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1 CDK The Chemical Development Kit
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2
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3 Copyright 1997-2007 The CDK Development Team
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4 License: LGPL, see doc/lgpl.license
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5
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6 1. Introduction
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7
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8 You are currently reading the README file for the Chemistry Development Project (CDK).
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9 This project is hosted under http://cdk.sourceforge.net
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10 Please refer to these pages for updated information and the latest version of the CDK.
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11
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12 The CDK is an open-source library of algorithms for structural chemo- and bioinformatics, implemented in
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13 the programming language Java(tm). The library is published under terms of the the
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14 GNU Lesser General Public License. This has implications on what you can do with sources and
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15 binaries of the CDK library. For details, please refer to the file LICENSE, which should have been
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16 provided with this distribution.
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17
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18 PLEASE NOTE: This is a library of useful data structures and algorithms to manipulated them
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19 from the area of structural chemo- and bioinformatics. As such, it is intended for the use by
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20 programmers, who wish to save some effort by reusing code. It is not intended for the enduser.
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21 If you consider yourself to be more like user, you might not find what you wanted.
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22 Please refer to other projects like the JChemPaint project (http://jchempaint.sourceforge.net)
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23 or the Jmol project (http://jmol.sourceforge.net) for programs that actually take advantage of the
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24 CDK library.
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25
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26 2. Compiling
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27
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28 Compiling and jar-ing the software is done with Jakarta's
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29 Ant (http://jakarta.apache.org/ant/) and requires Java 1.5.0 or better:
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30
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31 cdk/$ ls build.xml
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32 build.xml
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33 cdk/$ ant
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34
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35 "ant -p" gives a list of possible compilation targets. The default target is 'dist-all', which
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36 creates a number of .jar files in the 'dist' directory corresponding to subsets of the CDK
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37 functionality. For convenience, one large .jar file containing everything can be created using the
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38 target 'dist-large' (using the command "ant dist-large"). This is also created in dist/jar and is
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39 typically named something like 'cdk-cvs-20060303.jar'.
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40
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41 2.1 Creating the JavaDoc documentation for the API
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42
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43 The JavaDoc documentation for the API describes all of the CDK classes in detail. It functions as
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44 the user manual for the CDK, although you should also look at the list of examples and tutorials
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45 below. This documentation is created by 'ant' from the Java source code for the CDK as follows:
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46
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47 cdk/$ ls javadoc.xml
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48 javadoc.xml
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49 cdk/$ ant -buildfile javadoc.xml
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50
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51 The documenation is created as a series of .html pages in doc/api. If you use firefox, you can read
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52 the documentation using the following command:
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53
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54 cdk/$ firefox doc/api/index.html
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55
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56 3. Running tests
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57
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58 After you compiled the code, you can do "ant test-all" to run the test suite of non-interactive, automated
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59 tests. You might need to copy an appropriate junit.jar into your $ANT_HOME/lib
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60 directory or somewhere else in your classpath.
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61 Upon "ant dist-all test-dist-all test-all", you should see something like:
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62
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63 test:
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64 Running org.openscience.cdk.test.CDKTests
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65 Tests run: 1065, Failures: 7, Errors: 1, Time elapsed: 27,55 sec
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66
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67 As you can see, the vast majority of tests ran successfully, but that there
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68 are failures and errors. The $CDK_HOME/reports/results.txt file contains
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69 information about the outcome of the tests. Some tests might fail intentionally
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70 to mark know issues in CDK.
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71
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72 There are also run interactive tests, like the Controller2DTest. In order to try them, you can edit the "run"
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73 target in the build.xml file to look like this:
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74
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75 <target name="run" depends="dist">
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76 <java classname="org.openscience.cdk.test.ControllerTest" fork="yes">
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77 <arg value=""/>
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78 <classpath>
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79 <pathelement location="${dist}/jar/cdk.jar"/>
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80 <pathelement path="${java.class.path}"/>
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81 <pathelement location="."/>
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82 <fileset dir="jar">
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83 <include name="*.jar"/>
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84 </fileset>
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85 </classpath>
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86 </java>
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87 </target>
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88
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89 Then, a "ant run" should give you a window where you can add bonds to a given structure.
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90 Currently, there are more than 2500 test, of which a large part tests the data, datadebug and
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91 nonotify classes.
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92
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93 4. Using CDK
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94
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95 CDK is a class library intended to be used by other programs. It will not run
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96 as a stand-alone program, although it contains some GUI- and command
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97 line applications. In order to use the CDK in your program, you need to build
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98 the distribution jars by running "ant dist-all". They will end up in
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99 $CDK_HOME/dist/jar. Copy all cdk-*.jars as well as all jars from $CDK_HOME/jar
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100 to the lib directory of the project for which you intend to have CDK support and
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101 use them as you would use any other third party jar.
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102
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103 Alternatively, run "ant dist-large" to create a jar cdk-svn-YYYYMMDD.jar in
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104 $CDK_HOME/dist/jar. This large jar contains all the CDK code and all third
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105 party libraries that code depends on.
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106
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107 5. Examples and tutorials
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108
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109 To get started using the CDK, you may be interested in the following websites which contain
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110 examples and tutorials:
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111 * http://www.chemistry-development-kit.org
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112 * http://blue.chem.psu.edu/~rajarshi/code/java
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113 * http://www.redbrick.dcu.ie/~noel/CDKJython.html
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114
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115 Further examples can also be found in issues of the CDK News:
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116 * http://cdknews.org/
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117
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