Improved conversion of AtomContainer to CMLMolecule

Tools in the CML library tend to use the XMLContent value (see. [1])
Also ChemAxon MarvinSketch will not import with the bondStereo invalid
(probably a bug) but adding the XML value fixes this.

[1]
http://www.jarvana.com/jarvana/view/org/xml-cml/jumbo/6.0/jumbo-6.0-sour
ces.jar!/org/xmlcml/cml/tools/StereochemistryTool.java?format=ok

Change-Id: I141a43ca9e028b1da7cbf79cd13bf72934638012
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
CML Bond Conversion Test [patch:3530233]

- Added tests for correct wedge/hatch bond conversion
- Added ConvertorTest to libiocml test suite

Change-Id: Ia77be2d00267159ebb24ca3e43d3340914258e15
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Change the getHTML method to return the elements in the Hill System order (bug #3432131).

Change-Id: I0ca3c26a87f9af88de29e2c1a6b339a16b23ddf4
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated a method based on Ninas suggestion to avoid modifiying a atom container when looping over it. This avoids a concurrent modification exception. Also updated some Javadocs

Change-Id: If01762c6cff615d7a25de8b8f9bcee49c41eba16
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added Ninas modifcations to ensure that getting a molecular formula includes implicit hydrogens. Addressed bug 2983334. Also updated a unit test to take into account that H's are being considered

Change-Id: I9881e31c05d0f1bfb965393bd806e562a6158a0e
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:

	src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
Updated the README (fixes #3538451)

- updated outdated links and added the CDK G+ page
- updated the copyright line
- added an example on how to compile an individual module

Change-Id: I8b7232ffb5e2ee0e8804aa1f5bfb1c75aa238358
Update for a patch from cdk-1.4.x: s/NoNotification/Silent/

Change-Id: I0f9758b2abaed48647a314b3775c780ebebbdcce
Added a new author

Change-Id: I38cd6ba708f03da9c373e99249b0b66b37a49303
Added two more recent authors

Change-Id: I689138a7b198a3284d33ac49f1a3adf78e761d57
Added the option to specify element order as a parameter of getHTML()

Change-Id: Id4e37bb3ce2f30971ee3a533ad802ba4fb43e9e0
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Marked the getHillString() method as deprecated, because it is a duplicate of the getString() method.

Change-Id: I5f34a1af70af031d521e6ec75753f87e7040ae41
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Fixed a typo in test name (Whit -> With)

Change-Id: Idb2acc6511f980bfee05f41d797690f91ab8e69b
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Added a unit test for the perception of Co.plus (bug #3529082)

Change-Id: If0ad6e939fd3282fd8ba625bcf5070c9f8ed86a7
Added Co.plus atom type

Test for Co.plus is present in CDKAtomTypeMatcher but the actual type
did not exist in the cdk-atom-types.owl file

Change-Id: I02ce8af5153522d80b66c31d13f15de2a5337749
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated test for the bug fix in commit 37ca43cc4ea0f0a7efaf10edbbe60ef57a44e8ce to include the implicit hydrogens.

Change-Id: Iaef65d9172a333d8848fa844201853c9ee7a9f79

Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
Updated for the bug fix in commit 37ca43cc4ea0f0a7efaf10edbbe60ef57a44e8ce

Change-Id: I5cdf3b4df888084a723cb12fab5d54a21b724792

Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
Added a note about atom types to be perceived before using this class (closes #3513957)

Change-Id: I087e55e4899de389ae927860af4624749fa6ec42

Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
Added proper module assignment for RandomGenerator

Change-Id: If52be69be76f75a56daff782950f3c2b552c5662
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Merged in cdk-1.4.x: s/IMolecule/IAtomContainer/

Change-Id: I4b4f887b61b4fd5a07372a6e40055bdbc4e89cef
Added a missing dependency

Change-Id: I5fdab1a4bcfd260e20edacb386858eb5a3dcbb79

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