molcharge now uses the -method parameter for selecting a charge model. All
individual flags for charge models have been removed.
tautomers will now allow interconversion of
[NH2+]= and [NH3+]-.
tautomers now has a -warts option. Enabling this
options will number the output molecules with an @ symbol.
The default AM1BCC charge model in molcharge
now lightly restrains the AM1 geometry
optimization to the starting coordinates. This allows the important relaxation
of bond and angle degrees of freedom while greatly reducing the potential to
alter the molecule’s conformation away from its starting coordinates.
The AM1BCC charge models -method am1bccsym and -method am1bccspt in molcharge
now symmetrize the partial charges
over bond-topologically equivalent atoms, e.g. methyl hydrogens, in keeping
with the original model. This is especially important with conformationally
molcharge now has a .fail file to output molecules that do not charge correctly.
fixpka has been refined to reflect
feedback from collaborators. In particular isoxazoles and oxadiazoles were
added while pyrazoles and aryl sulfonamides were refined. Aryl sulfonamide
refinement also incorporated changes based on newly obtained experimental data.
tautomers will now properly set stereochemistry
on planar carbon to OEAtomStereo::Undefined. Previously, planar carbon could
inherit stereochemistry from an input molecule with stereochemistry set on a
A bug has been fixed in tautomers where 3D hydrogens where being suppressed.
fixpka now correctly addresses beta di-amino groups
so that if all other considerations are equivalent, secondary amines are
treated as most basic, followed by primary amines, with tertiary amine being
treated as least basic.
A few bugs have been fixed in fixpka involving
quaternary nitrogen and protonated aromatic nitrogens.
tautomers has been
fixed so that 3D molecules have 3D hydrogens instead of implicit
molcharge no longer inadvertently
converts reduced cysteine residues (CYS) to the oxidized form (CYX)
Amber partial charges to protein residues.
The -all flag has been removed from tautomers. Equivalent results can been achieved
with the following options: -level 7 -ch3 true. Level 7 will likely yield a plethora
of very unreasonable tautomers and is not recommended.