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Energetically reasonable coordinates for hydrogen atoms may be assigned
automatically using the OESet3DHydrogenGeom functions. The
overloaded functions which take only a molecule as an argument
traverse molecules and identify hydrogen atoms which are bonded to a
single atom, and have the same Cartesian coordinates of that atoms.
The functions then attempt to compute an energetically reasonable
position for the identified hydrogen atom based on either a
pre-assigned hybridization value for the parent atom. If no
hybridization value is found for the parent atom then the
hybridization will be assigned, if possible, from the molecule graph.
If hybridization assignment fails then new coordinates will not be
assigned for the hydrogen atom. An additional function is provided
which allows specification of the hydrogen for which new coordinates
are to be assigned. New coordinates for the hydrogen atom will be
computed regardless of whether the current coordinates of the hydrogen
are identical to the atom to which it is attached. If coordinates are
assigned correctly the method will return boolean 'true'. If the
function fails to compute a geometrically reasonable position the
method will return boolean 'false'.
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Version 1.3.1 | ||||
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