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Code Log


Commit Date  
[a1e1f1] by Egon Willighagen Egon Willighagen

Added JavaDoc testing to the QA task; removed module-uptodate which checked if the module was already compiled causing the target to be skipped

2010-05-14 12:01:31 Tree
[42b64e] by Stefan Kuhn Stefan Kuhn , pushed by Rajarshi Guha Rajarshi Guha

I made sure the MDLV2000Reader considers 0,0,0 coordinates in files with a single atom as 2d and 3d coordinates. The MDLReader does not handle the 0,0,0 case explicitly, so I just added a test for 2d. It might be better to have uniforma handling, but I will file a bug report for that.

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-12 13:50:16 Tree
[6ff55b] by Stefan Kuhn Stefan Kuhn , pushed by Rajarshi Guha Rajarshi Guha

The RXNReaders/Writers now all handle Atom-Atom-Mappings. This was only done in the MDLRXNReader till now

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-12 13:50:13 Tree
[6b787c] by Stefan Kuhn Stefan Kuhn , pushed by Rajarshi Guha Rajarshi Guha

Atom-Atom-Mapping is now read and written in MDL files. Note the reading until now was into ID field, which is not in line with description of ID field in ChemObject (Returns the identifier (ID) of this object). Also added tests for MDLWriter/Reader/2000Reader.

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-12 13:50:11 Tree
[d6d6ab] by mark_rynbeek mark_rynbeek , pushed by Rajarshi Guha Rajarshi Guha

Flexibility for ring start angles.

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-12 13:50:09 Tree
[353f93] by Stefan Kuhn Stefan Kuhn , pushed by Rajarshi Guha Rajarshi Guha

more mdl reader writer tests

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-12 13:50:08 Tree
[3b974e] by Stefan Kuhn Stefan Kuhn , pushed by Rajarshi Guha Rajarshi Guha

Revert "Additional constant"

This reverts commit 856197c02328369333f0442d664a02f33a7175bf.
the move arrows are no longer needed, mouse pointer is changed
the move arrows are no longer needed, mouse pointer is changed

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-12 13:50:05 Tree
[c4ea1d] by Stefan Kuhn Stefan Kuhn , pushed by Rajarshi Guha Rajarshi Guha

Added a test case for short line mol files. Patch by S.Kuhn, reworked by M.Rijnbeek.

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-12 13:50:04 Tree
[e36983] by Stefan Kuhn Stefan Kuhn , pushed by Rajarshi Guha Rajarshi Guha

MDL reading and writing UP_OR_DOWN

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-12 13:50:02 Tree
[fd1e57] by Egon Willighagen Egon Willighagen

Removal of references to removed R-CDK bridge

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-11 12:45:54 Tree
[5733da] by Rajarshi Guha Rajarshi Guha , pushed by Egon Willighagen Egon Willighagen

Removed the R-based model package and associated jar files and test code

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-05-11 12:45:38 Tree
[fcd762] by Egon Willighagen Egon Willighagen

Removed DocCheck from Eclipse' Build Path

2010-05-11 11:37:07 Tree
[b34423] by Egon Willighagen Egon Willighagen , pushed by Rajarshi Guha Rajarshi Guha

Removed obsolete castings, or replaced by more general ones

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

2010-04-29 18:11:13 Tree
[eebdb3] by Syed Asad Rahman Syed Asad Rahman

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

2010-04-26 11:55:31 Tree
[82b9fa] by Syed Asad Rahman Syed Asad Rahman

added CDKRMapHandlerTest

2010-04-26 11:50:50 Tree
[bb7bcb] by Syed Asad Rahman Syed Asad Rahman

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

2010-04-26 11:49:15 Tree
[10edb7] by Syed Asad Rahman Syed Asad Rahman , pushed by Egon Willighagen Egon Willighagen

The big SMSD patch.

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

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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

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

added more docs

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

added more docs

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

added more docs

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

commit de4c20898a6c81a43687fb421a4b718fb8306d65
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 25 00:39:13 2009 +0000

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

commit 713fc67a729d309e8ff6465c2cb5230607662299
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 25 00:30:52 2009 +0000

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

commit 9cbb2323dd6b16105c7f17dd246b0e2aee036d12
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 25 00:28:20 2009 +0000

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

commit 12b215fa6d162403e67cd8398c3b6d8227c81b61
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 24 19:38:24 2009 +0000

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

commit 21541a0eb8113656099e259b57826b4c95739b17
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 24 19:33:02 2009 +0000

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

commit 7e5b828fccb05fd86e9de41ea5d91e0b44c06cf3
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 24 19:32:47 2009 +0000

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

commit f07545c0c1640a25beeb80d5e83f187f3bedf538
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 24 19:30:16 2009 +0000

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

commit 5e3eb70efbe432337a6ce65ecca1eafbcc76793a
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 24 19:28:06 2009 +0000

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

commit 945202cfcf1304f3aa2a4544565a282f84a0a775
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 24 19:23:41 2009 +0000

test fixed for SMSD algorithm enum Signed-off-by: asad <asad@ebi.ac.uk>

commit f3d8180351cdb3b2f8343136ec4ea074080aaac3
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 24 19:23:10 2009 +0000

SMSD algorithm enum introduced Signed-off-by: asad <asad@ebi.ac.uk>

commit 037c9bfcd327b0c1ab71852a23a9ef765a0b9eb8
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 23 02:31:10 2009 +0000

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

commit 610cfd6906d95affe1e8d7bf126a2e74e7b61759
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 23 02:29:47 2009 +0000

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

commit df8ad04d0e8e74b408c9fd111b0eff3fa30a2b5f
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 23 02:25:09 2009 +0000

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

commit 0581d1366013132f807094ebf73cc696a3d40773
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 23 02:17:27 2009 +0000

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

commit e0a894c01978f5f18f92bcebc7c1852f7fae78b3
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 23 02:13:44 2009 +0000

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

commit 724add1f564cbce50c2e054fd7df242877aa82bd
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 23 01:57:45 2009 +0000

made McGregor modular, still more to do Signed-off-by: asad <asad@ebi.ac.uk>

commit 5f4786b9e2dad1dc995e792fd1e5bcc8249be026
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 17:59:27 2009 +0000

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

commit f9d4a7b1f7917568e01a13ebdbf764498aa0ea6a
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 17:54:23 2009 +0000

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

commit 8c4ed7407daefc076b94732fcd0ec625eff4e2cb
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 17:27:47 2009 +0000

Added CDK test cases as in UIT Test cases Signed-off-by: asad <asad@ebi.ac.uk>

commit 922d17b603e2f5984ae2eb0eba5f2bce09b42c30
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 17:27:16 2009 +0000

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

commit 0c37e00282033d3173fa7c871734dcaf2e204b2f
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 15:43:58 2009 +0000

Added CDK MCS UIT test cases Signed-off-by: asad <asad@ebi.ac.uk>

commit d88577912b60f47d0f3c30cdb317cf886b31f847
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 15:03:17 2009 +0000

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

commit 9554560b64874ee8880bd4da5088efd7f8599287
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 10:20:02 2009 +0000

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

commit d7ac02321da70631c22f447d7e881a43e39c9120
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 10:19:43 2009 +0000

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

commit 1af2e5833813f346668f0b5f243d3edc7eadc770
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 10:06:21 2009 +0000

PMD improvement on Mcgregor and Chemfilter Signed-off-by: asad <asad@ebi.ac.uk>

commit 3168c784800e719f9eb6cbd8943fdf20c33da5b9
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 09:30:26 2009 +0000

PMD improvement on Mcgregor and Chemfilter Signed-off-by: asad <asad@ebi.ac.uk>

commit 589aaca290666c8720f143a60aaada7150c22b9e
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 00:16:52 2009 +0000

SMSD example code added in the doc Signed-off-by: asad <asad@ebi.ac.uk>

commit 4f0244339d7df6a95df78f50fa585240d1789285
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 22 00:03:24 2009 +0000

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

commit e8f1b1f08285a277b694a50b339afa1f54047ab7
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 23:59:35 2009 +0000

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

commit 69db14f1a37520cbee0f36812257a9a4775abbc8
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 23:43:27 2009 +0000

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

commit 688795645e805a7d58d842e8d5c6ddb098860801
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 23:01:56 2009 +0000

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

commit f90b1725b0a613f4fac2c5ad3ad6a28af736f7d9
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 22:51:00 2009 +0000

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

commit f2fb3abed27a1fbc325aaa05f209732e290455ad
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 22:48:29 2009 +0000

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

commit 964c745a8fdf579155c037dd02efd211c6083bd8
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 20:33:21 2009 +0000

is stereo fixed and PMD improvement Signed-off-by: asad <asad@ebi.ac.uk>

commit 46e82b4625d8099312241e43be3e2905e141a495
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 20:15:07 2009 +0000

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

commit fdd4ba0aa7f2dd3f1e9ebc19501ba111bcbab364
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 19:53:21 2009 +0000

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

commit 6fbcbe226fbffb7195e12c60c965a93c9a2c6023
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 19:13:00 2009 +0000

return type fixed, comments Signed-off-by: asad <asad@ebi.ac.uk>

commit 4c54e4e1925f11a2d5e1a42490ac3d28f8404c1b
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 18:49:53 2009 +0000

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

commit de3ab92d91bd63e6457bd7f46205fde733a9d0df
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 18:46:16 2009 +0000

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

commit b4aa3f846a5c05efc3ff423e353ee62c73800193
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 17:56:24 2009 +0000

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

commit acd28f3df9a6a27521a7979c1c9e88009e735c8b
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 09:40:49 2009 +0000

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

commit d7c3715759f624fd5aa50208930898707655a248
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 00:51:44 2009 +0000

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

commit 32ce4a6543cf6c2a64a7285b0c3e88d77c9e25b6
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 00:49:35 2009 +0000

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

commit d82ea75128113f7f0179c459e5cfb5de34fa3730
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 21 00:49:17 2009 +0000

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

commit 3437593127186aa593558caeba31cee8bf2a1072
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 18:47:04 2009 +0000

PMD improvement, expected max violation 100, reduced from 800 Signed-off-by: asad <asad@ebi.ac.uk>

commit 5d805f87a168bb0c9e13d88be4bdfab10cbc0697
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 16:53:24 2009 +0000

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

commit 94bd21f9fa58155e2083997657456b6e62d17b5a
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 16:30:34 2009 +0000

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

commit 5b0873d752843d899d5b5aa08820bc53e939dafa
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 15:47:05 2009 +0000

Fixed SMSD Test cases PMD improvement Signed-off-by: asad <asad@ebi.ac.uk>

commit 0d95ce2e3ecc0cad1b1975f4169b71bcffbfd675
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 15:46:45 2009 +0000

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

commit a51d354ed7d1b738611825f5848e9786847cb3b3
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 10:28:49 2009 +0000

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

commit c450d1938e0c264fd5811861051f7d5c6bb6ebe7
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 10:06:45 2009 +0000

@TestClass("org.openscience.cdk.smsd.algorithm.vflib.VFLibTest") Signed-off-by: asad <asad@ebi.ac.uk>

commit 05832fa86a10bef763c1164c19367327ca1d4ae8
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 10:05:01 2009 +0000

@TestClass("org.openscience.cdk.smsd.algorithm.vflib.VFLibTest") Signed-off-by: asad <asad@ebi.ac.uk>

commit 352c53412f4a4bd614c8ec28309e73cc0518f93f
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 01:53:24 2009 +0000

2X speed improvement Signed-off-by: asad <asad@ebi.ac.uk>

commit 284387914ecd0475e680ed036e69bbfcb0cfad86
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 01:49:59 2009 +0000

2X speed improvement Signed-off-by: asad <asad@ebi.ac.uk>

commit af83a7097de8dd2514b1f49a38fe01d43f94b5d8
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 01:20:35 2009 +0000

SMSD refactoring and Speed optimization Signed-off-by: asad <asad@ebi.ac.uk>

commit 75bbb76e6a7110e8f52aa26f0dbec8ed383650bb
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 01:20:22 2009 +0000

SMSD refactoring and Speed optimization Signed-off-by: asad <asad@ebi.ac.uk>

commit 267aaa3aeaf3c0bd6e92ebea2dd0c290e30ef9ba
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 00:14:21 2009 +0000

changed SMSD Test for VFLib Signed-off-by: asad <asad@ebi.ac.uk>

commit c47922ab95c67df8db219a91f3cbf9c6e1183cf0
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 20 00:13:51 2009 +0000

Refactored SMSD, beautify the code Signed-off-by: asad <asad@ebi.ac.uk>

commit 41c7453d9e955808614f0e4726abdb021d638cbe
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 22:36:40 2009 +0000

removed unwanted space, beautify the code Signed-off-by: asad <asad@ebi.ac.uk>

commit 147d221e41e1e1467621a6bd69308afa665c780f
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 22:31:15 2009 +0000

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

commit 2a271d3ef631d83711407c97ee49755608becebe
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 22:28:21 2009 +0000

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

commit 29ec5e5337148275a424b7c798c79266aedee0ca
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 22:27:40 2009 +0000

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

commit 526c2f91e17bbd0e50e4b56401680b54cce5d2dc
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 22:04:14 2009 +0000

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

commit 3e2f5470b609876aff16f0ef2f40a775b03cfcfb
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 22:03:41 2009 +0000

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

commit f2078ca217df9929a62f77c4ffbac693f5a1cf2a
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 10:22:21 2009 +0000

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

commit fb3cf0e5b5bf9bebf2b106fbe10e60fedb7cc042
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 10:21:33 2009 +0000

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

commit a48578ad4961c424190d8807df23f4397ce6f21b
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 10:20:05 2009 +0000

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

commit e3eb7173f4d5e2c935d0c92e3be98b25e4f8757f
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 04:02:52 2009 +0000

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

commit bae11ae3b5e07ad3bab0ad8770750220111535f0
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 03:59:15 2009 +0000

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

commit bd03ba2ec8e853fd27120ebeca03af1b0116e583
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 03:52:55 2009 +0000

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

commit 97d19767e4cbcffdd6d31e236cf5cb4225edefa9
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 03:49:33 2009 +0000

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

commit c4bf68ff1585b9c2d3ab420c5062487b84bba5bb
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 03:44:57 2009 +0000

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

commit 2bf8f1de3a3a360d8f1df5b99dcaec3418b7cf0b
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 03:39:29 2009 +0000

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

commit 65898babc03ef95e7bac3785a50d72ec50b6535d
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 03:10:20 2009 +0000

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

commit f230b66412f15bdf61bb85b1d97938511431061a
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 03:08:30 2009 +0000

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

commit 8d2fa28882f943673bce18ee87bc73a74e08a83e
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 03:03:01 2009 +0000

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

commit dbe31253e270bc814d0f78c71462a1ece04c646c
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 02:44:40 2009 +0000

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

commit 4d25e2a3a6cf6f9b4b75116746a2d1023bc331bb
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 19 02:27:19 2009 +0000

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

commit fe926e6155f7d056cb6e7d4d320d44605b9e1dd4
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 23:25:06 2009 +0000

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

commit 776427b38d0eb3e232428e9d3bb398ffc17d701d
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 23:22:41 2009 +0000

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

commit 32cd88a3553efed7ddf4b6508044414c912866be
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 22:24:16 2009 +0000

PMD Vector to ArrayList Signed-off-by: asad <asad@ebi.ac.uk>

commit 33ef03ee9e6a86d9a86816b82a50fe4748083f7a
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 22:18:01 2009 +0000

PMD Vector to ArrayList Signed-off-by: asad <asad@ebi.ac.uk>

commit 0861c1bc41291246409bf5b28b6a0e5838c6a8dd
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 21:45:38 2009 +0000

Mcgregor Vector to ArrayList Signed-off-by: asad <asad@ebi.ac.uk>

commit 9aafa6dbd9999100049e83b8b9b0426ddbfcf730
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 21:44:03 2009 +0000

Mcgregor Vector to ArrayList Signed-off-by: asad <asad@ebi.ac.uk>

commit cfd1e4c15d4e3889b09fd2833a5df64f0fd15a7c
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 21:18:02 2009 +0000

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

commit b5d8616139673d2f32682402f946c05899f20b40
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 21:15:08 2009 +0000

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

commit 71aac6da4fa85d5300b73a1914c0f3ee7e14a7fb
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 21:14:06 2009 +0000

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

commit 9012a4c045dfc2d8b6f0b1b620cd229dec152367
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 20:11:15 2009 +0000

PMD fix for VFlib thread safe Signed-off-by: asad <asad@ebi.ac.uk>

commit 9bc2c8290c868db59abf1e895cedb189d5ca732e
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 20:09:47 2009 +0000

PMD fix for VFlib thread safe Signed-off-by: asad <asad@ebi.ac.uk>

commit f4b0dcf98b4ffe8073c89cfc55586133530391ae
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 20:08:38 2009 +0000

PMD fix for VFlib thread safe Signed-off-by: asad <asad@ebi.ac.uk>

commit 665680d07fc6920053fc894a1ef486c8193b8aa9
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 18:32:00 2009 +0000

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

commit 9455221b1041f801cb15724dd9d03b7edfe326d8
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 18:18:44 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit aeeadc3f147f65ce848601d97533f3361d21bf97
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 18:05:17 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 183ba74df553907690c11fdd487f39786a583514
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 18:02:56 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 2cdbbd91f0645b6dd21e1c3ccdd988f2404ec3a9
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:51:30 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 4ec4983734e17d8e9537f692d05bb05d30b3c115
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:44:25 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 504b0667d260519924c09d48e627e44308a12f4b
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:42:50 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 4a85e7142ca83f85f8358298fc60f2e1259a7e32
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:40:10 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 69934260e25d8efbc1ad6103a98909df9a9d3162
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:35:19 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 9be000a708b8a3f932dfc2de6e7756f2278195d6
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:34:12 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit d46c0bc898f49c8ad2abf24e04f1445787eca89c
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:33:12 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 4d81fd77296e0a0a5175cd1c89a718fd65ec3724
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:31:41 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 350145c1db1b63fca2a309ca4aa5209edff559bf
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:29:17 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit e1fb2b922998d5131c9bd25d0dc2209dabb8752a
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:28:38 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit cccdade729471663aae435b35b071d06ac912c0b
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:28:00 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit a4980a63bd240b6f2e6d02751e6956a13aee8ce9
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:25:02 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 5054948ea032d04896523cc280ad913810a8770e
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:23:29 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit cba554c6ac770f8f951fc5160e139ef528890c64
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:21:52 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit bbe717fd7be3bdd50dabd3e2608a6de4724182b9
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:21:09 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 901491e717c0136808d6e7e5048c8064ff87b081
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:20:19 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 054a72f02117107151cbeba3ceb12be560ca2555
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:19:41 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 3cf6fc8cd8d5d56e7c827010f4b58340773b2dff
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:19:04 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 4035ced86bb818d2146a668e7977823ed56bfe47
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:15:39 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit 9f4478f425becf10cfbe81bdcd814b9efeef58de
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 17:15:05 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit e80781e092c248732d792f49ecc7469e31f8db10
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 16:59:08 2009 +0000

PMD fix for GenerateCompatibilityGraph Signed-off-by: asad <asad@ebi.ac.uk>

commit ad28f17b410843be33b22527ffdd642ea38850f9
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 09:37:16 2009 +0000

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

commit ab0fd83647064fcca4b065f0527d02ceddb32b7b
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 09:33:57 2009 +0000

smsd module tag added Signed-off-by: asad <asad@ebi.ac.uk>

commit dc9741fb9c59473bdd6c824f97c32de8bb4f41fc
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 09:31:36 2009 +0000

smsd module tag added Signed-off-by: asad <asad@ebi.ac.uk>

commit 0ac2247fbe6a6796cd266791903a27a20b8bf09f
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date: Tue Nov 17 21:33:41 2009 +0100

Added new test class to module test

commit dfb25099bd0d0a3ad09572fcc3e3f2e8811a2727
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 18 09:19:32 2009 +0000

smsd module tag added Signed-off-by: asad <asad@ebi.ac.uk>

commit 0c0ee0af5f342c727e2b7bc359d661b2f061fbbe
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 17 10:23:34 2009 +0000

improved CDK doc and beautify it Signed-off-by: asad <asad@ebi.ac.uk>

commit c1fd83e81ad684ef754e0e829a73640871ebe382
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 17 10:07:43 2009 +0000

improved CDK doc and beautify it Signed-off-by: asad <asad@ebi.ac.uk>

commit 7dfcf20d2707e0fd29ae8b6a39fd547e07487149
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 17 09:59:27 2009 +0000

fixed non english codes Signed-off-by: asad <asad@ebi.ac.uk>

commit 394bb96a024e9c8b5ed936c5614ded86dc6ba985
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 17 09:55:07 2009 +0000

fixed non english codes Signed-off-by: asad <asad@ebi.ac.uk>

commit f51916301cbd2273c7a35450fe42848e3fce426c
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 21:03:02 2009 +0000

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

commit 940b21008a2c701a3cb5e5b0199fbec5fdc31db2
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 14:08:58 2009 +0000

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

commit 9317ac99a7be4afa686ad660c816bb4d548471df
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 14:07:21 2009 +0000

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

commit d5ac52fdd8f19ac69d355d4e98943f68d4dafc51
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 13:49:31 2009 +0000

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

commit ad9c5c1f1b352b7dfdc1426075dbd47bdc2366e4
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 13:42:09 2009 +0000

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

commit f5be3c2dd55e5a94e9f42215e48444141b0f6125
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 13:37:43 2009 +0000

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

commit e0468fff7cc0a084e449336cbd5ef7bc11cbb645
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 13:31:08 2009 +0000

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

commit 6d097294eac21562e660f321e6176fca1183a310
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 13:21:29 2009 +0000

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

commit b2c9fba19c1b5bc06ff36bdad41fcba6667b1167
Author: asad <asad@ebi.ac.uk>
Date: Mon Nov 16 13:19:04 2009 +0000

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

commit c7ba0fed7d4e0442ae9bf20da40184084bc4d63d
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 15 21:52:51 2009 +0000

removed unsed method or commented it, refactored some classes as per PMD reports Signed-off-by: asad <asad@ebi.ac.uk>

commit 0cef86f3c4979d8deaefccdefe5f7663f3642fe5
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 15 21:01:19 2009 +0000

removed unsed method or commented it, refactored some classes as per PMD reports Signed-off-by: asad <asad@ebi.ac.uk>

commit ce50ccd56f772802c18871c11653fac4112d0552
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 15 20:14:05 2009 +0000

removed unsed method or commented it, refactored some classes as per PMD reports Signed-off-by: asad <asad@ebi.ac.uk>

commit 635a8c307555f3e256395b1ed76ee5a78c19c4d5
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 15 19:13:26 2009 +0000

removed unsed method or commented it, refactored some classes as per PMD reports Signed-off-by: asad <asad@ebi.ac.uk>

commit 99c66af633dc42c5baf319a360ddd1ed8a82b03c
Author: asad <asad@ebi.ac.uk>
Date: Sun Nov 15 00:01:50 2009 +0000

refactored some classes as per PMD reports Signed-off-by: asad <asad@ebi.ac.uk>

commit b5970cdaff3a2a958af2253a1d44a1d6f0f1ffac
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 23:51:40 2009 +0000

refactored some classes as per PMD reports Signed-off-by: asad <asad@ebi.ac.uk>

commit ea3941923c2dd1bc6c6d49d1cbc76a49a9d56536
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 18:21:15 2009 +0000

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

commit 72a4aa992cb33efe93557274a5ae2f116f1f68e6
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 18:08:42 2009 +0000

removed Symbol feild from VFAtomMatcher Signed-off-by: asad <asad@ebi.ac.uk>

commit 582edf5ec83cfebeccdc1ecb5c2e8a042f476de1
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 17:09:08 2009 +0000

Added VFLib Test cases Signed-off-by: asad <asad@ebi.ac.uk>

commit c82aae7aedc6314344d89680146eff574da5f8a8
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 16:22:02 2009 +0000

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

commit d3d392b08963e4e609de5f5b90e54427f7e6c0f3
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 16:05:44 2009 +0000

remaned SubStructureFactory as SMSD, removed unsed classes and refactoring classes Signed-off-by: asad <asad@ebi.ac.uk>

commit 9aeef90478a2a0f4cdfab67aeb359cf62a5a24c3
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 15:50:51 2009 +0000

refactoring based on PMD results

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

commit 4afe7020d1c910efbc93ec35a59942197e0a2335
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 15:48:23 2009 +0000

refactoring based on PMD results

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

commit b0880cb6e9cd6a0536e570dc0f7ef086a6c34dd4
Author: Rajarshi Guha <rajarshi.guha@gmail.com>
Date: Sat Nov 14 09:37:59 2009 -0500

Refactored so that the custom atom and bond matchers for the vflib implementation are removed and usage is replaced with IQueryAtom and IQueryBond

commit 66340008a18190b074b851ea4de5e07650091821
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 14:44:33 2009 +0000

refactoring based on PMD results

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

commit 9d55f451586ac0f383435b5813eb42aa07c0799b
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 14:40:23 2009 +0000

refactoring based on PMD results

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

commit 35a1778da535f43b810a42ca89eb3be7f2e2ce18
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 13:54:05 2009 +0000

refactoring based on PMD results

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

commit 9166f8df4bcab0f19c49d2192035db357bb4a7e6
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 13:35:01 2009 +0000

remove EBIMCSCalculator

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

commit b10665d7d5a4f178a33f5eb6932ecaf0558a28f5
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 13:34:28 2009 +0000

point EBIMCSCalculator to SubStructureFactory

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

commit 6bb0f4c9cf7b33f0a367d080f7862bc6c68a0415
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 14 13:23:23 2009 +0000

MCSPlus code cleaning

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

commit 0269dadeb3802527d3dbefc1e54cb9cd30de80cf
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 13 17:31:47 2009 +0000

SMSD formatting

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

commit e65a9ee88823f93b7f639f2b1d386557d2e90b82
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 13 17:27:11 2009 +0000

SMSD formatting

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

commit 9e8a1578ad1e0dfaadf937f5cae6aa64ececc3f7
Author: Rajarshi Guha <rajarshi.guha@gmail.com>
Date: Fri Nov 13 08:32:33 2009 -0500

Added similarity methods to the similarity package so that we can drop the EBI Similarity class (even though it is not actually used in the other SMSD classes)

commit e7881cee638eebbe7c0a5f121cbc7290317b1481
Author: asad <asad@ebi.ac.uk>
Date: Fri Nov 13 17:11:38 2009 +0000

EBIException to CDKException

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

commit 9beeee0a0a3449a331b8ef2a14a02a5d049e204f
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date: Thu Nov 12 23:52:21 2009 +0100

Moved to the CoverageAnnotationTest approach

commit 1775699443e00a2a6d79533f9c086044d80ad073
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 12 10:44:45 2009 +0000

improved the java doc in the class

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

commit 39b3a8b059d0fbfea81ad10bf4ae53ca1975d070
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 12 10:38:20 2009 +0000

improved the java doc in the class

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

commit c0b91bc978ac62199c385721331ec1ce7002c9b0
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date: Thu Nov 12 00:14:25 2009 +0100

Hooked up quality control for the new module

commit c46c466ae75c09d3feacb3aa08dffe84a25ee3c6
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date: Thu Nov 12 00:11:36 2009 +0100

Set up a smsd test module

commit d10a4fa28f77a892b8343a0b8a6f3341016e500a
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date: Wed Nov 11 23:56:02 2009 +0100

Moved many more classes into the smsd module, which now compiles

commit 13752d8fa928d6a0721007d8edfb0c6dbc3256f8
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date: Wed Nov 11 21:45:25 2009 +0100

Moved all classes into a smsd module.

* added @cdk.module tags
* moved the copyright to above the 'package' statement here and there

commit a7a420e560c0df9af9bfe99d416c949f9fe30005
Author: Egon Willighagen <egonw@users.sourceforge.net>
Date: Wed Nov 11 21:45:19 2009 +0100

Require Java6

commit 143a8fb8a2383e4e7ccc9fe56ab3fb617e273a5b
Author: asad <asad@ebi.ac.uk>
Date: Wed Nov 11 00:14:45 2009 +0000

SMSD 2009 refer. added

commit 901810c17c790716e3b677f59d0d23ceced6852f
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 10 20:48:23 2009 +0000

SMSD Test cases introduced

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

commit f4afe15b2e0e530fb6d4eb4a4d4c00784df39c7f
Author: asad <asad@ebi.ac.uk>
Date: Tue Nov 10 20:47:46 2009 +0000

MCSPLus BKKCKCF fixed

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

commit b72f07a96e7584d2156c0f66ec01b2686080a6f2
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 7 03:01:05 2009 +0000

is subgraph fixed

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

commit dfba1577e256e5e6331c1f50a5a8bd1b5dbf39c4
Author: asad <asad@ebi.ac.uk>
Date: Sat Nov 7 01:58:26 2009 +0000

fixed license

commit b018dfb57afcfb09393fb3a695aac5d57c692df8
Author: asad <asad@ebi.ac.uk>
Date: Thu Nov 5 15:05:23 2009 +0000

fixed mcsplux index

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

commit 8b752580bfd118e5a38c951e277e0237022d598c
Author: sar <sar@192.168.1.2>
Date: Thu Nov 5 15:03:41 2009 +0000

fixed mcsplux index

commit 594b10ed3c13c3e9dee28ceab1ba3acc7c7c7eb2
Author: sar <sar@192.168.1.2>
Date: Sat Oct 31 09:53:00 2009 +0000

2007-2009 Syed Asad Rahman <asad@ebi.ac.uk>

Added CDK like license

* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/

commit f25c610fb7f2f0c39f433bdfbc78ffdfd27d54ec
Author: sar <sar@192.168.1.2>
Date: Mon Oct 26 22:16:20 2009 +0000

@Copyright (C) 2009 Syed Asad Rahman <asad@ebi.ac.uk> Updated the (C) Signed-off-by: asad

commit ab64ecc19606326db55eb88ffe7fb7ef5ec46699
Author: sar <sar@192.168.1.2>
Date: Mon Oct 26 21:59:35 2009 +0000

SMSD isSubgraph code updated

Signed-off-by: sar <sar@192.168.1.2>

commit 82af8aaf0276e4a447e5c958fbd7f7a8148d9bf7
Author: sar <sar@192.168.1.2>
Date: Mon Oct 26 21:52:34 2009 +0000

Changed Vector<foo> to List<foo> wherever appropriate

commit 8e4851bdcfcfedd868e3ddc2fe980be68d4a1084
Author: Asad <sar@Asad-Mac-2.local>
Date: Mon Oct 26 16:19:58 2009 +0000

added SMSD(Small Molecule Subgraph Detector) toolkit

2010-04-26 10:38:59 Tree
[f17fc8] by Egon Willighagen Egon Willighagen

Merge branch 'cdk-1.2.x'

2010-04-24 18:30:34 Tree
[b5fa3d] by Egon Willighagen Egon Willighagen

Fixed a ClassCastException in a unit test; I messed up (mea culpa)

2010-04-24 16:02:52 Tree
[25427b] by Egon Willighagen Egon Willighagen

Copied code from the DefaultChemObjectBuilder to handle the IBond constructor that takes an IAtom[] which I had forgotten to port to DebugChemObjectBuilder and NoNotificationChemObjectBuilder (fixes a few regressions)

2010-04-24 10:30:06 Tree
[426558] by Egon Willighagen Egon Willighagen

Merge branch 'cdk-1.2.x'

2010-04-24 10:26:50 Tree
[5f3489] by Egon Willighagen Egon Willighagen

Fixed NullPointerExceptions for LonePair's and SingleElectron's constructed with the no-argument constructors

2010-04-24 09:50:21 Tree
[2d4c12] by Egon Willighagen Egon Willighagen

Added missing cloning of single electrons

2010-04-24 09:50:13 Tree
[9672df] by Egon Willighagen Egon Willighagen

Do not try to clone the atom if it does not exist

2010-04-24 09:45:54 Tree
[c20a0e] by Stefan Kuhn Stefan Kuhn , pushed by Egon Willighagen Egon Willighagen

MDL reading and writing valency

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

2010-04-22 18:18:12 Tree
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