Provide the necessary project files for netBeans

Change-Id: I4e288a0a3cfa45c28ffc5ff6fe2b2b3f443dbe4a
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>
Release 1.4.11

Change-Id: Ia11cf99de6f5ba08681aec5f6f80c3d450963e1d
Open for bug fixing

Change-Id: I463c40bb68483c8753cf138b851d31abfa01c488
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>
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- updated outdated links and added the CDK G+ page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
Added a new author

Change-Id: I38cd6ba708f03da9c373e99249b0b66b37a49303
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>
Fixed the same problem as in DefaultChemObjectBuilder (see commit 3d0b0e5f329e9256638ce18e4b5024e2d348474a and 2a2aecc077add716309591e2fae9832dfcfc64cf)

Change-Id: I2c2e7ae356a62fda6dd3001693267bcf988aadec
Signed-off-by: ngn <jeliazkova.nina@gmail.com>