pdb2cex+charges

usage: pdb2cex+charges molecule.pdb charge.rules > molecule.cex

pdb2cex+charges is a shell script which runs pdbbonds to generate connectivity and double bonds from 3D-coordinates, runs pdb2cex to convert from pdb to CEX format, adds implicit hydrogens to the resulting SMILES, and finally runs smartscharge, which 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.