Yeah, it's also a LinkedHashMap (more memory due doubly linked list). I think all maps initialise to the default of ~14 slots in which case we can do some rough calculations, taking a conservative estimate of v=20 atoms… loading n=25,000 molecules. Each pointer (inc. null) is 8 bytes (64-bit system) so as a lower bound we get.

pointer x hash map lengthnull bytes x v x n
8 * 14 * 8 * 25,000 * 20 = 448000000 = 427 mb

J

On 11 Dec 2012, at 12:48, Nina Jeliazkova <jeliazkova.nina@gmail.com> wrote:

On 11 December 2012 07:54, Egon Willighagen <egon.willighagen@gmail.com> wrote:
On Sun, Dec 9, 2012 at 10:31 PM, John May <johnmay@ebi.ac.uk> wrote:
I noticed that what I term auxiliary atom type properties, such as PI_BONDCOUNT, LONEPAIR_COUNT, SINGLE_COUNT… etc. are never configured. Some algorithms try to use this information (e.g. this line in  CDKHueckelAromaticityDetector) but there is no obvious way to get at this information. It would be natural to add this to AtomTypeManipulator.configure() but as these are stored in a map it mean creating a HashMap on every single atom :/.

I think that method should configure all properties an atom type
definition file may contain, and thus that it should configure the
above properties. I consider this a bug.

Right, but in principle a HashMap per atom is a bit of overkill, if
this information is only used in few cases.

Regards,
Nina


It would be good to have these properties accessible but I can't see a useful way of doing it.

This information is used at some points, and I am not sure how it is
read there, if not via the configure() method... that I need to
explore.

Thanx for spotting and reporting this!

Egon

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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