Daylight's Depictions and JavaDepict
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Daylight's Depict toolkit currently serves to create depictions
of chemical entities and is used in all our applications.
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The Daylight Depict algorithm works by
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fixing relative angles in all cycles and for "directional"
bonds
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performing a restricted localized minimization around the
remaining free angles
to obtain depictions with atoms spread out as far as possible
from each other.
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The algorithm is quite stable and robust for layout. However
it could be improved by providing a little flexibility.
