Dear Greg,
Sorry I can't share the SMILES and SMARTS, they are proprietary. If you can
send me your structures I can test them with my program.
I double loop in the building of molecules and queries; the actual code is this:
for (i = 0; i < numsmi; i++)
{
mol = SmilesToMol(smiles[i].smiles);
numsims = 0;
fprintf(fpout, "%s,", smiles[i].smiles);
fprintf(stdout, "%d\n", i);
for (j = 0; j < numsma; j++)
{
pattern = SmartsToMol(smarts[j].smarts);
matchesfound = SubstructMatch(*mol,*pattern,matches, false,
false);
if (matchesfound == true)
{
numsims = numsims + 1;
if (numsims == 1) fprintf(fpout, "%s\n", smarts[j].smarts);
else fprintf(fpout, "%s,%s\n", smiles[i].smiles,
smarts[j].smarts);
}
delete pattern;
}
if (numsims == 0) fprintf(fpout, "\n");
delete mol;
}
The same double loop structure is used in the DL program. I could build the
molecules and queries at once as you suggest but I'm kind of testing my typical
situation that involves millions of molecules - not sure if that many of
molecules can be stored in memory.
Thanks a lot,
Gonzalo
-----Original Message-----
From: Greg Landrum [mailto:[email protected]]
Sent: 24 July 2012 15:08
To: Gonzalo Colmenarejo-Sanchez
Cc: [email protected]
Subject: Re: [Rdkit-discuss] speed of SMARTS matches calculations
A correction to my previous message:
On Tue, Jul 24, 2012 at 3:04 PM, Greg Landrum <[email protected]> wrote:
>
> molecules and queries once. Two of the regular benchmarks I run with
> the RDKit (http://code.google.com/p/rdkit/wiki/Benchmarking) involve
> substructure searching (t7 and t8 in that table) and there doing 428K
> matches takes about 6 seconds on my linux box. Another example
The 6 second number is for my MacBook Pro, not my Linux box.
-greg
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