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‎stylesheets/bio/pdb/pdb2svg.xsl‎

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<?xml version="1.0" encoding="UTF-8"?>
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<xsl:stylesheet
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version="1.0"
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xmlns:PDBx="http://pdbml.pdb.org/schema/pdbx-v50.xsd"
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xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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xmlns:svg="http://www.w3.org/2000/svg"
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xmlns:xlink="http://www.w3.org/1999/xlink"
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xmlns:h="http://www.w3.org/1999/xhtml"
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>
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<!--
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Motivation:
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transforms a pubchem xml result to SVG
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Author
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Pierre Lindenbaum PhD plindenbaum@yahoo.fr
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http://plindenbaum.blogspot.com
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Parameters:
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scale :=scale factor
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show-bounds := (true/false)
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xradius := scale factor for atoms
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-->
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<!-- ========================================================================= -->
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<xsl:output method='xml' indent='yes' omit-xml-declaration="no"/>
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<!-- ========================================================================= -->
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<!-- the margin of the SVG -->
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<xsl:param name="margin">100</xsl:param>
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<!-- the scale factor -->
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<xsl:param name="scale">30</xsl:param>
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<!-- the scale factor for atom radius-->
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<xsl:param name="xradius">1</xsl:param>
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<!-- array of atoms -->
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<xsl:variable name="a_array" select="/PDBx:datablock/PDBx:atom_siteCategory/PDBx:atom_site"/>
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<!-- number of atoms-->
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<xsl:variable name="count"><xsl:value-of select="count($a_array)"/></xsl:variable>
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<xsl:variable name="x_array" select="$a_array/PDBx:Cartn_x"/>
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<xsl:variable name="y_array" select="$a_array/PDBx:Cartn_y"/>
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<xsl:variable name="z_array" select="$a_array/PDBx:Cartn_z"/>
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<xsl:variable name="min-x">
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<xsl:for-each select="$a_array/PDBx:Cartn_x">
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<xsl:sort select="." data-type="number" order="ascending" />
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<xsl:if test="position() = 1">
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<xsl:value-of select="." />
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</xsl:if>
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</xsl:for-each>
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</xsl:variable>
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<xsl:variable name="max-x">
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<xsl:for-each select="$a_array/PDBx:Cartn_x">
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<xsl:sort select="." data-type="number" order="descending" />
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<xsl:if test="position() = 1">
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<xsl:value-of select="." />
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</xsl:if>
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</xsl:for-each>
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</xsl:variable>
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<xsl:variable name="min-y">
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<xsl:for-each select="$a_array/PDBx:Cartn_y">
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<xsl:sort select="." data-type="number" order="ascending" />
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<xsl:if test="position() = 1">
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<xsl:value-of select="." />
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</xsl:if>
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</xsl:for-each>
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</xsl:variable>
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<xsl:variable name="max-y">
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<xsl:for-each select="$a_array/PDBx:Cartn_y">
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<xsl:sort select="." data-type="number" order="descending" />
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<xsl:if test="position() = 1">
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<xsl:value-of select="." />
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</xsl:if>
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</xsl:for-each>
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</xsl:variable>
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<xsl:variable name="min-z">
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<xsl:for-each select="$a_array/PDBx:Cartn_z">
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<xsl:sort select="." data-type="number" order="ascending" />
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<xsl:if test="position() = 1">
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<xsl:value-of select="." />
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</xsl:if>
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</xsl:for-each>
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</xsl:variable>
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<xsl:variable name="max-z">
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<xsl:for-each select="$a_array/PDBx:Cartn_z">
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<xsl:sort select="." data-type="number" order="descending" />
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<xsl:if test="position() = 1">
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<xsl:value-of select="." />
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</xsl:if>
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</xsl:for-each>
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</xsl:variable>
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<xsl:variable name="length-x" select="$max-x - $min-x"/>
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<xsl:variable name="length-y" select="$max-y - $min-y"/>
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<xsl:variable name="length-z" select="$max-z - $min-z"/>
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<xsl:variable name="frame-width" select="($margin * 2 )+ ($length-x * $scale)"/>
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<xsl:variable name="frame-height" select="($margin * 2 )+ ($length-y * $scale)"/>
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<xsl:template match="/">
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<xsl:apply-templates select="PDBx:datablock"/>
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</xsl:template>
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<xsl:template match="PDBx:datablock">
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<xsl:element name="svg:svg">
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<xsl:attribute name="version">1.0</xsl:attribute>
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<xsl:attribute name="width"><xsl:value-of select="$frame-width"/></xsl:attribute>
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<xsl:attribute name="height"><xsl:value-of select="$frame-height"/></xsl:attribute>
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<svg:title><xsl:value-of select="@datablockName"/></svg:title>
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<xsl:comment>
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Author: Pierre Lindenbaum PhD plindenbaum@yahoo.fr
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http://plindenbaum.blogspot.com
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</xsl:comment>
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<!-- DEFINITIONS -->
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<xsl:element name="svg:defs">
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<xsl:call-template name="gradient">
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<xsl:with-param name="gid">o</xsl:with-param>
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<xsl:with-param name="start">white</xsl:with-param>
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<xsl:with-param name="end">blue</xsl:with-param>
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<xsl:with-param name="r">18</xsl:with-param>
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</xsl:call-template>
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<xsl:call-template name="gradient">
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<xsl:with-param name="gid">c</xsl:with-param>
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<xsl:with-param name="start">white</xsl:with-param>
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<xsl:with-param name="end">black</xsl:with-param>
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<xsl:with-param name="r">16</xsl:with-param>
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</xsl:call-template>
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<xsl:call-template name="gradient">
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<xsl:with-param name="gid">h</xsl:with-param>
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<xsl:with-param name="start">lightgray</xsl:with-param>
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<xsl:with-param name="end">gray</xsl:with-param>
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<xsl:with-param name="r">10</xsl:with-param>
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</xsl:call-template>
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<xsl:call-template name="gradient">
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<xsl:with-param name="gid">UN</xsl:with-param>
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<xsl:with-param name="start">green</xsl:with-param>
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<xsl:with-param name="end">red</xsl:with-param>
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<xsl:with-param name="r">10</xsl:with-param>
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</xsl:call-template>
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</xsl:element><!-- defs -->
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<xsl:element name="svg:rect">
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<xsl:attribute name="style">stroke:lightgray;fill:white;</xsl:attribute>
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<xsl:attribute name="x">0</xsl:attribute>
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<xsl:attribute name="y">0</xsl:attribute>
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<xsl:attribute name="width"><xsl:value-of select="$frame-width - 1"/></xsl:attribute>
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<xsl:attribute name="height"><xsl:value-of select="$frame-height - 1"/></xsl:attribute>
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</xsl:element>
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<xsl:element name="svg:g">
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<xsl:comment>BEGIN ATOMS</xsl:comment>
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<xsl:element name="svg:g">
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<xsl:apply-templates select="PDBx:atom_siteCategory/PDBx:atom_site"/>
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</xsl:element>
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<xsl:comment>END ATOMS</xsl:comment>
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</xsl:element>
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</xsl:element><!-- svg -->
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</xsl:template>
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<xsl:template match="PDBx:atom_site">
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<xsl:variable name="s"><xsl:value-of select="PDBx:auth_atom_id"/></xsl:variable>
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<xsl:element name="svg:use">
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<xsl:attribute name="xlink:href">#atom<xsl:choose>
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<xsl:when test="$s=&apos;o&apos; or $s=&apos;c&apos; or $s=&apos;h&apos;"><xsl:value-of select="$s"/></xsl:when>
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<xsl:otherwise>UN</xsl:otherwise>
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</xsl:choose></xsl:attribute>
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<xsl:attribute name="x"><xsl:call-template name="coord-x"><xsl:with-param name="atom" select="."/></xsl:call-template></xsl:attribute>
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<xsl:attribute name="y"><xsl:call-template name="coord-y"><xsl:with-param name="atom" select="."/></xsl:call-template></xsl:attribute>
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<xsl:attribute name="title"><xsl:value-of select="$s"/></xsl:attribute>
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</xsl:element>
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</xsl:template>
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<xsl:template name="gradient">
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<xsl:param name="gid">did</xsl:param>
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<xsl:param name="start">rgb(200,200,200)</xsl:param>
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<xsl:param name="end">rgb(0,0,255)</xsl:param>
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<xsl:param name="r">0</xsl:param>
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<xsl:element name="svg:radialGradient">
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<xsl:attribute name="id">radial<xsl:value-of select="$gid"/></xsl:attribute>
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<xsl:attribute name="cx">50%</xsl:attribute>
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<xsl:attribute name="cy">50%</xsl:attribute>
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<xsl:attribute name="r">50%</xsl:attribute>
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<xsl:attribute name="fx">30%</xsl:attribute>
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<xsl:attribute name="fy">30%</xsl:attribute>
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<xsl:element name="svg:stop">
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<xsl:attribute name="offset">0%</xsl:attribute>
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<xsl:attribute name="style">stop-color:<xsl:value-of select="$start"/>;stop-opacity:0.8;</xsl:attribute>
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</xsl:element>
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<xsl:element name="svg:stop">
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<xsl:attribute name="offset">100%</xsl:attribute>
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<xsl:attribute name="style">stop-color:<xsl:value-of select="$end"/>;stop-opacity:1;</xsl:attribute>
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</xsl:element>
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</xsl:element>
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<xsl:element name="svg:circle">
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<xsl:attribute name="id">atom<xsl:value-of select="$gid"/></xsl:attribute>
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<xsl:attribute name="r"><xsl:value-of select="number($r) * $xradius"/></xsl:attribute>
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<xsl:attribute name="style">stroke:black;fill:url(#radial<xsl:value-of select="$gid"/>);</xsl:attribute>
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</xsl:element>
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</xsl:template>
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<xsl:template name="coord-x">
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<xsl:param name="atom"/>
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<xsl:variable name="x" select="$atom/PDBx:Cartn_x"/>
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<xsl:value-of select="$margin + ($x - $min-x) * $scale"/>
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</xsl:template>
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<xsl:template name="coord-y">
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<xsl:param name="atom"/>
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<xsl:variable name="y" select="$atom/PDBx:Cartn_y"/>
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<xsl:value-of select="$margin + ($y - $min-y) * $scale"/>
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</xsl:template>
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</xsl:stylesheet>

‎stylesheets/comics/layout.flip.horizontal.xsl‎

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<?xml version='1.0' encoding="UTF-8" ?>
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<xsl:stylesheet
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xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
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xmlns:g="http://www.gexf.net/1.1draft"
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xmlns:viz="http://www.gexf.net/1.1draft/viz"
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xmlns:svg="http://www.w3.org/2000/svg"
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xmlns:h='http://www.w3.org/1999/xhtml'
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version='1.0'
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>
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<xsl:output method="xml" indent="yes"/>
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<xsl:variable name="width" select="number(100)"/>
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<xsl:variable name="height" select="number(150)"/>
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<xsl:template match="/">
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<xsl:apply-templates select="layouts"/>
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</xsl:template>
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<xsl:template match="layouts">
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<layouts>
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<xsl:apply-templates select="layout"/>
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</layouts>
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</xsl:template>
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<xsl:template match="layout">
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<xsl:copy-of select="."/>
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<layout>
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<xsl:attribute name="id">
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<xsl:value-of select="concat(@id,'.h')"/>
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</xsl:attribute>
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<xsl:apply-templates select="panel"/>
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</layout>
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</xsl:template>
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<xsl:template match="panel">
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<xsl:variable name="w">
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<xsl:for-each select="../panel">
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<xsl:sort select="number(@width) + number(@x)" data-type="number" order="descending"/>
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<xsl:if test="position() = 1"><xsl:value-of select="(number(@width) + number(@x))"/></xsl:if>
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</xsl:for-each>
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</xsl:variable>
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<panel>
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<xsl:attribute name="x">
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<xsl:value-of select="($w - number(@x) - number(@width))"/>
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</xsl:attribute>
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<xsl:copy-of select="@y" />
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<xsl:copy-of select="@width" />
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<xsl:copy-of select="@height" />
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</panel>
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</xsl:template>
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</xsl:stylesheet>
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‎stylesheets/comics/layout.flip.vertical.xsl‎

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<?xml version='1.0' encoding="UTF-8" ?>
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<xsl:stylesheet
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xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
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xmlns:g="http://www.gexf.net/1.1draft"
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xmlns:viz="http://www.gexf.net/1.1draft/viz"
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xmlns:svg="http://www.w3.org/2000/svg"
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xmlns:h='http://www.w3.org/1999/xhtml'
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version='1.0'
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>
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<xsl:output method="xml" indent="yes"/>
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<xsl:variable name="width" select="number(100)"/>
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<xsl:variable name="height" select="number(150)"/>
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<xsl:template match="/">
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<xsl:apply-templates select="layouts"/>
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</xsl:template>
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<xsl:template match="layouts">
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<layouts>
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<xsl:apply-templates select="layout"/>
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</layouts>
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</xsl:template>
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<xsl:template match="layout">
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<xsl:copy-of select="."/>
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<layout>
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<xsl:attribute name="id">
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<xsl:value-of select="concat(@id,'.v')"/>
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</xsl:attribute>
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<xsl:apply-templates select="panel"/>
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</layout>
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</xsl:template>
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<xsl:template match="panel">
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<xsl:variable name="h">
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<xsl:for-each select="../panel">
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<xsl:sort select="number(@height) + number(@y)" data-type="number" order="descending"/>
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<xsl:if test="position() = 1"><xsl:value-of select="(number(@height) + number(@y))"/></xsl:if>
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</xsl:for-each>
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</xsl:variable>
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<panel>
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<xsl:copy-of select="@x" />
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<xsl:attribute name="y">
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<xsl:value-of select="($h - number(@y) - number(@height))"/>
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</xsl:attribute>
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<xsl:copy-of select="@width" />
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<xsl:copy-of select="@height" />
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</panel>
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</xsl:template>
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</xsl:stylesheet>
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