Thank you very much Greg, Couple of more things to clarify: - in documentation you have mentioned pickle files. Can you please give an example read/write for this kind of files; - in SDF the records separated by quite definite sequence which allow us to create an index file and have direct access to particular record number. Is it possible with pickle files?
Regards, Evgueni 2009/4/30 Greg Landrum <greg.land...@gmail.com>: > 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 <ekolos...@gmail.com> 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 <greg.land...@gmail.com>: >>> Yes, the database containing the 214K molecules is 167MB >>> >>> >>> On Thu, Apr 30, 2009 at 7:55 PM, Evgueni Kolossov <ekolos...@gmail.com> >>> 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 <greg.land...@gmail.com>: >>>>> [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) >> ekolos...@gmail.com >> Tel. +44(0)1628 627168 >> Mob. +44(0)7812070446 >> > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
