Atom type perception is no longer part of SMILES parsing

Change-Id: I1ea866590bccb4f9fb433c73f91634a677cb363b

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
The new SMILES parser just kekulizes by default

Change-Id: Ie3db8b1f22d520474a96e458662129abcc72e608

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Updated the atom indices: the new parser has the atom orders in the carbonyl bonds the other way around

Change-Id: I810930c27ed0457b4165d2bbd7bacb82290ff66b

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added three tests which cannot be kekulized

Change-Id: I427968fbea64e1e174e9c860656de902e1ac61cc

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed a test of which the SMILES was outright broken

Change-Id: I17655987e3fc641e7fe8e3b6e0ddb2e1756420c3

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
The SMILES parser no longer automatically recognized aromaticity (it's OpenSMILES, not old SMILES), but the test was expecting IS_AROMATIC flags, so added perception

Change-Id: Iba02d1099d6c036a7b19fd81ba9ad978922b55a2

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
The assertion was wrong: with or without a double bond, this thing is aromatic; also added testing that the oxygen is not marked as aromatic

Change-Id: If0f046fdf583e9500239f907a5ecdf6a0ac2c2e3

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Ignore tests for unimplemented features

Change-Id: I72efc90a96efd33f0f8bd6e6e080bef7f33961ca

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Additional unit test of CID 42475007 stereoisomer.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
If the central atom is found in the ligand list replace it with an implicit hydrogen.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Removes the safety checked for implicit tetrahedral neighbours.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Can also now apply basic CIP rules to sulfinyl.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
We'll never agree on aromaticty... what model does Sybyl use anyway?

Change-Id: I6ae5b7e4938f376130635322a15a5756ae58db7a
Detection of out-of-ring planarity due to pi-pi interaction is out of scope of our algorithms right now

Change-Id: Ia7fbe93bd959ea00d919d953507a5f000f3ddd53
A NO2 nitrogen is N.pl3 in Sybyl

Change-Id: I53d0203c75dcdbf174e4f0efced823fd79d343b5
Nitrate oxygens are not O.co2's

Change-Id: Iec167c8b83887e25a9f32e67dd13e793ed4d2254
Implemented perception of the Sybyl O.co2 atom type

Change-Id: I3002340b5e7c6d2ed54d3fcd292f305ef020b110
Added mappings for Mo

Change-Id: I904d7e87778ef1026689070f01850401897b5678
Added rudimentary detection of the chromium atom types

Change-Id: I4a09a271e6b683b054b71975cb0f8b594597aec1
Added rudimentary detection of the Co.oh atom type

Change-Id: I2379c9a886f731f72c0e4dfeb4d3511334e57291