Added a unit test to check for multithreaded usage in PubchemFingerprint. Tests for bug 3510588

Change-Id: I2ee5c46b49846b1072949d9c0c06ec715fad8cb7
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removed to unused imports, one of which causes trouble with free Java systems

Change-Id: Ida389c59ad41b605b4243b557421c88c09cd02e4
Updated PubchemFingperinter to not use static variables. Allows it to be used in multithreaded scenarios

Change-Id: Iaa9481fd1fa5793cb5fe3b449219aeb7958a983d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added the missing cdk-test.jar (patch by Jonty Lawson)

Change-Id: I0408c9e03ace32aea9a7b9c4a7f031b4cc1dc62e
But the test data should be added too

Change-Id: I926c869d94562bb6b086b5556b02359c46abc597
Added testing of the number of double bonds found (fixes #3514176)

Change-Id: I1d2740ce310a767c9fa236be5b602ac64ee9b5d9
Signed-off-by: ngn <jeliazkova.nina@gmail.com>
Double bond orders are not properly assigned when using the SilentCOB

Change-Id: I299374c6ad0bf75f1e97ace99de52cb813e5c221
Signed-off-by: ngn <jeliazkova.nina@gmail.com>
Fixed bond order assignment when using the SilentCOB

Change-Id: Ic6427e6399d645b600f5e6f1c0f438335cd91298
Signed-off-by: ngn <jeliazkova.nina@gmail.com>
Bumped version number to 1.4.9

Change-Id: I524b508f28a5ca6ee1a97dd4210c511fe1b40dbb
Open for bug fixing

Change-Id: If0050db9e515a91feabb927b1dd091561e22f4c8
ForceFieldConfigurator checkForceFieldType correction

Change-Id: I665d38273b6381f775ddf35df22af2b6b71abc59
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updates with the SMARTS specs, among others to fix 'Sc' parsing (patch by Dazhi Jiao; fixes #2786624)

Change-Id: I34ad117aef815c89978223f7625c5b6558e2d62d

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Fixes recursion errors (patch by Dazhi Jiao)

Change-Id: I65f2afcbc85aa72041f3af8ed75819d644090a8a

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Fixed the tests to have the right match counts (patch by Dazhi Jiao)

Change-Id: Ib8e6b9f11aeee2623abe76a6ad616a8250b3af44

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Added test case for bug 3513954, OOM in equivalent class partitioner

Change-Id: Idc905aa1a60b3c8d58a3b675ec66f111422ae525
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Upgraded to JavaCC 5.0

Change-Id: I77b8fb2d3433f3bdb9691f98f5d8f188d6a91671

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Patch to report candidate constructors when failing to instantiate a class because of an incorrect number of passed parameters. (fixes #2987186)

Example output:

No constructor found for NNAtom with the given number of parameters.
Candidates are: NNAtom(), NNAtom(String), NNAtom(IElement),
NNAtom(String, Point3d), NNAtom(String, Point2d)

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Added a unit test to see if we get suggestions

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Added code to make suggestions to the silent builder too

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Updated TPSA descriptor to properly cast to IRing rather than different Ring implementations. Added unit test

Change-Id: I613cdf7728b2f9f9f9ece9a2742104d0c012fa6b
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>