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[Cdk-commits] CVS: cdk/doc/source agenda.xml,1.3,1.4 bibliography.xml,1.2,1.3 cdkdocs.xml,1.8,1.9 changelog.xml,1.3,1.4 libraries.xml,1.1,1.2 projectref.xml,1.6,1.7
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From: Egon W. <eg...@us...> - 2001-12-02 08:24:48
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Update of /cvsroot/cdk/cdk/doc/source In directory usw-pr-cvs1:/tmp/cvs-serv32523 Modified Files: agenda.xml bibliography.xml cdkdocs.xml changelog.xml libraries.xml projectref.xml Log Message: - Updated changelog - Added more used libraries to list - Updated Agenda - Added a new reference Index: agenda.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/source/agenda.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** agenda.xml 2001/09/07 11:29:00 1.3 --- agenda.xml 2001/12/02 08:24:46 1.4 *************** *** 7,10 **** <para>A substructure search</para> </listitem> </itemizedlist> ! </para> --- 7,16 ---- <para>A substructure search</para> </listitem> + <listitem> + <para>A energy minimizer / moleculare dynamics module</para> + </listitem> + <listitem> + <para>An interface API to other programs and implementation</para> + </listitem> </itemizedlist> ! </para> Index: bibliography.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/source/bibliography.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** bibliography.xml 2001/09/07 11:29:00 1.2 --- bibliography.xml 2001/12/02 08:24:46 1.3 *************** *** 1,3 **** ! <bibliography> <biblioentry id="BLE91"> <abbrev>BLE91</abbrev> --- 1,3 ---- ! <bibliography> <biblioentry id="BLE91"> <abbrev>BLE91</abbrev> *************** *** 196,239 **** <biblioentry id="PMR99"> <abbrev>PMR99</abbrev> ! <biblioset relation="article"> ! <authorgroup> ! <author> ! <firstname>P.</firstname> ! <surname>Murray-Rust</surname> ! </author> ! <author> ! <firstname>H. S.</firstname> ! <surname>Rzepa</surname> ! </author> ! </authorgroup> <title>Chemical Markup, XML, and the Worldwide Web. 1. Basic ! Principles</title> ! <pagenums>928-942</pagenums> ! <pubdate>1999</pubdate> ! </biblioset> ! <biblioset relation="journal"> ! <title>Journal of Chemical Information and Computer Sciences</title> ! </biblioset> ! <bibliomisc> <phrase>For constantly updated documentation of Chemical Markup ! Language (CML) please see <ulink url="http://www.xml-cml.org/">http://www.xml-cml.org/</ulink>.</phrase></bibliomisc> - - </biblioentry> ! <biblioentry id="XML"> ! <abbrev>XML</abbrev> ! <bibliomisc> <phrase>XML is a recommendation written by the World Wide Web ! Consortium (W3C). Info on this standard can be found at <ulink url="http://www.w3.org/TR/1998/REC-xml-19980210">http://www.w3.org/TR/1998/REC-xml-19980210</ulink>. ! </phrase> </bibliomisc> ! </biblioentry> ! <biblioentry id="WEI88"> ! <abbrev>WEI88</abbrev> ! <biblioset relation="article"> <authorgroup> <author> --- 196,239 ---- <biblioentry id="PMR99"> <abbrev>PMR99</abbrev> ! <biblioset relation="article"> ! <authorgroup> ! <author> ! <firstname>P.</firstname> ! <surname>Murray-Rust</surname> ! </author> ! <author> ! <firstname>H. S.</firstname> ! <surname>Rzepa</surname> ! </author> ! </authorgroup> <title>Chemical Markup, XML, and the Worldwide Web. 1. Basic ! Principles</title> ! <pagenums>928-942</pagenums> ! <pubdate>1999</pubdate> ! </biblioset> ! <biblioset relation="journal"> ! <title>Journal of Chemical Information and Computer Sciences</title> ! </biblioset> ! <bibliomisc> <phrase>For constantly updated documentation of Chemical Markup ! Language (CML) please see <ulink url="http://www.xml-cml.org/">http://www.xml-cml.org/</ulink>.</phrase></bibliomisc> ! </biblioentry> ! ! <biblioentry id="XML"> ! <abbrev>XML</abbrev> ! <bibliomisc> <phrase>XML is a recommendation written by the World Wide Web ! Consortium (W3C). Info on this standard can be found at <ulink url="http://www.w3.org/TR/1998/REC-xml-19980210">http://www.w3.org/TR/1998/REC-xml-19980210</ulink>. ! </phrase> </bibliomisc> ! </biblioentry> ! <biblioentry id="WEI88"> ! <abbrev>WEI88</abbrev> ! <biblioset relation="article"> <authorgroup> <author> *************** *** 256,262 **** ! <biblioentry id="WEI89"> ! <abbrev>WEI89</abbrev> ! <biblioset relation="article"> <authorgroup> <author> --- 256,262 ---- ! <biblioentry id="WEI89"> ! <abbrev>WEI89</abbrev> ! <biblioset relation="article"> <authorgroup> <author> *************** *** 269,281 **** <volumenum></volumenum> <issuenum></issuenum> ! <pagenums>97-101</pagenums><pubdate>1989</pubdate> </biblioset> <biblioset relation="journal"> ! <title>Journal of Chemical Information and Computer Sciences</title> </biblioset> ! <bibliomisc> </bibliomisc> ! </biblioentry> --- 269,302 ---- <volumenum></volumenum> <issuenum></issuenum> ! <pagenums>97-101</pagenums><pubdate>1989</pubdate> </biblioset> <biblioset relation="journal"> ! <title>Journal of Chemical Information and Computer Sciences</title> </biblioset> ! <bibliomisc> </bibliomisc> ! </biblioentry> + <biblioentry id="WILLIGHAGEN2001"> + <abbrev>WILLIGHAGEN2001</abbrev> + <biblioset relation="article"> + <authorgroup> + <author> + <othername role="initials">E.L.</othername> + <surname>Willighagen</surname> + </author> + </authorgroup> + <title>Processing CML Conventions in Java</title> + <volumenum>4</volumenum> + </biblioset> + <biblioset relation="journal"> + <title>Internet Journal of Chemistry</title> + </biblioset> + <bibliomisc> + <phrase>The abstract can be found at <ulink + url="http://www.ijc.com/abstracts/abstract4n4.html">http://www.ijc.com/abstracts/abstract4n4.html</ulink>. + </phrase> + </bibliomisc> + </biblioentry> Index: cdkdocs.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/source/cdkdocs.xml,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** cdkdocs.xml 2001/05/14 23:02:07 1.8 --- cdkdocs.xml 2001/12/02 08:24:46 1.9 *************** *** 36,41 **** <author> <authorblurb> ! <para> The author is a student of chemistry at the ! <ulink url="http://www.kun.nl/">University of Nijmegen</ulink> in the Netherlands. </para> </authorblurb> --- 36,42 ---- <author> <authorblurb> ! <para> The author is a PhD student at the <ulink url="http://www.kun.nl/">University of ! Nijmegen</ulink> in the Netherlands at the subject of ! <ulink url="http://www-cac.sci.kun.nl/people/egonw/">molecular representation</ulink>. </para> </authorblurb> Index: changelog.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/source/changelog.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** changelog.xml 2001/09/03 07:04:18 1.3 --- changelog.xml 2001/12/02 08:24:46 1.4 *************** *** 1,7 **** ! <para> Revision History of the CDK: <itemizedlist> ! <listitem><para>CVS Version <itemizedlist> <listitem><para>Added TestCases for PDBReader, Monomer, Polymer and ChemObject.</para></listitem> <listitem><para>Added get/setProperty and get/setRemark to ChemObject.</para></listitem> --- 1,33 ---- ! <para> Revision History of the CDK: <itemizedlist> ! <listitem><para>CVS version <itemizedlist> + <listitem><para>Nothing yet</para></listitem> + </itemizedlist> + </para></listitem> + </itemizedlist> + <itemizedlist> + <listitem><para>Preview 20011201 + <itemizedlist> + <listitem><para>Splitted required libraries from CDK source</para></listitem> + <listitem><para>Fixed (again) CML reading</para></listitem> + </itemizedlist> + </para></listitem> + </itemizedlist> + <itemizedlist> + <listitem><para>Preview 20011015 and 20011013 + <itemizedlist> + <listitem><para>Improvements to SingleRandomStructureGenerator</para></listitem> + <listitem><para>Added Log4J as (optional) logging tool</para></listitem> + <listitem><para>Fixed a problem in PathTools.breadthFirstTargetSearch()</para></listitem> + <listitem><para>Added to convenience methods to XMLTools for serializing + and de-serializing</para></listitem> + </itemizedlist> + </para></listitem> + </itemizedlist> + <itemizedlist> + <listitem><para>Preview 20010909 + <itemizedlist> <listitem><para>Added TestCases for PDBReader, Monomer, Polymer and ChemObject.</para></listitem> <listitem><para>Added get/setProperty and get/setRemark to ChemObject.</para></listitem> *************** *** 9,12 **** --- 35,40 ---- <listitem><para>Added classes for complex numbers, vectors and matrices</para></listitem> <listitem><para>Change name from Job to ClosedShellJob</para></listitem> + <listitem><para>Added Factories for AtomType, Element and Isotope as well as + their testcases.</para></listitem> </itemizedlist> </para></listitem> Index: libraries.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/source/libraries.xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** libraries.xml 2001/02/06 22:42:32 1.1 --- libraries.xml 2001/12/02 08:24:46 1.2 *************** *** 1,9 **** ! <para>Libraries that the CDK uses: ! <itemizedlist> ! <listitem> <para><ulink url="http://java.sun.com/products/java-media/3D/index.html">javax.vecmath</ulink></para> <para>Version: ??</para> <para>License: ??</para> <para>Sun's java library for vector algebra from the Java3D package.</para> </listitem> </itemizedlist> --- 1,50 ---- ! <para>Below is a list of libraries that are used by CDK. They can be downloaded manually, and some ! might even be installed on your machine already. They can also be downloaded in one bundle as ! <ulink url="https://sourceforge.net/project/showfiles.php?group_id=20024">cdk-libs</ulink>. ! </para> ! <para> ! <itemizedlist> ! <listitem> <para><ulink url="http://java.sun.com/products/java-media/3D/index.html">javax.vecmath</ulink></para> <para>Version: ??</para> <para>License: ??</para> <para>Sun's java library for vector algebra from the Java3D package.</para> + </listitem> + <listitem> + <para><ulink url="http://xml.apache.org/xerces-j/">Xerces</ulink></para> + <para>Version: 1.3.0</para> + <para>License: Apache Software License, Version 1.1</para> + <para>Apache's XML parser.</para> + </listitem> + <listitem> + <para><ulink url="http://xml.apache.org/xalan-j/">Xalan</ulink></para> + <para>Version: 2.0.1</para> + <para>License: Apache Software License, Version 1.1</para> + <para>Apache's XSLT processor.</para> + </listitem> + <listitem> + <para><ulink url="http://jakarta.apache.org/log4j/docs/">Log4J</ulink></para> + <para>Version: ??</para> + <para>License: ??</para> + <para>Apache's logging tool.</para> + </listitem> + <listitem> + <para>JUnit</para> + <para>Version: ??</para> + <para>License: ??</para> + </listitem> + </itemizedlist> + </para> + <para>Additionally, a number of database drivers are used: + <itemizedlist> + <listitem> + <para>MySQL</para> + <para>Version: ??</para> + <para>License: ??</para> + </listitem> + <listitem> + <para>PostgreSQL</para> + <para>Version: ??</para> + <para>License: ??</para> </listitem> </itemizedlist> Index: projectref.xml =================================================================== RCS file: /cvsroot/cdk/cdk/doc/source/projectref.xml,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -r1.6 -r1.7 *** projectref.xml 2001/09/16 11:42:39 1.6 --- projectref.xml 2001/12/02 08:24:46 1.7 *************** *** 145,150 **** <para> Ensembles of Molecules, like those involved in a chemical reaction, can be organized in a ! <ulink url="api/org/openscience/cdk/SetOfMolecules.html">SetOfMolecules</ulink> ! class. </para> <para> Due to the dedication of the Model/View/Controller paradigm, the programmer will find a --- 145,150 ---- <para> Ensembles of Molecules, like those involved in a chemical reaction, can be organized in a ! <ulink url="api/org/openscience/cdk/SetOfMolecules.html">SetOfMolecules</ulink> ! class. </para> <para> Due to the dedication of the Model/View/Controller paradigm, the programmer will find a *************** *** 162,166 **** <itemizedlist> <listitem><para>&MDLReader;</para></listitem> ! <listitem><para>&CMLReader;</para></listitem> <listitem><para>&XYZReader;</para></listitem> </itemizedlist> --- 162,166 ---- <itemizedlist> <listitem><para>&MDLReader;</para></listitem> ! <listitem><para>&CMLReader; <xref linkend="WILLIGHAGEN2001"/></para></listitem> <listitem><para>&XYZReader;</para></listitem> </itemizedlist> |