Normalised all getFlag and setFlag usages to use the CDKConstants

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Converted flags from incremental integers to bit masks

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Implemented new flag storage on IChemObject implementations. Flags are now stored on a single numeric value (currently a short) and flags are accessed/mutated via bit shifting of this value. This implementation provides space saving over using a boolean array however getFlags() and setFlags() now have a overhead due to conversion from the array to the numeric value. Usage however indicates the singular setFlag/getFlag is used >1000 times where as the setFlags/getFlags is used ~50.

Also removing debug statement from AbstractChemObjectTest

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
A go at @cdk.ioopionts

Change-Id: I2bc951328de7bbb551271b24a59b71db91ba6c5c
Added the dependencies to the taglet so that it can use reflection to extract the IO settings synamically; thanx to Stefan Ferstl, see http://stackoverflow.com/a/11819202/217943

Change-Id: I336b5e2158e6ed1c646779d35362446a1c188489
Merged the toString(Tag) and expand(Tag) methods, and complete all output

Change-Id: I25383304ea41e5232c1cc428f759a67f26e22101
Added @cdk.iooptions to all IO classes

Change-Id: I7e81241212d1b734fb6df9cdf460ba0cb5c76b6a
- StringBuilder instead of buffer - Separated the determination of the class name to a method - Separated the processing of the IOSetting to a method - Added default value as an extra column in the output - Added table headers for the output - Added closing </dd> - Replaced "/" with "File.Separator" - Added logging statements for null settings/no default constructors - Made toString(Tag[]) return empty string - Added @override/@inheritDoc (not really need)

Change-Id: Id7f039669c339136eb5d6d7eb0c31a7c88569efd
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
- Added properties for JVM arguments this allows us to switch on/off debugging and stdout via ant. This is useful as it can be seen from the run target debug had been commented out. The properties allow us to explicitly turn off debugging (on by default) - Used properties for junit-test, run-test and run targets - Added jarTestData as a required target before junit-test can be run

Change-Id: I7b94641a6893fa1e3ec1047a1a67b7291b03a6e2
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added output of ITetrahedralChirality to InChI

Change-Id: Ie69b3b3e38790f2ab99f61c11738535dcc1b8cea
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Implemented test for conversion of SMILES with a topological chiral centre.

Change-Id: I7703e9c2ca89baa4f3c55ab8b7b58f465510a12b
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added null check before input close. If the reader was created with a URL the input is never created and invoking '.close()' will throw a null pointer exception
Implementing fix for bugs 3557907 and 3553328 3557907: Previously only the dictRef attribute of bondStereo was supported. This patch adds support for the 'content/text' of the bondStereo element to be set. This patch allows the bondStereo to be added from the charContent when the end of the element is detected. 3553328: Added support for CML files missing atomic number information. As the starting atom is a Hydrogen in the passer if no atomic number is provided the atomic number will default to '1'. This fix checks if the atom 'hasAtomicNumber' before the atom data is stored - if there is no atomic number specified but the symbol has been the atomic number is looked up in the periodic table (as per Atom constructor).

Corrected bug

Signed-off-by: Ralf Stephan <ralf@ark.in-berlin.de>
Added unit tests for two CML bugs - both use the same molecule to test - 3553328: Atoms missing explicit atomic number default to 1. - 3557907: Only support for bond stereo with attribute dictRef

Signed-off-by: Ralf Stephan <ralf@ark.in-berlin.de>
added commons math library Signed-off-by:Syed Asad Rahman <s9asad@gmail.com>

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
added code dependencies for the Shortest path fingerprinter Signed-off-by:Syed Asad Rahman <s9asad@gmail.com>

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
added test case Signed-off-by:Syed Asad Rahman <s9asad@gmail.com>

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
added test case to test module Signed-off-by:Syed Asad Rahman <s9asad@gmail.com>

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
added ShortestPathFingerprinter with recommended changes Signed-off-by:Syed Asad Rahman <s9asad@gmail.com>

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
added ShortestPathFingerprinter with recommended changes Signed-off-by:Syed Asad Rahman <s9asad@gmail.com>

Signed-off-by: John May <john.wilkinsonmay@gmail.com>