Correctly replace atom in MDLV3000Reader. Setting just the atom does not update the bonds that reference that atom.

Change-Id: Ib52bf59b365fd927208e6c54644acef19599179a
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Define MACCS 166 Bit 44 definition - see http://www.dalkescientific.com/writings/diary/archive/2014/10/17/maccs_key_44.html

Change-Id: If22edf2444ff6be0103c9130ebe04eafb88dbb3b
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve remaining PMD naming violations in SMSD classes.

Change-Id: I91f1c89c9cd47c3fc68129e59c25b2f35e7b6204
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve PMD variable naming violations in SMSD mcplus classes.

Change-Id: Ie327be5bc7702f1946da2e915ac5638bd59751fd
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve PMD variable naming violations in various SMSD classes.

Change-Id: I9a59bde2d34be4203697c0db8a011d8d571ad6c2
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve PMD variable naming violations in SMSD mcgregor classed

Change-Id: Ia555adf371d0d6ed5ad83731f263dbfbb709505d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>