DOCK chem.defn file

["Zuccotto, Fabio" <fz24314 %-% at %-% glaxowellcome.co.uk>]

Dear CCL users,
 	the atom labelling parameters used by DOCK (chemical matching option) are
 contained in the file chem.defn.There, a set of atom definition rules (based on
 .mol2 atom types) is used to define acceptor, donor, polar hydrophobic atoms.
 For instance a carboxylate carbon is defined as
 C.2 (2 O.co2)
 where ( ) specify atoms that must be bounded to the parent atom. Similarly [ ]
 specify atoms that must not be bound to the parent atom. (*) specify any atom
 type (page 96 of the manual).
 Looking at the chem.defn file (page 98 of the manual) it contains, for instance,
 entries such as:
 F [*]  for polar
 C.3 [*] for hydrophobic
 O. [H] [N.] (*) for acceptor
 The way I read these entries is:
 F [*]  = a fluorine atom with nothing attached to it
 C.3 [*] = an sp3 carbon with nothing attached to it
 O. [H] [N.] (*) = any kind of oxygen with any atom attached to it but  H or N
 Clearly it is not possible that DOCK is defining the labels as isolated fluorine
 or carbon atoms as it is not possible that the definition of acceptor does not
 include -OH. Any better way to interpret these definitions?
 Thank you very much.
 fabio