There really isn't a maximum. It depends on the number of atoms, number of bonds, and number of conformers.
On Thu, Apr 30, 2009 at 9:09 PM, Evgueni Kolossov <[email protected]> wrote: > Ok , so the average size 781 byte. What's the max size of one molecule > can be in theory? > > 2009/4/30 Greg Landrum <[email protected]>: >> 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 >>>> >> > > > > -- > Dr. Evgueni Kolossov (PhD) > [email protected] > Tel. +44(0)1628 627168 > Mob. +44(0)7812070446 >
