ligandtypes assigns PMF atom types based on the SMARTS rules in
"atomtype.rules". These rules have been defined to
replicate as closely as possible the types defined by Muegge and
Martin
proteintypes
usage: proteintypes < protein.cex
proteintypes assigns PMF atom types to protein atoms based on their
standard PDB residue and atom names. Cofactor and coenzyme atom types
are currently not assigned; these atoms will be ignored.
plptypes
usage: plptypes donor.rules < molecule.cex
plptypes assigns PLP atom types. Types are based on standard protein atom and residue names. For atoms not recognized as in standard protein residues, types are assigned based on the SMARTS rules in
"donor.rules".
References
PMF: I. Muegge and Y.C. Martin, J. Med. Chem., 42,
791-804 (1999).
