smartscharge

usage: smartscharge charge.rules < molecule.cex

smartscharge assigns partial charges based on SMARTS substructure rules in "charge.rules". These rules are processed in order: rules at the end of the file will override rules at the beginning. The rules are defined for most types of functional groups encountered in medicinal chemistry and for proteins and nucleic acids.

smartscharge requires molecules in CEX datatree format. Utilities pdb2cex and tdt2cexid may be used to convert from PDB or Daylight TDT format to cex.