Hi all,
I have had a strange issue that I can't seem to find a way around. The
following code block consumes a ton of memory, which is strange as just
using the SD File reader I have no memory issues. I think that the issue
is related to the java garbage collection not being picked up, even though
I have attempted to force that (to no success).
All the following block does is iterate through an SD file and look for the
highest (or lowest) scoring molecule for each molecule. The assumption is
that all molecules of the same type will be next to each other in the file
(which is not my problem). Running this on a SD file of around 400K
molecules consumes around 23GB of memory, so if anyone has an idea I will
be most appreciative!
public static void main(String argv[]) throws IOException,
InterruptedException
{
CommandLineParser cParser;
String[] modes = {};
String[] parms = {"-in", "-filterTag", "-direction", "-out"};
String[] reqParms = {"-in", "-filterTag", "-direction", "-out"};
String rdkitSO = System.getenv("RDKIT_SO");
System.load(rdkitSO);
String currentDir = System.getProperty("user.dir");
File dir = new File(currentDir);
cParser = new
CommandLineParser(EXPLAIN,0,0,argv,modes,parms,reqParms);
ROMol rdmol = null;
ROMol rdmol2 = null;
SDMolSupplier suppl = new SDMolSupplier(cParser.getValue("-in"));
SDWriter writer = new SDWriter(cParser.getValue("-out"));
int count = 0;
while (!suppl.atEnd())
{
count++;
if (count % 1000 == 0)
{
System.out.println(count);
}
rdmol = suppl.next();
if (rdmol2 == null)
{
// rdmol2.delete();
rdmol2 = new ROMol(rdmol);
continue;
}
if (rdmol.MolToSmiles().equals(rdmol2.MolToSmiles()))
{
if ( cParser.getValue("-direction").equals("highest") )
{
double value1 =
Double.parseDouble(rdmol.getProp(cParser.getValue("-filterTag")));
double value2 =
Double.parseDouble(rdmol2.getProp(cParser.getValue("-filterTag")));
//System.out.println("Val1 " + value1 + " Val2 " + value2);
if (value1 > value2)
{
rdmol2.delete();
rdmol2 = new ROMol(rdmol);
}
}
else
{
if (
Double.parseDouble(rdmol.getProp(cParser.getValue("-filterTag"))) <
Double.parseDouble(rdmol2.getProp(cParser.getValue("-filterTag"))) )
{
rdmol2.delete();
rdmol2 = new ROMol(rdmol);
}
}
} else {
writer.write(rdmol2);
rdmol2.delete();
rdmol2 = new ROMol(rdmol);
}
}
}
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