Yes, the database containing the 214K molecules is 167MB
On Thu, Apr 30, 2009 at 7:55 PM, Evgueni Kolossov <[email protected]> wrote: > Thanks Greg, > > Unfortunately I do not quite got it - you mean the size of your > example is 167240704 bytes? > > Regards, > Evgueni > > 2009/4/30 Greg Landrum <[email protected]>: >> [redirecting to list since this may be of general interest] >> >> Yes, I generally store molecules in databases in blob columns >> containing the pickles. The primary reason for this is that one can >> then skip all the work of parsing the molecule, perceiving the >> chemistry, etc. >> >> I don't have a good general answer for how long pickles are. It really >> depends on the molecules. One example I have handy is a sqlite >> database containing the pubchem screening deck. The molecules are >> stores as follows: >> sqlite> .schema >> CREATE TABLE molecules (compound_id varchar not null unique,molpkl blob); >> sqlite> select count(*) from molecules; >> 214178 >> >> % ls -l Compounds.sqlt >> -rw-r--r-- 1 landrgr1 staff 167240704 Nov 22 07:28 Compounds.sqlt >> >> There is, no doubt, some overhead associated with the sqlite data, but >> this gives a rough estimate. >> >> -greg >>
