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1 CDK - The Chemical Development Kit
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2
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3 Copyright 1997-2012 The CDK Development Team
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4 License: LGPL v2, see doc/lgpl.license
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5
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6 1. Introduction
7
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.
11
12 The CDK is an open-source library of algorithms for structural chemo- and bioinformatics, implemented in
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 v2. 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
16 provided with this distribution.
17
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18 PLEASE NOTE: This is a library of useful data structures and algorithms to manipulate them
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19 from the area of structural chemo- and bioinformatics. As such, it is intended for the use by
20 programmers, who wish to save some effort by reusing code. It is not intended for the enduser.
21 If you consider yourself to be more like user, you might not find what you wanted.
22 Please refer to other projects like the JChemPaint project (http://jchempaint.sourceforge.net)
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23 or the Jmol project (http://www.jmol.org/) for programs that actually take advantage of the
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24 CDK library.
25
26 2. Compiling
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27
28 Compiling and jar-ing the software is done with Jakarta's
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29 Ant (http://jakarta.apache.org/ant/) 1.7.1 or better and Java 1.6.0 or better:
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30
31 cdk/$ ls build.xml
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
36 creates a number of .jar files in the 'dist' directory corresponding to subsets of the CDK
37 functionality. For convenience, one large .jar file containing everything can be created using the
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-1.2.7.jar'.
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40
41 2.1 Creating the JavaDoc documentation for the API
42
43 The JavaDoc documentation for the API describes all of the CDK classes in detail. It functions as
44 the user manual for the CDK, although you should also look at the list of examples and tutorials
45 below. This documentation is created by 'ant' from the Java source code for the CDK as follows:
46
47 cdk/$ ls javadoc.xml
48 javadoc.xml
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49 cdk/$ ant -buildfile javadoc.xml html
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50
51 The documenation is created as a series of .html pages in doc/api. If you use firefox, you can read
52 the documentation using the following command:
53
54 cdk/$ firefox doc/api/index.html
55
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56 3. Running tests
57
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58 IMPORTANT: this requires the Git version of the sources.
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59
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60 After you compiled the code, you can do "ant test-all" to run the test suite of non-interactive, automated
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61 tests. You might need to copy an appropriate junit.jar into your $ANT_HOME/lib
62 directory or somewhere else in your classpath.
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63 Upon "ant dist-all test-dist-all test-all", you should see something like:
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64
65 test:
66 Running org.openscience.cdk.test.CDKTests
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67 Tests run: 1065, Failures: 7, Errors: 1, Time elapsed: 27,55 sec
68
69 As you can see, the vast majority of tests ran successfully, but that there
70 are failures and errors. The $CDK_HOME/reports/results.txt file contains
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71 information about the outcome of the tests.
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72
73 There are also run interactive tests, like the Controller2DTest. In order to try them, you can edit the "run"
74 target in the build.xml file to look like this:
75
76 <target name="run" depends="dist">
77 <java classname="org.openscience.cdk.test.ControllerTest" fork="yes">
78 <arg value=""/>
79 <classpath>
80 <pathelement location="${dist}/jar/cdk.jar"/>
81 <pathelement path="${java.class.path}"/>
82 <pathelement location="."/>
83 <fileset dir="jar">
84 <include name="*.jar"/>
85 </fileset>
86 </classpath>
87 </java>
88 </target>
89
90 Then, a "ant run" should give you a window where you can add bonds to a given structure.
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91 Currently, there are more than 15000 test, of which a large part tests the data, datadebug and
92 silent classes.
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93
94 4. Using CDK
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95
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96 CDK is a class library intended to be used by other programs. It will not run
97 as a stand-alone program, although it contains some GUI- and command
98 line applications. In order to use the CDK in your program, you need to build
99 the distribution jars by running "ant dist-all". They will end up in
100 $CDK_HOME/dist/jar. Copy all cdk-*.jars as well as all jars from $CDK_HOME/jar
101 to the lib directory of the project for which you intend to have CDK support and
102 use them as you would use any other third party jar.
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103
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104 Alternatively, run "ant dist-large" to create a jar cdk-svn-YYYYMMDD.jar in
105 $CDK_HOME/dist/jar. This large jar contains all the CDK code and all third
106 party libraries that code depends on.
107
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108 5. Examples and tutorials
109
110 To get started using the CDK, you may be interested in the following websites which contain
111 examples and tutorials:
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112
113 * http://pele.farmbio.uu.se/planetcdk/
114 * http://rguha.net/code/java/
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115 * http://www.redbrick.dcu.ie/~noel/CDKJython.html
116
117 Further examples can also be found in issues of the CDK News:
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118 * http://cdknews.org/
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119
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