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>
Map the CDK atom type 'C.allene' to SYBYL 'C.1'.

Change-Id: Ic3d045d3b6cc969a1791c50bdf946b7e9d99483f
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Null safe check for setting "am" bond order.

Change-Id: I57f02e16a33c9ef192461022fa0c4419dbe2ad54
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve formula regressions in cdk-data. A new test was added to check for NPEs when adding formula, only cdk-silent updated.

Change-Id: I858ff5ddb64f44a1b9c99653b382ffdd3b47e307
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Test that RGroups don't cause a NPE in exact/major mass of molecular formula.

Change-Id: I2abb863888e9508a7e60920a815c6ba9e4d4bc61
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve variable naming violations due to sentence case or underscores in qsarmolecular.

Change-Id: I1eba117a1666eeb0999482c3e3602e6a125578a6
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Capitalize variable naming violation in constant resulting from copy paste between qsarmolecular classes.

Change-Id: I23199e8e06033f29c6520d3aa4f29a2013bdc057
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Capitalize other constants in qsarmolecular.

Change-Id: I6058a709712f71dfdee6f3d28c77f12aa2ba13dd
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Revert captialisation of non-constant field.

Change-Id: Ie12693bed5546f8f45ed18686086126ac7134a54
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve variable naming violations in qsaratomic.

Change-Id: I3511315c52edc30d810c70e0ff1d8166adfb40ad
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Resolve PMD variable naming violations in other qsar modules.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Allow SMARTS expressions of the form [h0] and [!h0] analogous to [H0] and [!H0]. Previously this was not possible to null handling semantics.