3.3 Selecting Potential Hydrogen Bonds

Once the hydrogen positions have been determined as far as possible, each
donor/acceptor pair is examined in turn to see if it fits the geometric
criteria.  

It is intended that geometric criteria will tend to be determined by the
purpose of the study.  For maximum comparability, this program defaults to
the same minimum angles and maximum distances as Baker and Hubbard (1984).
These are : -

Maximum Distances D-A of 3.9 Angstroms
	 	  H-A of 2.5 Angstroms
Minimum Angles  D-H-A of 90.0 degrees
               D-A-AA of 90.0 degrees
	       H-A-AA of 90.0 degrees

Maximum Angles D-A-AX of 20.0 degrees } for amino-aromatic interactions
               H-A-AX of 20.0 degrees } (AX is at L to aromatic plane)

The -d -h -b -B -a and -A command line options exist to allow the criteria
to be customised.

There are rules to cover contingencies.  If the hydrogen on the donor is
not fixed then the point on the hydrogen's locus that is closest to the
acceptor being investigated is selected.  If no position was given for the
hydrogen on the donor (for instance, for a water oxygen or an unrecognised
nitrogen) then it is assumed to be directly between the donor and acceptor,
one angstrom away from the donor.  If the acceptor is covalently bound to
more than one heavy atom, yielding more than one possible "angle at the
acceptor", the lower value is given.

The algorithm is slightly inflexible.  It finds potential hydrogen bonds
rather than real ones, and frequently, such as in the case of those donors
for which the hydrogen could not be positioned (eg serine, threonine or
tyrosine oxgygens), the hydrogen bonds can be mutually exclusive.  If a
pair of atoms could act both as donor and acceptor to each other, for
instance a "SER OG " and a "HOH O ", then they are listed as forming two
hydrogen bonds.  If more than one location is given for any particular atom
then the different locations are treated as different atoms that simply
happen to have the same name.  In these circumstances, a donor / acceptor
pair can have two hydrogen bonds listed with different geometries.