Removing print to stdout.
We'll never agree on aromaticty... what model does Sybyl use anyway?

Change-Id: I6ae5b7e4938f376130635322a15a5756ae58db7a

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Detection of out-of-ring planarity due to pi-pi interaction is out of scope of our algorithms right now

Change-Id: Ia7fbe93bd959ea00d919d953507a5f000f3ddd53

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
A NO2 nitrogen is N.pl3 in Sybyl

Change-Id: I53d0203c75dcdbf174e4f0efced823fd79d343b5

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Nitrate oxygens are not O.co2's

Change-Id: Iec167c8b83887e25a9f32e67dd13e793ed4d2254

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Implemented perception of the Sybyl O.co2 atom type

Change-Id: I3002340b5e7c6d2ed54d3fcd292f305ef020b110

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added mappings for Mo

Change-Id: I904d7e87778ef1026689070f01850401897b5678

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added rudimentary detection of the chromium atom types

Change-Id: I4a09a271e6b683b054b71975cb0f8b594597aec1

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added rudimentary detection of the Co.oh atom type

Change-Id: I2379c9a886f731f72c0e4dfeb4d3511334e57291

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
According to me example data, a nitro nitrogen is N.pl3

Change-Id: Iec32f8615e49a484921bc3dfb0f3540780f0c3da

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Strip trailing white space to git can match up the next commit.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Don't use IAtomParities when generating InChIs.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Load ITetrahedralChirality instead of IAtomParity with InChI.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove test from AtomContainerManipulator

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Copy stereo elements correctly. No longer use the single method which just copied IAtomParity.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Replaced IAtomContainer test using IAtomParity with ITetrahedralChirality.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Don't test chem object builders for creation of IAtomParity.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove IChemObject builder instance registration.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove atom parity test classes

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Remove atom parity from CDKToBeam converter.

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