Added finally cause to ensure the file is closed
Missing Se.2 atom type and test case

Change-Id: I3e47f8cc35bd7101c53d8146f68f5a3b691ec6ff
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated Gilleain's code to hook in with the other two new selenium atom types

Change-Id: I08649abd4dcf62c6ad23c50222156383360f2ed9
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
[bug:1274] added conditional to ensure that when multiple bond stereo is specified as attributes and characters only one is used. This is achieved by using the existing flag to determine if a stereo bond value has already been provided.

Change-Id: I2a4e64b1df2cbfdc5a3dfe5d8ff9a13c11f94e98
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
[bug:1275] added check to ensure that when String.substring is called the string is long enough
Fixed loading of the right class when reporting possible alternative constructors

Change-Id: I91c1682c8a46dcd520616d381ca365ad2c74dbf4
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed a bug present in many readers: it would not accept a subclass if ChemFile (e.g. NNChemFile) even if ChemFile itself was accepted

Change-Id: Ic8c00d63d9b11ebdda27198588b25293f97c1d86
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Accept that bonds are sometimes unset (and except them to have a SINGLE_OR_DOUBLE flag then), and no longer use IBond.Order ordinals for comparison, but do it the proper way.

Change-Id: I87a20792ae6249bf1f06d57e11e3b44defef2311
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added detection of C.sp2 atom types with SINGLE_OR_DOUBLE bonds

Change-Id: Ia25ce5449e70922ece571c0b02f97ab86ff806a7
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added a unit test for C.sp2 perception with SINGLE_OR_DOUBLE bonds

Change-Id: Ic1de95e700e6d52adc3b89f97dc2caf78d07ddac
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
unit test for bug 1269 (atom... not placed by SDG, causing NPE), remove catch statements, set expected

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

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

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Merged in cdk-1.4.x patches: s/IMolecule/IAtomContainer/ an s/Nonotification/Silent/

Change-Id: I642a9b12b4f90baf9b61f0e33b8157c7de38d20d
Added a missing dependency

Change-Id: I5ff09850deefad62f8e927adced4462ba2c3218e
Fixed a big goof up: 1. IBond.Order.UNSET was not considered; 2. when SINGLE_OR_DOUBLE the type bond order can also be SINGLE, and in fact must be SINGLE or DOUBLE, as the flag name suggests

Change-Id: Ifa960198b15737c3a51e8bee8858ff6d2303262f
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added perception of N.sp2 and N.planar3 when SINGLE_OR_DOUBLE is used

Change-Id: Ib2b045f6801bfd23479d89d148dae7b777067079
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added a field to the bond order enumeration allow access to the numeric value for that order.

Change-Id: I69b108218a127dad9ca73994de76558f977a304d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:
	src/main/org/openscience/cdk/interfaces/IBond.java
Replaced IBond.Order.ordinal() usages with IBond.Order.numeric()

Conflicts:
	src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
	src/test/org/openscience/cdk/smiles/FixBondOrdersToolTest.java

Change-Id: I53a0e74dfbc138e49f7fc85ce6fd226444608f0b