Release August 2013

New Features

  • 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 flexible molecules.

  • 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.

Bug Fixes

  • 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 tetrahedral carbon.

  • 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 hydrogens.

  • molcharge no longer inadvertently converts reduced cysteine residues (CYS) to the oxidized form (CYX) when assigning Amber partial charges to protein residues.

Other changes

  • 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.

  • This will be the last release to support SuSe 10.