Evaluator slow during pka evaluation, old test version fast

User 677b9c22ff

09-12-2006 23:46:05


I tested different evaluator versions, because I wanted to do some (massive) pka calculations, however there seems to be a speed bug.

I used something like:

java -Xmx200m -classpath C:\chemistry\jchem-test\lib\jchem.jar; chemaxon.jep.Evaluator -e Z:\pka-acid.txt Z:\pubchem-1000.smi

where PubChem.smi is a smiles file with 1000 smiles and pka-acid.txt

contains the term to calculate the most acidicpka: pKa('acidic', '1')

JCHEM 3.2.2 = 3.38 min

JCHEM 3.2 = 4 min

JCHEM-TEST = 3.30 min (Version Version TEST_2006_12_04) (latest)

JCHEM-TEST = 30 seconds (Version TEST_2006_08_25) (OLD)

(This also affects Instant-JChem).

Kind regards

Tobias Kind

User 851ac690a0

10-12-2006 00:08:40


I have this data for the speed of the pKa calculation: 65-70 molecules/second. (Windows XP, Pentium (4) 3GHZ, 1GB RAM)

One of my colleague will respond for the 'speed bug' problem you found.


User 677b9c22ff

10-12-2006 00:37:27


its really the evaluator, if you do it via

timethis ""java" -Xmx200m -classpath "C:\chemistry\jchem\lib\jchem.jar;" chemaxon.marvin.Calculator Z:\pubchem-1000.smi pka"

it always takes 30 seconds for all JChem versions (I am running the client version for this example.)

java version "1.5.0_06"

Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-b05)

Java HotSpot(TM) Client VM (build 1.5.0_06-b05, mixed mode, sharing)

If I run the server version (2,8 GHz Opteron, WINXP-32-bit, JAVA 1.5 server) its like 19 seconds.

And the speed is really depending on this specific sample (it takes long time for the first 600 and the last 400 are just fast).

IF you would take only these and multiply them, the 1000 smiles pka calculation is finished in 6 seconds, which translates to 1000/6 = 166 smiles/sec).

But I am more interested in the evaluator difference, because Instant-JChem is still slow for complex pka terms because of that problem.


ChemAxon e08c317633

11-12-2006 17:32:43


We will fix this Evaluator bug ASAP.