Now uses an extension of the MMFF94 force field for tricoordinate boron compounds. Most compounds containing B-X bonds where X=C,N,O,S, and H are covered with the following exceptions: X=N(imine),N(sulfonamide), N(pyridinium) and N(quaternary). Also not supported are compounds in which boron is bonded to X=F,Cl,Br,I,B and Si, or makes a bond angle BYX. Compounds in which boron is a part of four-membered rings of B1CCC1 type are also not available in the current parameterization because their existence is questionable: Ab initio calculations at the MP2/6-31G** level failed to identify stable structures for them (highly polar structures in which boron is four-coordinated are formed).
Fixed a bug where OMEGA wasn’t checking if 3D construction of fragment generation was successful.
Fixed a bug where output from flipper could still fail in OMEGA for missing stereo chemistry. Now the rules for required stereo chemistry are consistent.
Fixed a bug where setting stereo chemistry in too small of a ring could cause a crash. Now only rings greater than 7 members and only one double bond will be set with flipper.
Fixed a bug where OMEGA wasn’t checking if user generated fragment libraries were in OEB format. Fragment libraries must be in OEB format.
Fixed bugs related to nonsense values for command line parameters. User-supplied parameters must be a legal value. The ‘–help <parameter>’ command will print out the legal values.
Fixed a bug where SD tagged data wasn’t passed along to output molecules.