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The big SMSD patch.
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Squashed commit of the following:

commit fb32925db2cf56a0b782db97d968dfd66d59750f
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Fri Apr 23 17:07:00 2010 +0200

    Compile fixes for the rebase on the current master:

    * two imports that got lost due to several manual commit conflict fixes
    * updated for the recent IChemObjectBuilder API change

commit dbd1431408285faac5657c2d81b64e07f1ef534c
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Fri Apr 23 12:43:45 2010 +0200

    Fixed TestClass annotation

commit 27363278b4fb44aa7582fe58253b69bbc51c0989
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Fri Apr 23 12:27:23 2010 +0200

    Removed DocCheck from classpath too

commit a9e60e6a01ffe3e475420a4129288b6df9e312fc
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Wed Apr 21 10:23:08 2010 +0100

    atomContainer.getbuilder Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 7e9568fe47e8198ffa67dc7be7223071381a97f2
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Wed Apr 21 10:23:00 2010 +0100

    atomContainer.getbuilder Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 97117f4ca9313728a648c47976dd5caadac97728
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 21:34:36 2010 +0100

    updated builder plus removed System.gc() Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 02af5aa39578c305c4d1cdedeecc1ed8484f5f76
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 16:42:27 2010 +0100

    MCS plus test cases added

commit d2845c242d2fb4092027249b7ede5011d4483f8c
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 16:42:02 2010 +0100

    updated /** * @author Syed Asad Rahman <asad@ebi.ac.uk> * * @cdk.module test-smsd */ Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit ae9ef8929bd8eaf6be2619bbc343c2ecad6b9f38
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 15:21:31 2010 +0100

    updated /** * @author Syed Asad Rahman <asad@ebi.ac.uk> * * @cdk.module test-smsd */ Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit b9a5a6b9d988b574be96cbd3a01214d70dd08fe6
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 15:17:50 2010 +0100

    org.openscience.cdk.smsd.algorithm.single Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 8a82b2ec8206ad276a3790ddcfed700ea12b2a79
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 15:01:42 2010 +0100

    org.openscience.cdk.smsd.algorithm.single Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 400aa528564bf5fb3c0d4993ff688b10a3ac99f5
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 14:52:49 2010 +0100

    MCS plus test cases added

commit b8c4f79b55077a404aa65fc56001956ef011ede9
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 14:48:45 2010 +0100

    MCSplus test cases added Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 573c65fec0012cb7e05695da7ea1014be24596ff
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 14:21:24 2010 +0100

    all classes

commit f52d7732bf9883bd251112fa98e27f91187f798f
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 14:19:51 2010 +0100

    added test case SMSDNormalizer

    Signed-off-by: Asad <s9asad@gmail.com>

    Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 987cd5376ec5cbf2b319934eb8fc17be3ee4ae82
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 14:13:15 2010 +0100

    is subgraph example code improved

    Signed-off-by: Asad <s9asad@gmail.com>

commit 5ace2c811d437c5fc111aadd201aae3e77b696e5
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 13:03:10 2010 +0100

    all classes

commit 6a95815de4e5feea6cc2be4caf14cb3112b4be5d
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 12:43:45 2010 +0100

    SMSD Test annotation Added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 6001621612105dc899daf372fcb27b73685db509
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 12:39:44 2010 +0100

    SMSD McGregor TestAdded

    Signed-off-by: Asad <s9asad@gmail.com>

    Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit c11108df6bf232e70934130bbf5ef87edb153ef7
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 12:39:15 2010 +0100

    CDK Resolution graph test added

    Signed-off-by: Asad <s9asad@gmail.com>

    Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 24dc66d4ad8fa4c718d35a17282a3621b0ae25a2
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 12:19:34 2010 +0100

    fixed Text license doc for SMSD

    Signed-off-by: Asad <s9asad@gmail.com>

    Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 2231dae2dcf2378353165d04fc48d16b993ab4b9
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Apr 20 11:01:21 2010 +0100

    fixed java doc for SMSD

    Signed-off-by: Asad <s9asad@gmail.com>

    Signed-off-by: Syed Asad Rahman <s9asad@gmail.com>

commit 3b4aa28b68541d2ad086359151834aeb15bda9dd
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 15:09:08 2010 +0100

    added missing classes

commit fb8eb30f2bd1f6ba30c04d8f933df2743e52b400
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 15:08:36 2010 +0100

    added missing classes

commit 37a18d611b853f30cd097b99fa95b9ac2cda3f46
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 14:55:31 2010 +0100

    Filters @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 77dae9ea8760ac65161ca6e7132da35a43fd3c12
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 14:49:51 2010 +0100

    factory @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 18cf781f34351cf8bba40808d1f528431a51603d
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 14:32:04 2010 +0100

    global @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 2f104f90ebdaa468052ff0c09e3313e692a8341b
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 14:29:17 2010 +0100

    helper @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 0774a4a234e6f9d7447b357b31c5c2578638a22a
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 14:18:14 2010 +0100

    tools @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit a9095f5d7694af7babf9dd3573a15c67effa3092
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 14:05:35 2010 +0100

    VFlib class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit ba9828058a6e71f6d11a3350b37757eef1107d69
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 14:03:49 2010 +0100

    VFlib class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 095ef1c76e00174748d60a70f87dd501efa386c8
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 14:03:40 2010 +0100

    VFlib class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 8efbc8607cbdce9397962442e8e4daa40d76b73e
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 13:57:08 2010 +0100

    VFlib class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit e507e5f5574a32e5707a2e91500b8253c342e228
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 13:07:57 2010 +0100

    Single mapping class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 722f3a2cc947b5ba5cdbee064ffd856cf0aadc9a
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 13:00:49 2010 +0100

    MCSPlusHandler class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit c1fba0751eb8b9146314016917a39d027fbb7601
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 13:00:18 2010 +0100

    MCSPlusHandler class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit b10f400487072fe33254e2d6b964e26dee429f94
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 12:56:24 2010 +0100

    CDKMCSHandler class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 7e4806f6f3d710c3c490e0c9fc4af1502c20ade2
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 12:48:08 2010 +0100

    SMSD class @TestMethod added

    Signed-off-by: Asad <s9asad@gmail.com>

commit 8b71d7a5db8a5ab548ca3f58a616507ac8346388
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 10:11:33 2010 +0100

    added docs for Test

    Signed-off-by: Asad <s9asad@gmail.com>

commit d2df6658c7bafe91721e459f7abc2f50bd38dc35
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 10:02:26 2010 +0100

    added Mcgregor test

    Signed-off-by: Asad <s9asad@gmail.com>

commit c80530e4141683ecab52a309dfecfcfb99006e5a
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 09:57:25 2010 +0100

    added Mcgregor test

    Signed-off-by: Asad <s9asad@gmail.com>

commit 47bbb48781150cc5f9a9ccfd18f44f0237b4e719
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 09:55:47 2010 +0100

    test cases

commit 134ecaf3e6ad813d3394def739dfd95188e7d514
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Wed Apr 7 09:57:10 2010 +0200

    Limit to one class, to comply to the current @TestClass limitation

commit f0e600745ee190b5e69538a698e3fd29f96ff60a
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Wed Apr 7 09:56:48 2010 +0200

    Added missing test class name

commit 465293f3ad9213acad510a5420d1bbd08fbce2e0
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Wed Apr 7 09:45:57 2010 +0200

    Just point to one unit test class

commit e18700bdcd19021f3fa8efa531afb0a2dabe7fc5
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Wed Apr 7 09:44:27 2010 +0200

    Use assertTrue(foo) rather than assertEquals(true,foo)

commit f1c0c4bfdc42f86e5c276e4de19b6b9024bff416
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Wed Apr 7 09:43:07 2010 +0200

    Point to just one test class; added missing @TestMethod annotation

commit 0b64414c250fab596da65b494ef119808239f5a0
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 07:31:04 2010 +0100

    no notify not supported in test

    Signed-off-by: Asad <s9asad@gmail.com>

commit ed76d558960d97132ea64eea9d691036557baa44
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 07:18:54 2010 +0100

    no notify not supported in test

    Signed-off-by: Asad <s9asad@gmail.com>

commit 3b038c3dc195db9f995f1407fe193c58c9ee76ea
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 07:13:59 2010 +0100

    added

    * @cdk.module test-smsd

    Signed-off-by: Asad <s9asad@gmail.com>

commit 60b85aa74e1d5c7ac2c615da5763d64b84f88e1f
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 07:05:25 2010 +0100

    smsd test suite updated

    To do
    Mcgregor suite and Bond sens

    Signed-off-by: Asad <s9asad@gmail.com>

commit 13efe98931c48d8982d44a949b02c31637ddd74a
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 06:57:30 2010 +0100

    Test suite works

    To do
    Mcgregor suite and Bond sens

    Signed-off-by: Asad <s9asad@gmail.com>

commit 84e33d6321b0ba8d7f1aebcf021e57a0b87eb5ed
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 06:43:26 2010 +0100

    Interface test

    Signed-off-by: Asad <s9asad@gmail.com>

commit da914adb55cf8b48d78758f0edbbe53b19dbe465
Author: Asad <s9asad@gmail.com>
Date:   Wed Apr 7 06:39:11 2010 +0100

    String mol file reader mcs test done

    Signed-off-by: Asad <s9asad@gmail.com>

commit 5ff0243dfe92a30d07f0e47d8c77fe258b7fca0a
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 22:16:39 2010 +0100

    test cases

commit f6bdc67b124bc0baa91ec14f1e0a74faf84df678
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 21:40:40 2010 +0100

    CDK MCS UIT handler suite works

    TO DO

    String mol file reader test

    Signed-off-by: Asad <s9asad@gmail.com>

commit 29b4462de43d68bbae1369f55192cf38522a40c1
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 21:40:33 2010 +0100

    CDK MCS UIT handler suite works

    TO DO

    String mol file reader test

    Signed-off-by: Asad <s9asad@gmail.com>

commit 9401025471a5e809d83847eace239d8de246a90c
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 18:37:06 2010 +0100

    MCSPlus handler suite works

    TO DO

    String mol file reader test

    Signed-off-by: Asad <s9asad@gmail.com>

commit 93cbdef6785448b889c51268e15bb50124accb0f
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 18:33:08 2010 +0100

    Single mapping suite works

    TO DO

    String mol file reader test

    Signed-off-by: Asad <s9asad@gmail.com>

commit 302e3716fb88c26bad3f7d056f1e892d1b14eb20
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 18:32:20 2010 +0100

    Single mapping return type assigned

    Signed-off-by: Asad <s9asad@gmail.com>

commit 012eb090ea16c31b03c6b65ab7355bfc628c3efa
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 18:18:24 2010 +0100

    Single mapping return type assigned

    Signed-off-by: Asad <s9asad@gmail.com>

commit 7c5bc166ac954200348dfeb8f89a11caaccde03b
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 18:14:38 2010 +0100

    Single mapping return type assigned

    Signed-off-by: Asad <s9asad@gmail.com>

commit 149e51e5b3fd4aadb2eacb1c5df54f504fa6130f
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 18:06:34 2010 +0100

    VFlib suite working

    TODO
    String mol file reader test

    Signed-off-by: Asad <s9asad@gmail.com>

commit 59d2af96e16116576c885b6fa5ff1007fca8e10c
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 18:05:44 2010 +0100

    VFlib suite working

    TODO
    String mol file reader test

    Signed-off-by: Asad <s9asad@gmail.com>

commit 7a9b783150acc9871d076f108efb041d507c7d61
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 18:04:50 2010 +0100

    VFlibMCSHandler algrithm. X factor increase in Speed, removed unwanted System.gc()

    Signed-off-by: Asad <s9asad@gmail.com>

commit b1481d50715cc8e8b17962b2883987faf54b10b7
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 16:41:52 2010 +0100

    Factory suite is working!!

    Signed-off-by: Asad <s9asad@gmail.com>

commit b0506d23be7718198795bfe826c002b9149ca155
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 16:24:50 2010 +0100

    added @cdk.module test-smsd Factory suite working TO DO Fragment factory

    Signed-off-by: Asad <s9asad@gmail.com>

commit 411932bde354fd7db59feb0b4fd9cea9cce4d405
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 16:24:41 2010 +0100

    added @cdk.module test-smsd Factory suite working TO DO Fragment factory

    Signed-off-by: Asad <s9asad@gmail.com>

commit 0a5da70e5b1d8a7dde3101acba0b9a780bb1d9fa
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 15:43:26 2010 +0100

    Filters suite working

    Signed-off-by: Asad <s9asad@gmail.com>

commit f465453050ee347d504472c8101e7a9845c57036
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 14:23:00 2010 +0100

    test cases

commit 23c710c799aad3783bd9929bffaacc3b999491f0
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 14:21:06 2010 +0100

    test cases updated

    Signed-off-by: Asad <s9asad@gmail.com>

commit 96b19ea2f2d35f319192365185f23aa43d464be1
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 13:57:44 2010 +0100

    Test Global Suite working

    Signed-off-by: Asad <s9asad@gmail.com>

commit 8bd428d1f7b59b30d512660b4279dd0cae951ef8
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 13:56:08 2010 +0100

    Test toolsSuite working

    Signed-off-by: Asad <s9asad@gmail.com>

commit bad3c071a10861df52816cfb4ac0d636baedda08
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 13:55:41 2010 +0100

    labelContainer and Final mapping optimised

    Signed-off-by: Asad <s9asad@gmail.com>

commit 0445de111a62c7a278f34488016e9fa333ee346c
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 13:55:17 2010 +0100

    helper suit working

    Signed-off-by: Asad <s9asad@gmail.com>

commit 49bd248400cfdfa23d1fdbf0da48f53133c3ad3c
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 12:41:59 2010 +0100

    Fixed label container

    Signed-off-by: Asad <s9asad@gmail.com>

commit 1cc906781cd39cb09df70b0c7a7d90d5425d9cf1
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 10:57:42 2010 +0100

    Global Test Suite works

    Signed-off-by: Asad <s9asad@gmail.com>

commit 952c3bdb93fb05594fcde8b5e486492a3f46132b
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 10:43:37 2010 +0100

    added junit test cases skeleton To DO: add meat to the skeleton

    Signed-off-by: Asad <s9asad@gmail.com>

commit d325bcac21cda555f38d7250d244c92f56ecfaf5
Author: Asad <s9asad@gmail.com>
Date:   Tue Apr 6 10:41:22 2010 +0100

    doc improvements

    Signed-off-by: Asad <s9asad@gmail.com>

commit 779c8d685045c9d621ee82d07a62d841f357681e
Author: Asad <s9asad@gmail.com>
Date:   Mon Apr 5 10:14:35 2010 +0100

    optimiser

    Signed-off-by: Asad <s9asad@gmail.com>

commit 4402b25ed4805694b33790a379ae5f75c0405e44
Author: Asad <s9asad@gmail.com>
Date:   Mon Apr 5 10:02:15 2010 +0100

    optimiser

    Signed-off-by: Asad <s9asad@gmail.com>

commit 8d6caeedb05a57a562f69a2d59eb3c230597055e
Author: Asad <s9asad@gmail.com>
Date:   Mon Apr 5 10:02:00 2010 +0100

    cdk logging tool

    Signed-off-by: Asad <s9asad@gmail.com>

commit 469fa854f80322c809894329bee441e992f5bfb8
Author: Asad <s9asad@gmail.com>
Date:   Sat Apr 3 11:41:37 2010 +0100

    removed "_"

    Signed-off-by: Asad <s9asad@gmail.com>

commit 0cc54e177e7709bf66f3257050d807b37938e574
Author: Asad <s9asad@gmail.com>
Date:   Sat Apr 3 08:43:46 2010 +0100

    doc added

    Signed-off-by: Asad <s9asad@gmail.com>

commit dbe7fbd383096233f269f1a053a1550980e29ba2
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Sat Apr 3 09:40:58 2010 +0200

    Renamed another abstract class from IFoo to AbstractFoo.

commit 9057066a5c42f34abe0e64baff0f0e95e3624e0e
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Sat Apr 3 09:25:17 2010 +0200

    Added missing periods at end of first sentenced in JavaDoc

commit 86cf0491c1cb963a18a1a067661fa39289047e31
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Sat Apr 3 09:23:52 2010 +0200

    Fixed class name: interfaces start with I, abstract classes no, but with, for example, Abstract

commit 54f95fafe6431f9394966fc6b7af4550829e0b14
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Sat Apr 3 09:20:47 2010 +0200

    Added missing test class annotation

commit db48887b8cb4e806341a22b163204b48d81ef49f
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Sat Apr 3 09:08:54 2010 +0200

    Added a stub for a unit test for the searchMCS() method

commit 799c56215f3e26a5cf33d7d74c6d1a0e1970aef7
Author: Asad <s9asad@gmail.com>
Date:   Sat Apr 3 08:22:12 2010 +0100

    doc

    Signed-off-by: Asad <s9asad@gmail.com>

commit cd7da0328b1c083d6fdb8f876ca2c048cb1f0422
Author: Asad <s9asad@gmail.com>
Date:   Sat Apr 3 08:19:44 2010 +0100

    doc

    Signed-off-by: Asad <s9asad@gmail.com>

commit d01c9aa59648eb91ebff1cc88fcb3e1b7ca05ead
Author: Asad <s9asad@gmail.com>
Date:   Sat Apr 3 08:15:58 2010 +0100

    changes in the IMCSAlgorithm

    Signed-off-by: Asad <s9asad@gmail.com>

commit 5a5f91dafd339964c7485cfda66b68fb00a3434e
Author: Asad <s9asad@gmail.com>
Date:   Sat Apr 3 07:00:37 2010 +0100

    Second round of Major java doc update

    Signed-off-by: Asad <s9asad@gmail.com>

commit 4b4f436d1571dd25eb667a8979d8ab192e3aa9ee
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 22:28:16 2010 +0100

    Major java doc update

    Signed-off-by: Asad <s9asad@gmail.com>

commit f1e295bc750cec13c3e3b8daf93462e47dcd3d42
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 19:36:00 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit 8e6ca9685c6a8b24f83fd59c387d7493dea56c27
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 19:30:48 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit 34c44c80a6d66d6863eaacbb7248f25a603b8001
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 13:08:09 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit 77b558a165e29f52ddc7b4e4d20aae230990226a
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 13:04:56 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit fdf58253d9a12ae6750a582aaee267dd813d433e
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 12:58:55 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit b81709b26d61e49c77710d4eb86a758ebd082c34
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 12:49:27 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit ae0e7a177806888a152ce1811aa22351723c7c91
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 12:44:57 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit 8348dd3c36fc3ed75f1c69d72bf3a745be0103b0
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 12:42:03 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit 15d85fdae4768043683d570700848ee91a8de445
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 12:39:07 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit ef841f2e78f0b639a6e55c795044d9f744344569
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 12:32:54 2010 +0100

    added more docs

    Signed-off-by: Asad <s9asad@gmail.com>

commit 5d62da8704f5372eec099e1faf42f033683b22f7
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 07:09:42 2010 +0100

    added test cases

commit 4a99caa5b50a727145f3427e4ae6bfd019fb0ee3
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 07:08:47 2010 +0100

    Decoupled and added more test cases

    Signed-off-by: Asad <s9asad@gmail.com>

commit 4d2db273838f01749015e378c90fcbc0849f21a3
Author: Asad <s9asad@gmail.com>
Date:   Fri Apr 2 07:08:26 2010 +0100

    Pattern design change in the SMSD

    Signed-off-by: Asad <s9asad@gmail.com>

commit f60750a23af706be4733949ea6ea0304d70910ef
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 12:03:23 2010 +0100

    test cases

commit a0f0baf8a8232152fee4f7e99110f641209c5c3c
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 11:53:35 2010 +0100

    formating

commit 0e92ba2da2b680de4208a92d726fc7ea733466be
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 07:18:10 2010 +0100

    doc

    Signed-off-by: Asad <s9asad@gmail.com>

commit bc363210eef49189a3b81a841af3152c127c76c1
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 07:14:41 2010 +0100

    mcgregor helper public to protected

    Signed-off-by: Asad <s9asad@gmail.com>

commit ed14bfdb4ccb8a2e1124d818f4619824e2ae4aa6
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 07:09:58 2010 +0100

    exact mapping main doc last commit for overall java doc

    Signed-off-by: Asad <s9asad@gmail.com>

commit ff9d59433da65c4e9555e7810a22a0ebc3ef8c0c
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 06:59:50 2010 +0100

    few more java docs -> VFlib

    Signed-off-by: Asad <s9asad@gmail.com>

commit 74dc3164570dd1c755defe5308768f122de593bf
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 06:50:48 2010 +0100

    few more java docs -> VFlib

    Signed-off-by: Asad <s9asad@gmail.com>

commit 58595dcd9614db0e20e89621ae55022b13540f26
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 06:48:46 2010 +0100

    few more java docs -> VFlib

    Signed-off-by: Asad <s9asad@gmail.com>

commit 0f511ff1c9994f4451bef86b525475eddbc1b1af
Author: Asad <s9asad@gmail.com>
Date:   Wed Mar 31 06:40:21 2010 +0100

    add main java doc VFlib

    Signed-off-by: Asad <s9asad@gmail.com>

commit 60091540990c679d77f578ef1a9c2d69f41c50ea
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 18:35:21 2010 +0100

    org.openscience.cdk.smsd.algorithm.cdk doc added Signed-off-by: Asad <s9asad@gmail.com>

commit 1568b7a76800e8ab82d7ab34af8b2ab5fcce41e4
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 18:31:36 2010 +0100

    Single mapping and MCSPlus doc improved Signed-off-by: Asad <s9asad@gmail.com>

commit 38ed5b6da61374afe8948eda37c487d483a77e40
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 17:51:17 2010 +0100

    Mcgregor package doc improved Signed-off-by: Asad <s9asad@gmail.com>

commit 0aec00c1e59b3ab37cf78072842d1920b2e477d7
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 17:38:25 2010 +0100

    some more main class annotation Signed-off-by: Asad <s9asad@gmail.com>

commit 0c57b7a107f28e906f89dc17d826cd1b1bd914c2
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 17:30:51 2010 +0100

    main class comments

commit ffba7920ddfef4bc0734fe8eed085a4c6c2bdf22
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 17:12:25 2010 +0100

    bond typoe class return Signed-off-by: Asad <s9asad@gmail.com>

commit 19b4995a4a31672ca11be69da33bd9e67a8357b0
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 17:09:14 2010 +0100

    added /** * @cdk.module smsd * @cdk.githash * @author Syed Asad Rahman <asad@ebi.ac.uk> */

    Signed-off-by: Asad <s9asad@gmail.com>

commit 8cff667bbf15779ca197943acf4cde46541d1127
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 17:06:12 2010 +0100

    added /** * @cdk.module smsd * @cdk.githash * @author Syed Asad Rahman <asad@ebi.ac.uk> */

    Signed-off-by: Asad <s9asad@gmail.com>

commit fc5f3576f4dbf35c3f204ce4590400e876cb5ef8
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 15:10:25 2010 +0100

    some more returns

commit 38ea40d0c7098d5cc033c53989ffba6a799b258b
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 15:03:34 2010 +0100

    some more returns

commit ba001b4ebb6c2b09385a5283e03edddab90b34b7
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 15:00:37 2010 +0100

    some more returns

commit 89eb5ef1ba8d37ea16e73664581deab4bda8b5cd
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:58:37 2010 +0100

    some more returns

commit 2f1de11f0d3f9923431fdcfa933c7b7b6d085afd
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:58:06 2010 +0100

    some more returns

commit 4eed47ba4c4924641c57dba17ee6b7652291a05f
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:55:03 2010 +0100

    some more returns

commit 366cd9048b16546d92ee26dfae1e653d2f7dff55
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:53:26 2010 +0100

    some more returns

commit 66697ffd6ed08ea135ec2404733e2504ff7c9783
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:48:43 2010 +0100

    some more returns

commit dd85841cc8a95c3bb22f66d77dacf79f686fb229
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Tue Mar 30 16:22:06 2010 +0200

    Added missing @cdk.githash tags

commit 530daf8f99ccfed3aef5fa9d842ca14ec6c2aff8
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:42:49 2010 +0100

    some more returns

commit 8c2c59879949927a66e96cabe99b63adc472e633
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:40:58 2010 +0100

    some more returns

commit 4108cb04aa66ac7d27482d305352be8679860b5f
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:39:08 2010 +0100

    some more returns

commit e96d04e81043e9dca53b307d31efa699bdb8ff81
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:37:40 2010 +0100

    some more returns

commit 0941fcf94c008081d7458442607386b9153b2103
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:35:28 2010 +0100

    some more returns

commit 48759748feb8f84f19bfd4ab43314f480920b4c7
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:28:07 2010 +0100

    some more returns

commit df5a33aff2cc28e74f3f79b00843049d19b59af9
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 14:09:08 2010 +0100

    some more returns

commit bd8b907c613f7a2c818b9aad661f889c0f05c451
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 13:10:06 2010 +0100

    /** {@inheritDoc} *

    Signed-off-by: Asad <s9asad@gmail.com>

commit 27cfb489efde0b8e2eecb3983ea3036fd45d2441
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 13:07:51 2010 +0100

    /** {@inheritDoc} *

    Signed-off-by: Asad <s9asad@gmail.com>

commit c84be5771d9ba9362a069d2ae721c89f15cab2c2
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 12:58:22 2010 +0100

    /** {@inheritDoc} *

    Signed-off-by: Asad <s9asad@gmail.com>

commit 1e675d119fe55f696c7d731c9a9e8843d9b5bdd4
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 12:55:53 2010 +0100

    /** {@inheritDoc} *

    Signed-off-by: Asad <s9asad@gmail.com>

commit 64be147a60b16b9670a0867028e425026b11d2e2
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 11:16:35 2010 +0100

    Algorithm type doc upadted

    Signed-off-by: Asad <s9asad@gmail.com>

commit 2006448b600bae1476d8abc0fd5257a54c8bb90a
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 11:15:58 2010 +0100

    Algorithm type doc upadted

    Signed-off-by: asad <s9asad@gmail.com>

commit d51a4325bf46125611740a9046dd5e589f0da11e
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 11:09:38 2010 +0100

    {@link org.openscience.cdk.smsd.interfaces.Algorithm}

commit aa9948cd1b6fa598b9d46f9547aefd7a8e98117c
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 10:48:53 2010 +0100

    algorithm added

commit fe2610fcaa9fa5230481f38c6fdcb335ef94e903
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 10:40:14 2010 +0100

    merged copyrights

commit 652ec0cf364c8d6648ed29444cc8fdc495b36310
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Mar 30 02:32:57 2010 -0700

    Test cases doc updated as per Egon

commit 91c9848ecdbca279f5b74b4e8d097e833a26d8ff
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 07:50:34 2010 +0100

    updated Copyright (C) 2009-2010

commit fc311a68db47ec06f678c5f6e4be4cd8a4dcda6b
Author: Asad <s9asad@gmail.com>
Date:   Tue Mar 30 07:38:23 2010 +0100

    updated docs

commit 676a68c77848b252100ab924821549e831009773
Author: Syed Asad Rahman <Asad@asad.local>
Date:   Tue Mar 30 07:30:07 2010 +0100

    updated Copyright (C) 2006-2010

commit da3c50f5379197bfd6514ee116be90c8e2543cff
Author: Syed Asad Rahman <Asad@asad.local>
Date:   Tue Mar 30 07:22:54 2010 +0100

    moved algorithm to interface class

commit 4e8f7788895cb1d32b55a800a9316a166fe1c22b
Author: Syed Asad Rahman <Asad@asad.local>
Date:   Tue Mar 30 07:15:25 2010 +0100

    Java doc improved for SMSD

commit 699a3878e580bf2adce5b4a675c224b9542ae552
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Mon Mar 22 12:57:09 2010 -0700

    GenerateCompatibilityGraph updated

commit d704b24958f6f142fab7afd7b511b46f4880e41f
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Mon Mar 22 12:32:15 2010 -0700

    Updated the compatibility graph generator

commit 37739514e7b8b8207a888f3e2a008b1951bf0f91
Author: Asad <Asad@192.168.0.102>
Date:   Sun Mar 21 09:45:14 2010 +0000

    added new test Signed-off-by: asad <asad@ebi.ac.uk>

commit 26f21edf7cc1f1d8e6a6a5982a3cc2560cd774b4
Author: Asad <Asad@192.168.0.102>
Date:   Sun Mar 21 09:20:00 2010 +0000

    Garbagge collecter Signed-off-by: asad <asad@ebi.ac.uk>

commit 2305856c2bddd7bcced67760911101b23e46aafc
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:56:18 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 8bfd8af78884d0ec57249b0318c517f19af72c31
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:54:51 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit f5ed27125f763c866672c62ecae7945601ce7071
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:52:17 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 334d54b101439991c9feb29cadd5a0b54d9862d5
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:51:49 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 60a83f9d6224e48cc8cc05689c71894f79fbab24
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:50:43 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit b47601e3b2b9cb8ab955b8b17811d210d9ead2be
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:50:37 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit dce87f1c059e5c46cafb4be7c79497fd0ad72c00
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:50:31 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit bafa8ba8c7604d059484e7c24b73598488528fcb
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:50:24 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 2012ede9a0977d04b24cba893598382bb850f19e
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:50:18 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 21e0f4f2f3dbd4740f9b638f06d326b004ce3eff
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:50:11 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 01853eec66da3773fe93e6fc18b0ee76b1f027e7
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:49:42 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 3e8a26a31dffaa47a3a96b2ecd6d1e28d97f58b1
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:49:34 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit eae2eadb19688ad42b80f78d632729b554462945
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:49:28 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 212cf45c9e556b531ca60c90df90d6033c7e6a08
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:49:20 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit e5d6749c31882f04d2e73b092d47a26f33d9d276
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:49:13 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 5a61ddc99da45a865d67f612526b50001dc35356
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 20 01:48:33 2010 +0000

    OVERHAULING of the SMSD performance with code optimisation Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 085c13b4bd751cae7761a088cb7023149a71d6cb
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 13 20:01:13 2010 +0000

    bond match code improvised Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 196cc8d522ba23a43c70be6747f1b40390291631
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 13 10:19:41 2010 +0000

    // continue search in case of substructures // return false in case of mcs state else it keeps on searching, fixed Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 2b83ef2e441eaafc6adc9544d353994b6f191076
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 13 05:21:58 2010 +0000

    // return false else it keeps on searching, fixed Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit fbacaa64e715c910c0c3c5a99cfde6020fc0f9fa
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 13 04:24:35 2010 +0000

    cleaned code Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 9295b595f5922911a8937ac5f851c09c92b9f425
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 13 04:06:59 2010 +0000

    isSubgraph code fixed and optimised Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit d35a31b8ab47957ee2fd893dc9cb0a508219123c
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 13 04:06:04 2010 +0000

    Bond matcher improved in VFlib Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 39390a958743ff82037e801aedaaaa5a36429fad
Author: Asad <Asad@192.168.0.102>
Date:   Sat Mar 13 04:05:35 2010 +0000

    test case optimised Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit 6b1bd27d38b3a2ab853c19d4345c9a8c68af1d61
Author: Asad <Asad@192.168.0.102>
Date:   Fri Mar 12 20:34:48 2010 +0000

    fixed the bond matching in VFLib so that its not AGGRESSIVE! Signed-off-by: asad <asad@ebi.ac.uk>

    Signed-off-by: Asad <Asad@192.168.0.102>

commit c082f087780544b6aa8d70494d9a7368fdb6b029
Author: asad <asad@ebi.ac.uk>
Date:   Thu Mar 11 21:04:30 2010 +0000

    fixed single mapping CDKMCS patch Signed-off-by: asad <asad@ebi.ac.uk>

commit 90ca4eb4b2f4d52ab3c72eaba5ad2c93306d5794
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Mar 11 13:20:26 2010 -0700

    Ext Container updated

commit 52a6fb5b81dcaa159b62207beefc6ff71b963242
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Mar 11 04:02:55 2010 -0700

    Added testdata.jar CDK test were falling out as this jar was missing

commit 1f7cf92d07610b02688395f436d7e8daaeaa4ec0
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Tue Mar 9 05:18:55 2010 -0700

    Doc fixed time manager

commit 16b59c3b61de4f88b802391d1d35577cd5a2211f
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Mar 4 13:50:19 2010 -0700

    Add label fixed

commit f1de271db00c37b094c92aa03cabb4fb7fae2cca
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Mar 4 13:40:18 2010 -0700

    Add few doc comments

commit 0da7240fe7027230da48ac6752e45190314bedfb
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Mar 4 13:12:43 2010 -0700

    Improved the speed with pre calculated atom count

commit 0d1be5d135b26730d1e4986aa38b38d3f1665b45
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Mar 4 13:11:24 2010 -0700

    Improved the speed with pre calculated atom count

commit 085c286407ef6f95b7295c457adb7be047c6d55b
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Wed Mar 3 00:07:31 2010 -0700

    Formatting

commit cdfff12fa5cb87d4be2231ae24b730b590fe9461
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Wed Mar 3 00:04:45 2010 -0700

    Chem-filters made robust with default values and stereo matches improved

commit 0e8464a89d537916e4c4f9981747527f78547b76
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Fri Feb 19 18:46:52 2010 -0700

    get stereo fixed as first mcs was null

commit 12305ab113c7717228a1984b8223273ede09436d
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Feb 18 05:19:52 2010 -0700

    Set Chem Filters fixed

commit b97919bae0da1886872ab4b7572a53ea85db62f0
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Feb 18 04:41:15 2010 -0700

    is subgraph optimised

commit ccb1e2bb0192cb8b02c4349c9c8d8f7d08c23747
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Feb 18 04:39:19 2010 -0700

    Is Subgraph optimised

commit f06a8d0bff60a04450ed4c107d5b63ac9a175cfa
Author: Syed Asad Rahman <s9asad@gmail.com>
Date:   Thu Feb 18 04:37:00 2010 -0700

    Fixed the chem filter return type its its null

commit ad6ca775e878d41384132c83a3b14832936922bf
Author: asad <asad@ebi.ac.uk>
Date:   Tue Feb 2 11:06:44 2010 +0000

    updated files

commit 322941e2e59ad10081d93f9928a04a4bdb5ca756
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Thu Jan 14 10:16:57 2010 +0100

    Removed some redundant files from the root folder

commit d1718fce63c1216ca68c13109c9e3d764a54e148
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Tue Feb 2 07:46:57 2010 +0100

    Fixed missing test-smsd module annotation

commit c9321c9beff5a38f8e4c36a14ff630ca259c64ff
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Thu Jan 14 17:54:59 2010 +0100

    Added a bunch of missing unit tests. Most are stubs, with a few really basic tests. Unit tests can be added AbstractMCSAlgorithmTest and will automatically be part of the subclassing unit tests: the class is basically a holder for unit tests for methods in the IMCSAlgorithm interface.

commit cccf9cc50d61697ac773d4a468e30231112d2cd0
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date:   Thu Jan 14 16:03:18 2010 +0100

    Enabled OpenJavaDocCheck checking for the SMSD module

commit 88c71f607b1b7e51414dec0a842f7bac0b350c2c
Author: asad <asad@ebi.ac.uk>
Date:   Wed Jan 27 13:42:50 2010 +0000

    netbean project renamed Signed-off-by: asad <asad@ebi.ac.uk>

commit ac170252ac15efa8b003e903d9a32f3841f1dfa0
Author: Syed Asad Rahman <asad@ebi.ac.uk>
Date:   Thu Jan 14 12:09:36 2010 +0100

    Added Normalizer methods used by the SMSD patch

commit 30314a37343c9895165a491c86b73ad18287adb3
Author: asad <asad@ebi.ac.uk>
Date:   Wed Jan 6 16:10:39 2010 +0000

    Bond matcher updated Signed-off-by: asad <asad@ebi.ac.uk>

commit 531572a09d347772353f1e8104392666cba2add7
Author: asad <asad@ebi.ac.uk>
Date:   Tue Dec 22 15:24:23 2009 +0000

    cdkmcs fixed for pmd Signed-off-by: asad <asad@ebi.ac.uk>

commit b375fc6ce58c92862801f860261e385cab770dc2
Author: asad <asad@ebi.ac.uk>
Date:   Tue Dec 22 07:52:52 2009 +0000

    nb updated

commit 52451d06cf10576d2c514bbeeed24439eeb78718
Author: asad <asad@ebi.ac.uk>
Date:   Tue Dec 22 07:52:03 2009 +0000

    test case updated

commit bda79b980dec7a0b2fb8342307fb192bf6518149
Author: asad <asad@ebi.ac.uk>
Date:   Mon Dec 21 18:00:12 2009 +0000

    updated McGregor files

commit c1efc06998f6e087adb8017c169c5a35b537cf1b
Author: asad <asad@ebi.ac.uk>
Date:   Mon Dec 21 17:59:08 2009 +0000

    added new files after bug fix

commit 5d43ea185c1431488c154adf5d03e587776eceb0
Author: asad <asad@ebi.ac.uk>
Date:   Mon Dec 21 17:56:53 2009 +0000

    few files deleted and updated as a bug creeped in while performing PMD fixes

commit f3d0c9c34010e3d9c08336e86bb224ffd94417ec
Author: asad <asad@ebi.ac.uk>
Date:   Mon Dec 21 15:39:56 2009 +0000

    CDK RGraph complexity fixed Signed-off-by: asad <asad@ebi.ac.uk>

commit 2ff8b1eefc8f5353cc16d5743199b56df049b660
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 20 10:51:03 2009 +0000

    PMD fixes and improved code Signed-off-by: asad <asad@ebi.ac.uk>

commit 741926718147a92c7a9c85cb62d2c22450465ed4
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 20 10:50:22 2009 +0000

    PMD fixes and improved code Signed-off-by: asad <asad@ebi.ac.uk>

commit 1d9dc2174f425460168232ca0670bf5fdc054df2
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 20 10:49:55 2009 +0000

    PMD fixes and improved code Signed-off-by: asad <asad@ebi.ac.uk>

commit 54fe63b84f206779f52515b5fb953247882bbff3
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 20 09:21:14 2009 +0000

    PMD fixes Signed-off-by: asad <asad@ebi.ac.uk>

commit 2755b7b4e6aa097e1449ff90f59d5da77da1bd28
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 20 09:15:06 2009 +0000

    PMD fixes Signed-off-by: asad <asad@ebi.ac.uk>

commit 5f6ca53d1e509e19576b375b8dba740d499471a4
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 20 08:42:06 2009 +0000

    PMD fixes Signed-off-by: asad <asad@ebi.ac.uk>

commit 9a31ef4f8436b12db55a9dda70218b0bc3736bc6
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 22:15:04 2009 +0000

    some more class annotation Signed-off-by: asad <asad@ebi.ac.uk>

commit 126967a0e3c78a41bd6b8daf216ab43cb4514049
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 22:13:37 2009 +0000

    some more class annotation Signed-off-by: asad <asad@ebi.ac.uk>

commit 78bce1409a2b3d4062de1bcecb5aa56b6aef9141
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 22:04:07 2009 +0000

    some more class annotation Signed-off-by: asad <asad@ebi.ac.uk>

commit c2477e9f733dd5a4bd397481ec84ff47344cfd53
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 19:56:00 2009 +0000

    120 lines format for SMSD Signed-off-by: asad <asad@ebi.ac.uk>

commit 3cf1a57dc7970afc846cb1c6d9f30ea93a8edb3b
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 19:14:16 2009 +0000

    CDKMCS Test updated Signed-off-by: asad <asad@ebi.ac.uk>

commit e3b798fa2d2bff7d6695dea103bf3ae0552a3eb1
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 19:03:07 2009 +0000

    CDKMCS added few methods like single mapping Signed-off-by: asad <asad@ebi.ac.uk>

commit a9e3b902df0dfa0f9210cc4d41c7ec8d28e99011
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 15:06:32 2009 +0000

    CDKMCS PMD improvement

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 2c08a18f6be320db0db97ff7a283306e3c4802c7
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 15:01:51 2009 +0000

    CDKMCS PMD improvement

    Signed-off-by: asad <asad@ebi.ac.uk>

commit f322c79385ad211711631368a65b674e66b13f49
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 14:59:35 2009 +0000

    CDKMCS PMD improvement

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 7a8818aa0acee0a581163b6558a6ad58279007cf
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 19 10:16:02 2009 +0000

    CDKMCS PMD improvement

    Signed-off-by: asad <asad@ebi.ac.uk>

commit b21e8780939b556c340e224faee6accff01a8cd7
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 18 22:33:37 2009 +0000

    CDKMCS PMD improvement

    Signed-off-by: asad <asad@ebi.ac.uk>

commit d5a98e9d5dbae9422fa2fd9e79f3047e77070e0e
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 18 19:49:41 2009 +0000

    Stereo Fixed in the ExtAtomContainer

    Signed-off-by: asad <asad@ebi.ac.uk>

commit d93451bb26c5cbbb13d6dfc8e7b012fd58ff88e6
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 18 08:53:35 2009 +0000

    Fixed PMD for the classes CDKMCS and McGregor

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 551ce520eaf5b4bca1d772cc4d9b94d5263fcd76
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 18 08:41:09 2009 +0000

    Fixed PMD for the classes CDKMCS and McGregor

    Signed-off-by: asad <asad@ebi.ac.uk>

commit a2854764474c721e0af1d7369dff8b6bc0fa5166
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 17 14:51:31 2009 +0000

    Fixed PMD for the classes

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 16813c1621ad9c9c1acecf5b0478356305a627c2
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 17 07:53:32 2009 +0000

    removed unused class

    Signed-off-by: asad <asad@ebi.ac.uk>

commit d62fcc37a1be9a0660df59ed2e5c00d45f0dc1cd
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 17 07:50:41 2009 +0000

    removed unused class

    Signed-off-by: asad <asad@ebi.ac.uk>

commit cd95c204e48b0f6261759bc8606434cb23e37dc7
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 17 07:46:14 2009 +0000

    PMD improvement for more classes

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 824cdd3505ac87dcf563fbfa80b997f7d51183cb
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 17 07:24:20 2009 +0000

    PMD improvement McGregor

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 67b84a94662cfcb6d0faf03f24fd037542a87abf
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 17 07:21:50 2009 +0000

    PMD improvement McGregor

    Signed-off-by: asad <asad@ebi.ac.uk>

commit a6fa2b2bf3f8e2aa1ce90630eee08e317a35e44e
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 16 23:17:40 2009 +0000

    PMD improvement McGregor

    Signed-off-by: asad <asad@ebi.ac.uk>

commit d6aa861c16ef7c35ebfbee699b49c40c8c1810bc
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 16 23:14:47 2009 +0000

    PMD improvement McGregor

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 91028c0b3ec4018dfd7b04437f9730e4ec93640d
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 16 23:14:37 2009 +0000

    PMD improvement McGregor

    Signed-off-by: asad <asad@ebi.ac.uk>

commit a980d627767bbe1fab21089e11e3588cda67f451
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 16 23:13:01 2009 +0000

    PMD improvement McGregor

    Signed-off-by: asad <asad@ebi.ac.uk>

commit e2e0ebacd6816cb06d9739aa515e9269d404ab51
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 16 17:10:01 2009 +0000

    PMD improvement of few classes

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 9cf895cd4cf54042132d1fb127fde9595a390418
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 16 17:06:16 2009 +0000

    PMD improvement of few classes

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 53774e81acca1e2881c55b579194b0b5b6c57775
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 16 17:01:29 2009 +0000

    PMD improvement of few classes

    Signed-off-by: asad <asad@ebi.ac.uk>

commit 4888383f4c44ee7df1be83574448e45ee54bdbc3
Author: asad <asad@ebi.ac.uk>
Date:   Mon Dec 14 08:08:59 2009 +0000

    PMD improved Signed-off-by: asad <asad@ebi.ac.uk>

commit 4004573dcbff6029033b61887ae144f514ffc66d
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 13 22:22:40 2009 +0000

    remove unused methods from ExtAtomContainerManipulator Signed-off-by: asad <asad@ebi.ac.uk>

commit 163f24c730a853cb8ca01b90cafd5a65df7ee9dd
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 13 22:19:33 2009 +0000

    Improved BKKCKCF as per the PMD report Signed-off-by: asad <asad@ebi.ac.uk>

commit 3cd8d74cc7af7d39858470b158397c88082ad8fd
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 13 22:15:42 2009 +0000

    Improved TargetProcessor as per PMD Signed-off-by: asad <asad@ebi.ac.uk>

commit 5ac770f9474c5cad7c3baaeab8eb2a6d15d12092
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 13 19:37:02 2009 +0000

    Bond energy error for spl symbols fixed Signed-off-by: asad <asad@ebi.ac.uk>

commit 2f4a46333e84b158a0b390b6b03e7c60581b950d
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 13 09:04:52 2009 +0000

    PMD Improvement Signed-off-by: asad <asad@ebi.ac.uk>

commit 25b1603d41f3415ea947aac6484619a2bb90d538
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 12 22:53:24 2009 +0000

    PMD Improvement Signed-off-by: asad <asad@ebi.ac.uk>

commit 7dde86b691f40d145243f38326f7c3ff08959a45
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 12 21:45:15 2009 +0000

    Bond Energy with Helper class added Signed-off-by: asad <asad@ebi.ac.uk>

commit 0fb99f3afd619a257b931aa99576d8d1349ba849
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 12 00:57:37 2009 +0000

    PMD Chemfilter improved Signed-off-by: asad <asad@ebi.ac.uk>

commit dbf26f80e753b34090835047bace9607b53505b3
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 12 00:39:23 2009 +0000

    /** * @cdk.module smsd */ Signed-off-by: asad <asad@ebi.ac.uk>

commit 28acafcbd5a04996affe92315d86f6274d9817c9
Author: asad <asad@ebi.ac.uk>
Date:   Sat Dec 12 00:36:37 2009 +0000

    /** * @cdk.module smsd */ Signed-off-by: asad <asad@ebi.ac.uk>

commit 15fdc2378e5649b62efae576baf86bdd07a4a99b
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 10 20:59:52 2009 +0000

    bond matcher, null exception fixed Signed-off-by: asad <asad@ebi.ac.uk>

commit 4f498f669171b23a6b9c584d90822cde952ba3f4
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 9 07:52:46 2009 +0000

    fixed McGregor veryNodes Signed-off-by: asad <asad@ebi.ac.uk>

commit d81fcb079589175edb9c31b74693e05f20abaa5f
Author: asad <asad@ebi.ac.uk>
Date:   Tue Dec 8 17:45:36 2009 +0000

    PMD Update Signed-off-by: asad <asad@ebi.ac.uk>

commit 748aa05cbd6bbe64addff9546651adad90e39131
Author: asad <asad@ebi.ac.uk>
Date:   Tue Dec 8 09:04:41 2009 +0000

    PMD Update Signed-off-by: asad <asad@ebi.ac.uk>

commit dbdadd27e16a2f4b186dbce52af8980186117172
Author: asad <asad@ebi.ac.uk>
Date:   Tue Dec 8 08:52:21 2009 +0000

    subgrph test Signed-off-by: asad <asad@ebi.ac.uk>

commit bf3754612d234e236ef01d1478294600b81d7d9b
Author: asad <asad@ebi.ac.uk>
Date:   Mon Dec 7 08:04:25 2009 +0000

    subgrph test Signed-off-by: asad <asad@ebi.ac.uk>

commit c812ebfb1e5ae78ffd78fe9d58712d5b5fcb3e39
Author: asad <asad@ebi.ac.uk>
Date:   Mon Dec 7 08:01:30 2009 +0000

    Smiles instead of mol reader Signed-off-by: asad <asad@ebi.ac.uk>

commit a8da42fde1a8f95488131ba1ffb891c1b9e9f372
Author: asad <asad@ebi.ac.uk>
Date:   Mon Dec 7 07:59:35 2009 +0000

    Smiles instead of mol reader Signed-off-by: asad <asad@ebi.ac.uk>

commit 026b820b734e9cefa44e45bc44d57660e467c147
Author: asad <asad@ebi.ac.uk>
Date:   Sun Dec 6 08:35:59 2009 +0000

    PMD improvement for BKKCKCF, McGregor Signed-off-by: asad <asad@ebi.ac.uk>

commit bd9fbd2e1f5741abac6e922c5a7cd2f87ff7540c
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date:   Fri Dec 4 15:20:35 2009 +0100

    Added a missing test class for BondEnergies

commit 5dfd8223dd25843d47538e421a0865bc178f3700
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date:   Fri Dec 4 15:14:58 2009 +0100

    Moved copyright header to show up before the package declaration

commit 3f1e0b9daa9c331e79354fa25ce86e188c18b3fd
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date:   Fri Dec 4 15:13:32 2009 +0100

    Added a missing test class for TimeManager

commit 75acf3bad374db1dca4ee96e9a3249b907aac8dc
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date:   Fri Dec 4 15:12:21 2009 +0100

    Added new CDKMCSTest to suite

commit 4fd3694aa5e21c1c1bbd50aee3de870c1c0002cb
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date:   Fri Dec 4 15:05:47 2009 +0100

    Moved copyright header to show up before the package declaration

commit cf4eb0afa2a0b421c67d888c49fb1ec9e60af5b5
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 4 02:36:58 2009 +0000

    PMD improvement for BKKCKCF Signed-off-by: asad <asad@ebi.ac.uk>

commit d14314404481e6961a1d421a4b0771f12a8acdc8
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 4 02:13:46 2009 +0000

    PMD improvement for McGregor Signed-off-by: asad <asad@ebi.ac.uk>

commit ed4ec4efb05f5d8b7173fb907c508ac9b272296a
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 4 01:52:48 2009 +0000

    PMD improvement Signed-off-by: asad <asad@ebi.ac.uk>

commit 88cf57af1dd96efe308fd5d0faedcb8afe4b44d0
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 4 01:08:15 2009 +0000

    updated imports Signed-off-by: asad <asad@ebi.ac.uk>

commit 20b77f38611d0d07cb03f3de39e36d3ea48f7d71
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 4 01:02:57 2009 +0000

    added new mols for test Signed-off-by: asad <asad@ebi.ac.uk>

commit 262dab00df2aa82445f4dbb0a528be5be20444a2
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 4 00:52:16 2009 +0000

    VFlib revisited Signed-off-by: asad <asad@ebi.ac.uk>

commit d016f8564dbaaf717a105e304833aa1a3bbd109b
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 4 00:20:48 2009 +0000

    added large subgraph test Signed-off-by: asad <asad@ebi.ac.uk>

commit e778f32785242e2c3b80790d003054b3fd589f97
Author: asad <asad@ebi.ac.uk>
Date:   Fri Dec 4 00:20:06 2009 +0000

    VFLibHandler organised, fixed PMD and bug Signed-off-by: asad <asad@ebi.ac.uk>

commit 0d7421450fa428ef90cf53516b5504f2cfe89b86
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 23:25:14 2009 +0000

    test case adapted to the new factory format Signed-off-by: asad <asad@ebi.ac.uk>

commit 9fe5fc6edef1f97642358ea4aced46e225a8849c
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 23:22:29 2009 +0000

    cleaner algorithm selection method Signed-off-by: asad <asad@ebi.ac.uk>

commit d999ae84ae762b918b78ba2b9e7b3e481c080975
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 23:17:13 2009 +0000

    improved doc Signed-off-by: asad <asad@ebi.ac.uk>

commit bdd9b71333a9e4608f9b4db9ae19060306671a91
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 23:13:36 2009 +0000

    Substructure search algorithm factory made generic as a plugin More MCS/Substructure search algorithm can be added in the near future Signed-off-by: asad <asad@ebi.ac.uk>

commit 525f548572c07f6c015cecbbb3bf6c9cc84a79ea
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 23:13:22 2009 +0000

    Substructure search algorithm factory made generic as a plugin More MCS/Substructure search algorithm can be added in the near future Signed-off-by: asad <asad@ebi.ac.uk>

commit ec14501d7653cab35d569ea6627111a916fdea2d
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 23:10:18 2009 +0000

    optimised Algorithm Factory as plugin Signed-off-by: asad <asad@ebi.ac.uk>

commit 44cb449692b403d02c2e6a9f975855425634171a
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 17:45:21 2009 +0000

    PMD optimisation Signed-off-by: asad <asad@ebi.ac.uk>

commit 098fcde63954c6014638ba1dcffb4702dfe2aac6
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 10:17:08 2009 +0000

    nb build changed Signed-off-by: asad <asad@ebi.ac.uk>

commit b7862b9ba12868bdb2666801013a2b311a900fac
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 08:38:45 2009 +0000

    PMD improvement Signed-off-by: asad <asad@ebi.ac.uk>

commit 0d263329fe3afc8ade9cda405e807a866ad43196
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 08:32:53 2009 +0000

    VFLib MCS non redundent hits Signed-off-by: asad <asad@ebi.ac.uk>

commit 3066ba6a4ad8ac37b5ed1faa19752d9e53fa2977
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 08:28:50 2009 +0000

    VFLib MCS non redundent hits Signed-off-by: asad <asad@ebi.ac.uk>

commit afc3fab6766a3ad64fd19adf13191876f962545a
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 08:14:53 2009 +0000

    Test modules added Signed-off-by: asad <asad@ebi.ac.uk>

commit 889c77e34efa01c4466b80e20aac2cec9e68f995
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 08:14:35 2009 +0000

    MCSVF lib improved Signed-off-by: asad <asad@ebi.ac.uk>

commit 7828b1c7f474a37bb78b050552cd580922560868
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 02:33:33 2009 +0000

    organised test modules Signed-off-by: asad <asad@ebi.ac.uk>

commit 980f6597a256677f46ddec8c0d0e8f6d97064100
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 02:32:49 2009 +0000

    organised test modules Signed-off-by: asad <asad@ebi.ac.uk>

commit 816e971caf790bb2dc403b7262d156ad9a0fc7b0
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 02:26:55 2009 +0000

    Doc improved Signed-off-by: asad <asad@ebi.ac.uk>

commit f07cc32b8722557ddca47bbd6ac63a01c8772e43
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 02:26:00 2009 +0000

    McGregor improved and made modular to decrease the code complexity Signed-off-by: asad <asad@ebi.ac.uk>

commit 7d3bdf958a96f3101a8aa4d640bea49d5e8a85dc
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 02:24:17 2009 +0000

    McGregor improved and made modular to decrease the code complexity Signed-off-by: asad <asad@ebi.ac.uk>

commit 69ef929e4f33874441fcaab182009a7245c16d61
Author: asad <asad@ebi.ac.uk>
Date:   Thu Dec 3 01:18:15 2009 +0000

    McGregor improved made modular Signed-off-by: asad <asad@ebi.ac.uk>

commit b4956625a90bb8ccc47b64a67f2c30c98f9512b2
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 22:56:59 2009 +0000

    McGregor improved with variables Signed-off-by: asad <asad@ebi.ac.uk>

commit d0f579dbf25186d90c6f8bcce4e34bd8e7b6ab39
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 22:43:19 2009 +0000

    McGregor improved Signed-off-by: asad <asad@ebi.ac.uk>

commit 1338bbd4184844c9c7239d8fa15516b0fa1f9577
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 18:18:00 2009 +0000

    Single Mapping Test introduced Signed-off-by: asad <asad@ebi.ac.uk>

commit da9cf1d34b277259317c161ea463fee0cfef2653
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 18:17:39 2009 +0000

    Single Mapping ranking fixed Signed-off-by: asad <asad@ebi.ac.uk>

commit 5e0dc48d2f975e51ccbf9ee70c46f7d3082a5fa7
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 14:58:57 2009 +0000

    Single Mapping optimised Signed-off-by: asad <asad@ebi.ac.uk>

commit 37c4d4b75f8cc091621b830b590d3eb28a3caacf
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 14:53:06 2009 +0000

    Single Mapping optimised Signed-off-by: asad <asad@ebi.ac.uk>

commit 61ef38b95f00684bdd34d7ef88c3745c611a72d3
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 13:55:04 2009 +0000

    Single Mapping optimised Signed-off-by: asad <asad@ebi.ac.uk>

commit 3a3c2c9bd8b25a064afe67ccc6ae357514f9bf13
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 13:15:17 2009 +0000

    optimising McGregor step 3 Signed-off-by: asad <asad@ebi.ac.uk>

commit b22f8dae4d97d1049a65ad08a7e32b6d398a3f70
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 12:36:15 2009 +0000

    optimising McGregor step 3 Signed-off-by: asad <asad@ebi.ac.uk>

commit 1dc7da189f27398de99a33c30e50e0c8684a3734
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 05:14:04 2009 +0000

    optimising McGregor step 2 Signed-off-by: asad <asad@ebi.ac.uk>

commit ca33b96b15081f3026283db274cd0706da40c65a
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 05:10:19 2009 +0000

    optimising McGregor step 2 Signed-off-by: asad <asad@ebi.ac.uk>

commit 3122ee1ce3df8f310056f1e6e252c6583b027065
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 05:09:26 2009 +0000

    optimising McGregor step 2 Signed-off-by: asad <asad@ebi.ac.uk>

commit 2c81e278b269f2eeaf8f7de1a184472a9067f326
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 04:58:18 2009 +0000

    optimising McGregor step by step Signed-off-by: asad <asad@ebi.ac.uk>

commit ec88c04ab0abdec7c2283bba506af104b8a0e36a
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 04:09:59 2009 +0000

    more robust testing modules Signed-off-by: asad <asad@ebi.ac.uk>

commit 72b03f125b5e5f4dc63a0e0b7b490b5a2d33747b
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 04:09:26 2009 +0000

    Reverted McGregor changes Signed-off-by: asad <asad@ebi.ac.uk>

commit f78ee588e45848170a4269b6c8e7a70af9093bf3
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 03:46:50 2009 +0000

    new mdl data for smsd test added Signed-off-by: asad <asad@ebi.ac.uk>

commit db0a815659033f19027b75cf84fe9071ba0fa882
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 03:46:13 2009 +0000

    Test added Signed-off-by: asad <asad@ebi.ac.uk>

commit 4447736cb1c8f384532813057a353838b08b9933
Author: asad <asad@ebi.ac.uk>
Date:   Wed Dec 2 03:45:44 2009 +0000

    compatibility graph made modular Signed-off-by: asad <asad@ebi.ac.uk>

commit 097ce57d9bf7bc69cde40800df1b56284e6847f4
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 12:19:31 2009 +0000

    Test Updated Signed-off-by: asad <asad@ebi.ac.uk>

commit fba66f386bbcb55d6ff63bdbfc17447471fca1cd
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 12:04:30 2009 +0000

    Test Updated Signed-off-by: asad <asad@ebi.ac.uk>

commit c96a8d6a256751c3b6c79bbb7d435bd2325191df
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 12:00:33 2009 +0000

    Reorganised the Interfaces Signed-off-by: asad <asad@ebi.ac.uk>

commit c1858bd6bb4af3d06ab3380b3953157cc0fae30e
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 11:57:31 2009 +0000

    moved files to proper folder Signed-off-by: asad <asad@ebi.ac.uk>

commit e22c2363091febc6946883e0818940b5c27f5a28
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 11:57:09 2009 +0000

    moved files to proper folder Signed-off-by: asad <asad@ebi.ac.uk>

commit a7b725000fe7a16e8ac8ee47f1bf735c44d24b4c
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 11:12:04 2009 +0000

    Fixed MCSPlus GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 705c70b436bc3a942c67850609cec986e089a45c
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 08:58:31 2009 +0000

    Improved McGregor To Do Fix MCSPlus for bond sensitive default algorithm changed for bond sensitive and insensitive Signed-off-by: asad <asad@ebi.ac.uk>

commit a9a21a735d2ac8f977598fa01edcc5ffa67b5ad8
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 08:09:54 2009 +0000

    default algorithm changed Signed-off-by: asad <asad@ebi.ac.uk>

commit 8b323e63258633dab081b3ee2802aa19dd1dc8a2
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 07:44:51 2009 +0000

    Doc improved Signed-off-by: asad <asad@ebi.ac.uk>

commit fb5906cff3ed62aecfee76648615265d0a9e8ffc
Author: asad <asad@ebi.ac.uk>
Date:   Mon Nov 30 07:41:22 2009 +0000

    Turbo MCS called SMSD Interface changed for IAtomContainer and IMolecule only Signed-off-by: asad <asad@ebi.ac.uk>

commit 711cdc6274b7f92735ed20f4ce5966c8b33254e3
Author: sar <sar@192.168.1.2>
Date:   Mon Nov 30 07:35:59 2009 +0000

    SMSD Interface changed for IAtomContainer and IMolecule only Signed-off-by: asad <asad@ebi.ac.uk>

commit 0acf184b5d9fcc0952173d86c677261442c23cf5
Author: sar <sar@192.168.1.2>
Date:   Mon Nov 30 01:32:16 2009 +0000

    SMSD Interface changed for turbo match based subgraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 270b503f9b8e8a494a9df889fdf8088bb15c1f82
Author: sar <sar@192.168.1.2>
Date:   Mon Nov 30 01:31:59 2009 +0000

    SMSD Interface changed for turbo match based subgraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 081e87e12500c53961833192b1a64c551ce86121
Author: sar <sar@192.168.1.2>
Date:   Mon Nov 30 01:31:21 2009 +0000

    Added subgraph test Signed-off-by: asad <asad@ebi.ac.uk>

commit 56afe37bd732ce1ea08fde95a2ee5e7b325c6292
Author: sar <sar@192.168.1.2>
Date:   Sun Nov 29 21:33:45 2009 +0000

    Improved the SMSD java doc Signed-off-by: asad <asad@ebi.ac.uk>

commit 788fba8d7a19ca43a496b0f677f82eac51133572
Author: asad <s9asad@gmail.com>
Date:   Sun Nov 29 13:08:41 2009 -0700

    Egon Willighagen <egonw@users.sourceforge.net> Added missing dependencies, for MDLV2000 (cdk-io) and QueryAtomContainer (cdk-isomorphism)

commit 7f7b1b9621d946727eac1796243bcd3086766fa1
Author: asad <asad@ebi.ac.uk>
Date:   Wed Nov 25 01:03:31 2009 +0000

    Doc imp Signed-off-by: asad <asad@ebi.ac.uk>

commit 70d3d50bb17402aa1de2bfaeb8b5ba00fec231f7
Author: asad <asad@ebi.ac.uk>
Date:   Wed Nov 25 01:01:50 2009 +0000

    Mcgregor Checks Signed-of…
  • Loading branch information
@egonw
Syed Asad Rahman authored and egonw committed Apr 26, 2010
1 parent f17fc8f commit 10edb71
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Showing 146 changed files with 26,970 additions and 6 deletions.
1 change: 1 addition & 0 deletions AUTHORS
View file
Expand Up @@ -49,3 +49,4 @@ Stephane Werner
Egon Willighagen
Yong Zhang
Daniel Zaharevitz
Syed Asad Rahman
10 changes: 5 additions & 5 deletions build.xml
View file
Expand Up @@ -259,7 +259,7 @@
<mkdir dir="${build}" />
<javac includes="net/sf/cdk/tools/MakeJavafilesFiles.java"
srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
debug="${debug}" deprecation="${deprecation}" source="1.5"/>
debug="${debug}" deprecation="${deprecation}" source="1.6"/>
<java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
<arg value="${src}/META-INF"/>
<arg value="${src}/main"/>
Expand Down Expand Up @@ -372,7 +372,7 @@

<!-- ok, now that we have a copy, compile this copy -->
<javac srcdir="${build.src}/${module}" destdir="${build}/${module}" optimize="${optimization}"
debug="${debug}" deprecation="${deprecation}" target="1.5" source="1.5">
debug="${debug}" deprecation="${deprecation}" target="1.6" source="1.6">
<classpath>
<fileset dir="${lib}" >
<exclude name="**/*" unless="module.libdepends.present" />
Expand Down Expand Up @@ -531,7 +531,7 @@
list="pdb,smiles,sdg,inchi,libiocml"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="control,extra,reaction,pdbcml,libiomd"/>
list="control,extra,reaction,pdbcml,libiomd,smsd"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="charges,smarts"/>
Expand Down Expand Up @@ -573,7 +573,7 @@
test-nonotify"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="test-qsarprotein,test-qsarionpot"/>
list="test-qsarprotein,test-qsarionpot,test-smsd"/>
</target>

<target id="jarTestdata" name="jarTestdata" description="Creates jar files with test data.">
Expand Down Expand Up @@ -1044,7 +1044,7 @@
smarts,fingerprint,smiles,qsar,qsaratomic,qsarbond,
qsarmolecular,qsarionpot,qsarprotein,pdb,pcore,inchi,
structgen,libiomd,libiocml,formula,render,extra,sdg,
ioformats,log4j"/>
ioformats,log4j,smsd"/>
</target>

<target id="limitations" name="limitations" depends="noJunit, dist-all"
Expand Down
12 changes: 12 additions & 0 deletions doc/refs/cheminf.bibx
View file
Expand Up @@ -990,4 +990,16 @@ Method </bibtex:title>
</bibtex:article>
</bibtex:entry>

<bibtex:entry id="SMSD2009">
<bibtex:article>
<bibtex:author>Rahman, S.A. and Bashton, M. and Holliday, G.L. and Schrader, R. and Thornton, J.M. </bibtex:author>
<bibtex:title>Small Molecule Subgraph Detector (SMSD) Toolkit</bibtex:title>
<bibtex:journal>Journal of Cheminformatics</bibtex:journal>
<bibtex:year>2009</bibtex:year>
<bibtex:volume>1</bibtex:volume>
<bibtex:pages>12</bibtex:pages>
</bibtex:article>
</bibtex:entry>


</bibtex:file>
2 changes: 2 additions & 0 deletions javadoc.xml
View file
Expand Up @@ -146,6 +146,7 @@
<antcall target="doccheck-module"><param name="module" value="valencycheck"/></antcall>
<antcall target="doccheck-module"><param name="module" value="charges"/></antcall>
<antcall target="doccheck-module"><param name="module" value="diff"/></antcall>
<antcall target="doccheck-module"><param name="module" value="smsd"/></antcall>
</target>

<target name="check-doccheck">
Expand Down Expand Up @@ -209,6 +210,7 @@
<antcall target="ojdcheck-module"><param name="module" value="valencycheck"/></antcall>
<antcall target="ojdcheck-module"><param name="module" value="charges"/></antcall>
<antcall target="ojdcheck-module"><param name="module" value="diff"/></antcall>
<antcall target="ojdcheck-module"><param name="module" value="smsd"/></antcall>
</target>

<target name="ojdcheck-module">
Expand Down
3 changes: 3 additions & 0 deletions manifest.mf
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@@ -0,0 +1,3 @@
Manifest-Version: 1.0
X-COMMENT: Main-Class will be added automatically by build

2 changes: 2 additions & 0 deletions pmd-migrating.xml
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Expand Up @@ -55,6 +55,7 @@
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="valencycheck"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="charges"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="diff"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="smsd"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="migrating-qm"/><param name="module" value="qm"/></antcall>
<!-- the test modules -->
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-core"/></antcall>
Expand All @@ -79,6 +80,7 @@
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-qsarprotein"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-diff"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-qm"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="migrating"/><param name="module" value="test-smsd"/></antcall>
</target>

<target id="test-module" name="test-module"
Expand Down
2 changes: 2 additions & 0 deletions pmd-unused.xml
View file
Expand Up @@ -56,6 +56,7 @@
<antcall target="test-module"><param name="module" value="charges"/></antcall>
<antcall target="test-module"><param name="module" value="diff"/></antcall>
<antcall target="test-module"><param name="module" value="qm"/></antcall>
<antcall target="test-module"><param name="module" value="smsd"/></antcall>
<!-- the test modules -->
<antcall target="test-module"><param name="module" value="test-core"/></antcall>
<antcall target="test-module"><param name="module" value="test-interfaces"/></antcall>
Expand All @@ -79,6 +80,7 @@
<antcall target="test-module"><param name="module" value="test-qsarprotein"/></antcall>
<antcall target="test-module"><param name="module" value="test-diff"/></antcall>
<antcall target="test-module"><param name="module" value="test-qm"/></antcall>
<antcall target="test-module"><param name="module" value="test-smsd"/></antcall>
</target>

<target id="test-module" name="test-module"
Expand Down
2 changes: 2 additions & 0 deletions pmd.xml
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Expand Up @@ -63,6 +63,7 @@
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="valencycheck"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="charges"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="diff"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="smsd"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom-qm"/><param name="module" value="qm"/></antcall>
<!-- the test modules -->
<antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-core"/></antcall>
Expand All @@ -87,6 +88,7 @@
<antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-charges"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-diff"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-qm"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-smsd"/></antcall>
<antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-log4j"/></antcall>
</target>

Expand Down
8 changes: 8 additions & 0 deletions src/META-INF/smsd.cdkdepends
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cdk-annotation.jar
cdk-interfaces.jar
cdk-core.jar
cdk-standard.jar
cdk-data.jar
cdk-io.jar
cdk-sdg.jar
cdk-smiles.jar
2 changes: 2 additions & 0 deletions src/META-INF/smsd.libdepends
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vecmath1.2-1.14.jar
commons-cli-1.0.jar
13 changes: 13 additions & 0 deletions src/META-INF/test-smsd.cdkdepends
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cdk-annotation.jar
cdk-interfaces.jar
cdk-core.jar
cdk-standard.jar
cdk-data.jar
cdk-smsd.jar
cdk-extra.jar
cdk-test.jar
cdk-smiles.jar
cdk-valencycheck.jar
cdk-io.jar
cdk-isomorphism.jar
cdk-testdata.jar
1 change: 1 addition & 0 deletions src/META-INF/test-smsd.devellibdepends
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junit-4.5.jar
4 changes: 4 additions & 0 deletions src/META-INF/test-smsd.libdepends
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vecmath1.2-1.14.jar
commons-cli-1.0.jar
log4j.jar
jgrapht-0.6.0.jar

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