Re: [Cdk-user] Reading large SD Files

2013-09-19 Thread Nina Jeliazkova
The RandomAccessReader mentioned above is exactly such low level indexer - it does not perceive chemistry when building the index. Lochana may have issues if trying to load all these molecules in memory - this is definitely not the way to go. Nina On 19 September 2013 03:07, Andrew Dalke

[Cdk-user] Reading large SD Files

2013-09-19 Thread lochana menikarachchi
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.

Re: [Cdk-user] Reading large SD Files

2013-09-19 Thread Joos Kiener
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.

Re: [Cdk-user] Reading large SD Files

2013-09-19 Thread lochana menikarachchi
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,