Scale AtomRadius in RadicalGenerator

Change-Id: I38f932505ba215e241e5732bf58f015c0e01bb79
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Changed the layout of radicals to have a smaller gap between them.

Updated radical spacing

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test if the monomer ID is read

Change-Id: Id5f8e7fd168a8b170cb1fb7f31943e3c5247a24c
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Links from the JavaDoc

Change-Id: I246f4b809f964ef0533412e12c67754bad51e931
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Use interfaces instead of implementations

Change-Id: I9d6c1764ea7c3ec6c9b58e2fd4408576b25e2467
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

Conflicts:
	src/main/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java
Factored out the test for PDB atom customization; also fixed the test to register the customizer (but there is more wrong)

Change-Id: I02ada008ab0736a0137544266566ef96c21d4c56
Signed-off-by: John May <john.wilkinsonmay@gmail.com>

Conflicts:
	build.xml
	src/test/org/openscience/cdk/io/cml/CML2Test.java
Do not output empty properties

Change-Id: I771bab0938c950635f236df229d9309d9fe3d0b1
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Output the monomers in a sorted manner, to make the CML output more reproducible

Change-Id: Ice68427060f642d9adec3754e8e068b893ffd697
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Do not output isotope info in PDB-CML files (fixing the last roundtripping inconsistency

Change-Id: I9166f590d91867f3fd35a319a8ca667b4ff15f62
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Updated murcko fragmenter to speed up preprocessing and avoid processing duplicate fragments in recursive calls.

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Updated to allow user specified molecule hash generator and included the orbital information in default molecular hash generator Removed reset method, no need for it Ensured that we output SMILES rather than fragment hashes Updated check for zero atom linkers to avoid redoing cycle detection. 5x speedup for large symmetric/branched structures Keep molecule hash as Long rather than String

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added dependency of frag module on hash module

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added inchi for macrocycle test case
Went back to use of spanning tree in check for zero atom linker
Added Javadoc annotation to indicate the class is not threadsafe

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Made the method threadsafe by removing static field

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Made the method threadsafe by removing static field
Avoided repeated calls to spanning tree by manually flagging ring bonds before starting search

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Dependency required by fragment.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Merge remote branch 'upstream/master'