Re: [Cdk-devel] interesting perf results

[Egon W. <ego...@gm...>]

Rajarshi,

thanx for posting this!

On Thu, Sep 11, 2008 at 4:50 PM, Rajarshi Guha <rg...@in...> wrote:
> What I was interested in was the memory usage for individual Atom and
> Bond objects. The shallow sizes for them are as follows:
>
> Object          Num Object              Size (bytes)    Avg Size (bytes)
> Atom            13,923                  1,447,992       104
> Bond            14,335                  688,080         48
> boolean[]       31,810                  764,800         24.04

I have had similar observations...

> I've included the entry for boolean[] just out of interest - I assume
> these correspond to the flags for each atom, bond (as well as
> IAtomContainer), so that explains the large number of them. But as
> expected the size if quite small.
>
> What is a little worrisome is the size of Atom objects!

Same here... this is why I like to see IAtomType, IElement, IIsotope
as fields, instead of using hierarchical structure.

But I'm sure there are other places where we can optimize... e.g.
using enum for the common CDKConstant's, short instead of integer for
atomic number (!), drop the use of Symbol is primary identifier and
rely on the atomic number (and use IPseudoAtom for every symbol for
which there is no symbol, which we expect people do anyway), use float
for coordinates instead of double.

Egon

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