xsl:template>
-
- <xsl:template match="*[name(.)='metadataList']">
- <xsl:apply-templates select="./*[name(.)='metadata']"/>
- </xsl:template>
-
- <xsl:template match="*[name(.)='metadata']">
- <xsl:if test="./@dictRef='reaction-types-metadata:reactionType'">
- <xsl:variable name="metaEntryID" select="substring-after(./@content, ':')"/>
- <xsl:text>This reaction is a </xsl:text>
- <xsl:element name="a">
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- <xsl:for-each select="$metadataDoc">
- <xsl:value-of select="key('entryKey',$metaEntryID)/@term"/>
- </xsl:for-each>
- </xsl:element><br />
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- <xsl:if test="./@dictRef='reaction-types-metadata:reactionClass'">
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- <xsl:text>This reaction is a </xsl:text>
- <xsl:element name="a">
- <xsl:attribute name="href">http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionMetadata#<xsl:value-of select="$metaEntryID"/></xsl:attribute>
- <xsl:for-each select="$metadataDoc">
- <xsl:value-of select="key('entryKey',$metaEntryID)/@term"/>
- </xsl:for-each>
- </xsl:element><br />
- </xsl:if>
- </xsl:template>
-
- <xsl:template match="*[name(.)='exemplesReaction']">
- <center><xsl:apply-templates select="./*[name(.)='imagedata']"/></center>
- </xsl:template>
-
- <xsl:template match="*[name(.)='imagedata']">
- <xsl:if test="./@dictRef='reactions-metadata:CML'">
- <xsl:variable name="ReactionCML" select="./@content"/>
- <applet code="org.openscience.cdk.applications.jchempaint.applet.JChemPaintViewerOnlyApplet"
- name="JCPApplet" archive="jar/jchempaint-applet-core.jar"
- width="500" height="150">
- <param name="load" value="{$ReactionCML}"/>
- <param name="compact" value="true"/>
- </applet>
- </xsl:if>
- </xsl:template>
-
-
- <xsl:template match="*[name(.)='relatedEntry']">
- <xsl:variable name="relationType" select="substring-after(./@type, ':')"/>
- <xsl:variable name="entryID" select="./@href"/>
- <xsl:element name="a">
- <xsl:attribute name="href">http://qsar.sourceforge.net/dicts/reaction-types-metadata/index.xhtml#<xsl:value-of select="$relationType"/></xsl:attribute>
- <xsl:for-each select="$metadataDoc">
- <xsl:value-of select="key('entryKey',$relationType)/@term"/>
- </xsl:for-each>
- </xsl:element>
- <xsl:text>: </xsl:text>
- <xsl:element name="a">
- <xsl:attribute name="href">#<xsl:value-of select="./@href"/></xsl:attribute>
- <xsl:value-of select="key('entryKey',$entryID)/@term"/>
- </xsl:element>
- </xsl:template>
-
- <xsl:template match="*[name(.)='bibtex:cite']">
- [<xsl:element name="a">
- <xsl:attribute name="href">#bibtex:<xsl:value-of select="./@ref"/></xsl:attribute>
- <xsl:value-of select="./@ref"/>
- </xsl:element>]
- </xsl:template>
-
- <xsl:template match="*[name(.)='bibtex:entry']">
- <xsl:element name="a">
- <xsl:attribute name="id">bibtex:<xsl:value-of select="./@id"/></xsl:attribute>
- [<xsl:value-of select="./@id"/>]
- </xsl:element>
- <xsl:apply-templates select="./*"/>
- <br/>
- </xsl:template>
-
+<?xml version="1.0"?>
+<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+ xmlns="http://www.w3.org/1999/xhtml"
+ version="1.0">
+
+ <!-- $Author: mrc $
+ $Date: 2006/05/08 17:00:44 $
+ $Revision: 0.1 $ -->
+
+ <xsl:output method="xml" indent="yes"
+ omit-xml-declaration="no" encoding="utf-8"
+ doctype-public="-//W3C//DTD XHTML 1.1 plus MathML 2.0 plus SVG 1.1//EN"
+ doctype-system="http://www.w3.org/2002/04/xhtml-math-svg/xhtml-math-svg.dtd"/>
+
+ <xsl:variable name="metadataDoc" select="document('reaction-types-metadata.xml')"/>
+
+ <xsl:key name="entryKey" match="*" use="@id"/>
+
+ <xsl:include href="bibtexml2xhtml.xsl"/>
+
+ <xsl:template match="*">
+ <xsl:apply-templates/>
+ </xsl:template>
+
+ <xsl:template match="*[namespace-uri(.)='http://www.w3.org/1998/Math/MathML']">
+ <xsl:element name="{name(.)}">
+ <xsl:apply-templates select="text()|*"/>
+ </xsl:element>
+ </xsl:template>
+
+ <xsl:template match="*[name(.)='mrow']">
+ <xsl:element name="math">
+ <xsl:element name="mrow">
+ <xsl:apply-templates select="*"/>
+ </xsl:element>
+ </xsl:element>
+ </xsl:template>
+
+ <xsl:template match="text()">
+ <xsl:value-of select="."/>
+ </xsl:template>
+
+ <xsl:template match="/">
+<html xml:lang="en">
+<head>
+<title><xsl:value-of select=".//*[name(.)='dictionary']/@title"/>
+[<xsl:value-of select=".//*[name(.)='dictionary']/@id"/>]</title>
+<style type="text/css">
+p.small {font-size: 70%}
+a:hover {background-color: #000000; color: white; text-decoration: none}
+div.toc { margin-left: 2em; }
+h1 {background-color: #CCCCCC}
+h2 {background-color: #DDDDDD}
+h3 {background-color: #EEEEEE}
+</style>
+</head>
+<body>
+<h1><xsl:value-of select=".//*[name(.)='dictionary']/@title"/></h1>
+<p>
+ <xsl:for-each select=".//*[name(.)='contributor']">
+ <xsl:if test="position()=last() and last()!=1"><xsl:text> and </xsl:text></xsl:if>
+ <i><xsl:value-of select="."/></i>
+ <xsl:if test="position() &lt; (last()-1)"><xsl:text>, </xsl:text></xsl:if>
+ </xsl:for-each>
+</p>
+<p>
+ <xsl:apply-templates select=".//*[name(.)='dictionary']/*[name(.)='description']"/>
+</p>
+<p>
+ <!-- table of content -->
+ [<a href="#Entries">Entries</a>]
+ [<a href="#Bibliography">Bibliography</a>]
+ [<a href="#FinalNotes">Final Notes</a>]
+</p>
+<xsl:if test="/*[name(.)='dictionary']/@id='reaction-types'">
+<h2><a name="TOC">Table of Contents</a></h2>
+<p>
+ <!-- entries index -->
+ <xsl:variable name="self" select="/"/>
+ <xsl:for-each select="$metadataDoc//*[name(.)='entry']//*[name(.)='relatedEntry' and @type='reaction-types-metadata:instanceOf' and (@href='reactionType' or @href='reactionClass')]">
+ <xsl:sort select="./@href"/>
+ <xsl:variable name="className" select="../@id"/>
+ <b><xsl:value-of select="../@term"/>s</b>
+ <xsl:for-each select="$self//*[name(.)='metadata' and @content=concat('reaction-types-metadata:', $className)]">
+ <div class="toc">
+ <xsl:element name="a">
+ <xsl:attribute name="href">#<xsl:value-of select="../../@id"/></xsl:attribute>
+ <xsl:value-of select="../../@id"/>
+ </xsl:element>
+ </div>
+ </xsl:for-each><br/>
+ </xsl:for-each>
+</p>
+</xsl:if>
+<h2><a name="Entries">Entries</a></h2>
+<xsl:for-each select=".//*[name(.)='entry']">
+ <xsl:sort select="./@term" order="ascending"/>
+ <xsl:apply-templates select="."/>
+</xsl:for-each>
+<h2><a name="Bibliography">Bibliography</a></h2>
+<p>
+<xsl:for-each select=".//*[name(.)='bibtex:entry']">
+ <xsl:sort select="./@id" order="ascending"/>
+ <xsl:apply-templates select="."/>
+</xsl:for-each>
+</p>
+<h2><a name="FinalNotes">Final Notes</a></h2>
+<p>
+ This dictionary
+ [<xsl:value-of select=".//*[name(.)='metadata' and ./@name='cvs:revision']/@content"/>]
+ was last modified by
+ [<xsl:value-of select=".//*[name(.)='metadata' and ./@name='cvs:last-change-by']/@content"/>]
+ on
+ [<xsl:value-of select=".//*[name(.)='metadata' and ./@name='cvs:date']/@content"/>].
+</p>
+<p>
+ <a href="http://validator.w3.org/check?uri=referer"><img
+ src="http://www.w3.org/Icons/valid-xhtml10"
+ alt="Valid XHTML 1.0!" height="31" width="88" /></a>
+</p>
+</body>
+</html>
+ </xsl:template>
+
+ <xsl:template match="*[name(.)='entry']">
+<h3><xsl:element name="a">
+ <xsl:attribute name="id"><xsl:value-of select="./@id"/></xsl:attribute>
+ <xsl:value-of select="./@term"/> (<xsl:value-of select="./@id"/>)
+ </xsl:element>
+</h3>
+<ul>
+<li><p>
+ <xsl:if test="./*[name(.)='definition']">
+ <b>Definition</b><br/>
+ <xsl:apply-templates select="./*[name(.)='definition']"/>
+ </xsl:if>
+</p>
+<p>
+ <xsl:if test="./*[name(.)='description']">
+ <b>Description</b><br/>
+ <xsl:apply-templates select="./*[name(.)='description']"/> Examples
+ with JChemPaint Viewer <xsl:element name="a">
+ <xsl:attribute name="href">http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/examples/"./@id"/>&amp;ie=UTF-8&amp;oe=UTF-8</xsl:attribute>
+ here
+ </xsl:element>
+
+ </xsl:if>
+</p>
+<p>
+ <xsl:if test="./*[name(.)='relatedEntry']">
+ <b>Relations</b><br />
+ <xsl:for-each select="./*[name(.)='relatedEntry']">
+ <xsl:apply-templates select="."/><br />
+ </xsl:for-each>
+ </xsl:if>
+ <xsl:if test="./*[name(.)='metadataList']">
+ <b>Classification</b><br />
+ <xsl:apply-templates select="./*[name(.)='metadataList']"/>
+ </xsl:if>
+</p>
+
+<!--<p>
+ <xsl:if test="./*[name(.)='exemplesReaction']">
+ <b>Exemple</b>
+ <xsl:apply-templates select="./*[name(.)='exemplesReaction']"/>
+ with JChemPaint Viewer <xsl:element name="a">
+ <xsl:attribute name="href">http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/examples/"./@id"/>&amp;ie=UTF-8&amp;oe=UTF-8</xsl:attribute>
+ here
+ </xsl:element>
+ </xsl:if>
+</p>-->
+
+ <!-- the Google.com search link -->
+<p>
+ <b>Implementations</b><br />
+ <xsl:text>Search implementations on </xsl:text>
+ <xsl:element name="a">
+ <!-- <xsl:attribute name="href">http://www.google.com/search?q=http%3A//qsar.sf.net/dicts/qsar-descriptors/%23<xsl:value-of select="./@id"/>&amp;ie=UTF-8&amp;oe=UTF-8</xsl:attribute> -->
+ <xsl:attribute name="href">http://www.google.com/search?<xsl:value-of select="./@term"/>&amp;ie=UTF-8&amp;oe=UTF-8</xsl:attribute>
+ Google.com
+ </xsl:element>
+</p>
+
+</li>
+</ul>
+<p class="small"><i>
+Contributed by:
+<xsl:for-each select="./*[name(.)='annotation']/*[name(.)='documentation']/*[name(.)='metadata' and @name='dc:contributor']">
+ <xsl:variable name="contributorID" select="./@content"/>
+ <xsl:value-of select="key('entryKey',$contributorID)/."/>
+ <xsl:if test="position()!=last()"><xsl:text>, </xsl:text></xsl:if>
+</xsl:for-each><xsl:text>.</xsl:text>
+Created on: <xsl:value-of select="./*[name(.)='annotation']/*[name(.)='documentation']/*[name(.)='metadata' and @name='dc:date']/@content"/>.
+</i></p>
+ </xsl:template>
+
+ <xsl:template match="*[name(.)='metadataList']">
+ <xsl:apply-templates select="./*[name(.)='metadata']"/>
+ </xsl:template>
+
+ <xsl:template match="*[name(.)='metadata']">
+ <xsl:if test="./@dictRef='reaction-types-metadata:reactionType'">
+ <xsl:variable name="metaEntryID" select="substring-after(./@content, ':')"/>
+ <xsl:text>This reaction is a </xsl:text>
+ <xsl:element name="a">
+ <xsl:attribute name="href">http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionMetadata#<xsl:value-of select="$metaEntryID"/></xsl:attribute>
+ <xsl:for-each select="$metadataDoc">
+ <xsl:value-of select="key('entryKey',$metaEntryID)/@term"/>
+ </xsl:for-each>
+ </xsl:element><br />
+ </xsl:if>
+ <xsl:if test="./@dictRef='reaction-types-metadata:reactionClass'">
+ <xsl:variable name="metaEntryID" select="substring-after(./@content, ':')"/>
+ <xsl:text>This reaction is a </xsl:text>
+ <xsl:element name="a">
+ <xsl:attribute name="href">http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionMetadata#<xsl:value-of select="$metaEntryID"/></xsl:attribute>
+ <xsl:for-each select="$metadataDoc">
+ <xsl:value-of select="key('entryKey',$metaEntryID)/@term"/>
+ </xsl:for-each>
+ </xsl:element><br />
+ </xsl:if>
+ </xsl:template>
+
+ <xsl:template match="*[name(.)='exemplesReaction']">
+ <center><xsl:apply-templates select="./*[name(.)='imagedata']"/></center>
+ </xsl:template>
+
+ <xsl:template match="*[name(.)='imagedata']">
+ <xsl:if test="./@dictRef='reactions-metadata:CML'">
+ <xsl:variable name="ReactionCML" select="./@content"/>
+ <applet code="org.openscience.cdk.applications.jchempaint.applet.JChemPaintViewerOnlyApplet"
+ name="JCPApplet" archive="jar/jchempaint-applet-core.jar"
+ width="500" height="150">
+ <param name="load" value="{$ReactionCML}"/>
+ <param name="compact" value="true"/>
+ </applet>
+ </xsl:if>
+ </xsl:template>
+
+
+ <xsl:template match="*[name(.)='relatedEntry']">
+ <xsl:variable name="relationType" select="substring-after(./@type, ':')"/>
+ <xsl:variable name="entryID" select="./@href"/>
+ <xsl:element name="a">
+ <xsl:attribute name="href">http://qsar.sourceforge.net/dicts/reaction-types-metadata/index.xhtml#<xsl:value-of select="$relationType"/></xsl:attribute>
+ <xsl:for-each select="$metadataDoc">
+ <xsl:value-of select="key('entryKey',$relationType)/@term"/>
+ </xsl:for-each>
+ </xsl:element>
+ <xsl:text>: </xsl:text>
+ <xsl:element name="a">
+ <xsl:attribute name="href">#<xsl:value-of select="./@href"/></xsl:attribute>
+ <xsl:value-of select="key('entryKey',$entryID)/@term"/>
+ </xsl:element>
+ </xsl:template>
+
+ <xsl:template match="*[name(.)='bibtex:cite']">
+ [<xsl:element name="a">
+ <xsl:attribute name="href">#bibtex:<xsl:value-of select="./@ref"/></xsl:attribute>
+ <xsl:value-of select="./@ref"/>
+ </xsl:element>]
+ </xsl:template>
+
+ <xsl:template match="*[name(.)='bibtex:entry']">
+ <xsl:element name="a">
+ <xsl:attribute name="id">bibtex:<xsl:value-of select="./@id"/></xsl:attribute>
+ [<xsl:value-of select="./@id"/>]
+ </xsl:element>
+ <xsl:apply-templates select="./*"/>
+ <br/>
+ </xsl:template>
+
</xsl:stylesheet>
View
348 ...ct/data/react/reaction-types-metadata.xml → ...ct/data/react/reaction-types-metadata.xml
@@ -1,175 +1,175 @@
-<dictionary
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.xml-cml.org/schema/cml2/core cmlAll.xsd
- http://bibtexml.sf.net/ bibtexml.xsd"
-
- xmlns="http://www.xml-cml.org/schema/cml2/core"
- xmlns:bibtex="http://bibtexml.sf.net/"
- xmlns:cvs="https://www.cvshome.org/"
- xmlns:dc="http://dublincore.org/"
-
- xmlns:reaction-types-metadata="http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionMetadata"
- id="reaction-types-metadata" title="REACTION.sf.net Metadata Dictionary">
-
- <annotation>
- <documentation>
- <metadata name="cvs:revision" content="$Revision: 0.1 $"/>
- <metadata name="cvs:last-change-by" content="$Author: mrc $"/>
- <metadata name="cvs:date" content="$Date: 2006/05/08 13:49:48 $"/>
- <metadata name="cvs:id" content="$Id: reaction-types-metadata.xml,v 0.1 2006/05/08 13:49:48 mrc Exp $"/>
- </documentation>
- <appinfo>
- <contributor id="mrc">Miguel Rojas</contributor>
- </appinfo>
- <documentation title="bibliography">
- <bibtex:file>
- <bibtex:entry id="REACTIONDICT">
- <bibtex:misc>
- <bibtex:author>The REACTION.sf.net Project</bibtex:author>
- <bibtex:title>REACTION types Dictionary</bibtex:title>
- <bibtex:url>http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict</bibtex:url>
- </bibtex:misc>
- </bibtex:entry>
- </bibtex:file>
- </documentation>
- </annotation>
-
- <description>
- This dictionary describes reactions used in the reaction-types <bibtex:cite ref="REACTIONDICT"/>
- dictionary.
- </description>
-
- <entry id="electronImpact" term="Electron Impact">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- This reaction type is a representation of the processes which occure in the mass spectrometer.
- </definition>
- <relatedEntry type="reaction-types-metadata:instanceOf" href="reactionType"/>
- </entry>
-
- <entry id="displacement" term="Displacement">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-06-08"/>
- </documentation>
- </annotation>
- <definition>
- This reaction type is a representation of displacement of the electron which are in a
- orbital pi.
- </definition>
- <relatedEntry type="reaction-types-metadata:instanceOf" href="reactionType"/>
- </entry>
-
- <entry id="rearrangementCharge" term="Rearrangement of Charge">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- This reaction type represents a rearrangment of charge .
- </definition>
- <relatedEntry type="reaction-types-metadata:instanceOf" href="reactionType"/>
- </entry>
-
-
- <entry id="reactionClass" term="Reaction Class">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- Class of reaction.
- </definition>
- <relatedEntry type="reaction-type-metadata:instanceOf" href="reactionClassifier"/>
- </entry>
-
- <entry id="reactionClassification" term="Reaction Classification">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- Classification of the reaction.
- </definition>
- </entry>
-
- <entry id="reactionClassifier" term="Reaction Classifier">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- Concept that allows reaction to be classified into groups.
- </definition>
- </entry>
-
- <entry id="reactionType" term="Reaction Type">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- Type of reaction.
- </definition>
- <relatedEntry type="reaction-type-metadata:instanceOf" href="reactionClassifier"/>
- </entry>
-
- <entry id="instanceOf" term="Is a">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- Indicates that the entry is a instance of the linked entry.
- </definition>
- </entry>
-
- <entry id="isAModificationOf" term="Is a Modification Of">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- Indicates a relation between two reactions of which the first is a
- modification of the second.
- </definition>
- </entry>
-
- <entry id="isModificatedAs" term="Is Modificated Into">
- <annotation>
- <documentation>
- <metadata name="dc:contributor" content="mrc"/>
- <metadata name="dc:date" content="2006-05-08"/>
- </documentation>
- </annotation>
- <definition>
- Indicates a relation between two reactions of which the second is a
- modification of the first.
- </definition>
- </entry>
-
-
-
-
-
+<dictionary
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.xml-cml.org/schema/cml2/core cmlAll.xsd
+ http://bibtexml.sf.net/ bibtexml.xsd"
+
+ xmlns="http://www.xml-cml.org/schema/cml2/core"
+ xmlns:bibtex="http://bibtexml.sf.net/"
+ xmlns:cvs="https://www.cvshome.org/"
+ xmlns:dc="http://dublincore.org/"
+
+ xmlns:reaction-types-metadata="http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionMetadata"
+ id="reaction-types-metadata" title="REACTION.sf.net Metadata Dictionary">
+
+ <annotation>
+ <documentation>
+ <metadata name="cvs:revision" content="$Revision: 0.1 $"/>
+ <metadata name="cvs:last-change-by" content="$Author: mrc $"/>
+ <metadata name="cvs:date" content="$Date: 2006/05/08 13:49:48 $"/>
+ <metadata name="cvs:id" content="$Id: reaction-types-metadata.xml,v 0.1 2006/05/08 13:49:48 mrc Exp $"/>
+ </documentation>
+ <appinfo>
+ <contributor id="mrc">Miguel Rojas</contributor>
+ </appinfo>
+ <documentation title="bibliography">
+ <bibtex:file>
+ <bibtex:entry id="REACTIONDICT">
+ <bibtex:misc>
+ <bibtex:author>The REACTION.sf.net Project</bibtex:author>
+ <bibtex:title>REACTION types Dictionary</bibtex:title>
+ <bibtex:url>http://almost.cubic.uni-koeln.de/jrg/Members/mrc/reactionDict/reactionDict</bibtex:url>
+ </bibtex:misc>
+ </bibtex:entry>
+ </bibtex:file>
+ </documentation>
+ </annotation>
+
+ <description>
+ This dictionary describes reactions used in the reaction-types <bibtex:cite ref="REACTIONDICT"/>
+ dictionary.
+ </description>
+
+ <entry id="electronImpact" term="Electron Impact">
+ <annotation>
+ <documentation>
+ <metadata name="dc:contributor" content="mrc"/>
+ <metadata name="dc:date" content="2006-05-08"/>
+ </documentation>
+ </annotation>
+ <definition>
+ This reaction type is a representation of the processes which occure in the mass spectrometer.
+ </definition>
+ <relatedEntry type="reaction-types-metadata:instanceOf" href="reactionType"/>
+ </entry>
+
+ <entry id="displacement" term="Displacement">
+ <annotation>
+ <documentation>