Joos,
You are right. I should use a local database instead of SD files...
Lochana
________________________________
From: Joos Kiener <j...@sunrise.ch>
To: lochana menikarachchi <locha...@yahoo.com>
Cc: "cdk-user@lists.sourceforge.net" <cdk-user@lists.sourceforge.net>
Sent: Thursday, September 19, 2013 9:37 AM
Subject: Re: [Cdk-user] Reading large SD Files
I played a round a bit and came up with a crude solution as I mentioned in my
initial response.
index all occurrences of "$$$$" -> takes 3-4 seconds for a file with 131'000
records
use separate thread to index to increase performance but current implementation
requires that index is fully built. This is an issue as you need to have 2
access mechanisms, index based and not-index based.
Use BufferedReader to go to the indexed line, eg
for (int i = 0; i < linesToRead; i++) {
bufferedReader.readLine();
}
yeah, not ideal but it actually is faster than I expected.
add caching to it.
But a question remains:
What is your actual goal? Why can't you use Marvin, for commercial use?
1 million is a lot. Using a real database comes to mind.
2013/9/19 lochana menikarachchi <locha...@yahoo.com>
Hi Nina,
>
>
>I did try the RandomAccessSDFReader. It took few minutes to build the index
>for an SD file with 50,000 structures. What I am saying is what ever
>MarvinView does to build index (if it is using an index) is much faster. I am
>wondering how it does that.
>
>Lochana
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