fixpka has been added. This application may be used to set a molecule to an energetically favorable ionization state for pH=7.4. This is the same pH model that was available in the Filter application. Additionally, the perception of acceptable valence states has been improved to include phosphorus as well as aromatic oxygen and sulfur with +1 formal charge.
In tautomers: Major improvement for carbon hybridization. Now carbon atoms with bonds to one, two, or three heavy atoms are able to change hybridization state. However, only carbons close to an appropriate heteroatom are allowed to change hybridization state. Additionally, unreasonable charge states of carbon have been removed. Now the enabling the -ch3 option will only generate tautomers appropriate for the given level.
In tautomers: Improvement of the -reasonable option, particularly involving exocyclic heteroatoms.
In tautomers: Added stereo preservation flag -savestereo with a default value of false. Stereo chemistry can be lost during creation and removal of double bonds, but if the user desires a certain stereo setting to be preserved this flag will prevent the associated atoms and bonds from taking part in tautomerization.
pkatyper now implicitly uses the -reasonable true setting for its internal call to tautomers. This provides a better reference tautomer when enumerating pKa states.
In pkatyper: Improvements to pka states.
In molcharge: Aromaticity settings on molecules are now unchanged on returned molecules. Aromaticity may be temporarily changed inside the function while charges are being calculated, but the molecule will have the same aromaticity after the function as before.
In molcharge: AmberFF94 charges can now be applied to standard protein residues.
In molcharge: A new -altlocs flag will retain all alternative locations in a disordered .pdb structure when charging. This option allows dictionary-based charges such as AmberFF94 to be applied to all atoms in a disordered molecule (but should not be used with conformation-dependent charges such as AM1BCC).
In tautomers, atom-ordering could in rare instances be inconsistent for output molecules. This led to cases where even though all associated tautomers led to the same unique tautomer, the unique tautomer could have different SMILES representations depending on the input structure. This has been fixed.