Public access to Oracle installation with PubChem database indexed by Bingo

[Dmitry Pavlov]

Hello all,

We have opened a public access to our Oracle server, so everybody
could try Bingo without installing it. Only a working Oracle client
is required.

Server: scitouch.net (actually this is a proxy)
Port: 1521
Database instance: orcl
User: pubchem_ro
Password: pubchem

You can do SELECT queries on pubchem.pccomp table.
Please see below for examples.

Please note that any commercial usage is disallowed.

With best regards,

Dmitry

$ sqlplus pubchem_ro/pub...@scitouch.net:1521/orcl

SQL> set linesize 1024;
SQL> set wrap off;
SQL> set timing on;
SQL> select cid, bingo.smiles(cmol) from pubchem.pccomp where bingo.sub(cmol, 'C(S([O-])(=O)=O)1=CC=C(C(=O)O)C=C1C')=1;

CID BINGO.SMILES(CMOL)
4050247 S([O-])(=O)(=O)C1=C(C(O[H])=O)C([H])=C(C(O[H])=O)C([H])=C1[H]
17897903 S([O-])(=O)(=O)C1=C(C(O[H])=O)C([H])=C(C(O[H])=O)C([H])=C1[H].[N+](C([H])([H])[H])([H])([H])[H]
20826299 S([O-])(=O)(=O)C1=C(C([H])([H])[H])C(C(O[H])=O)=C(C(O[H])=O)C(C([H])([H])[H])=C1[H].[Na+]
21406134 S([O-])(=O)(=O)C1=C(C2=C([H])C3C(=C(C(=C(C=3[H])[H])[H])[H])C([H])=C2[H])C(C(OC([H])([H])[H])=O)=C(C(OC([H])([H])[H])=O)C([H])=C1[H]
21406139 S([O-])(=O)(=O)C1=C(C2C3C(=C(C(=C(C=3[H])[H])[H])[H])C([H])=C([H])C=2[H])C(C(OC([H])([H])[H])=O)=C(C(OC([H])([H])[H])=O)C([H])=C1[H]
22352749 S([O-])(=O)(=O)C1=C(C2C(S(O[H])(=O)=O)=C([H])C([H])=C([H])C=2[H])C(C(O[H])=O)=C(C(O[H])=O)C([H])=C1[H]
22481358
S([O-])(=O)(=O)C1=C(C(OC(C(C2(C([H])([H])C([H])([H])C([H])([H])C([H])([H])C2([H])[H])[H])([H])[H])([H])[H])=O)C([H])=C(C(OC(C(C2(C([H])([H])C([H])([H])C([H])([H])C([H])([H])C2([H])[H])[H])([H])[H])([H])[H])=O)C([H])=C1C(OC(C(C1(C([H])([H])C([H])([H])C([H])([H])C([H])([H])C1([H])[H])[H])([H])[H])([H])[H])=O
22481363
S([O-])(=O)(=O)C1=C(C(OC(C2(C3(C([H])([H])C(C(C3([H])[H])([H])[H])([H])C2([H])[H])[H])[H])([H])[H])=O)C([H])=C(C(OC(C2(C3(C([H])([H])C(C(C3([H])[H])([H])[H])([H])C2([H])[H])[H])[H])([H])[H])=O)C([H])=C1C(OC(C1(C2(C([H])([H])C(C(C2([H])[H])([H])[H])([H])C1([H])[H])[H])[H])([H])[H])=O
22481392
S([O-])(=O)(=O)C1=C(C(OC(C23C([H])([H])C4(C(C(C2([H])[H])(C([H])([H])C(C4([H])[H])([H])C3([H])[H])[H])([H])[H])[H])([H])[H])=O)C([H])=C(C(OC(C23C([H])([H])C4(C(C(C2([H])[H])(C([H])([H])C(C4([H])[H])([H])C3([H])[H])[H])([H])[H])[H])([H])[H])=O)C([H])=C1C(OC(C12C([H])([H])C3(C(C(C1([H])[H])(C([H])([H])C(C3([H])[H])([H])C2([H])[H])[H])([H])[H])[H])([H])[H])=O
23670850 S([O-])(=O)(=O)C1=C(C(O[H])=O)C([H])=C(C(O[H])=O)C([H])=C1[H].[Na+]

10 rows selected.

Elapsed: 00:00:10.96
SQL> select cid, bingo.smiles(cmol) from pubchem.pccomp where bingo.exact(cmol, 'NC1=CC2=C(C=C1)C=C(O)C=C2', 'NONE')=1;

CID BINGO.SMILES(CMOL)
428605 O(C1=C([H])C2=C(C(=C(N([H])[H])C(=C2[H])[H])[H])C([H])=C1[H])[H]
4076990 O=C1C([H])([H])C([H])([H])C2=C(C(=C(C(N([H])[H])=C2[H])[H])[H])C1([H])[H]
13177879 O(C1=C([H])C2C(C(C(N([H])[H])(C([H])([H])C=2C([H])=C1[H])[H])([H])[H])([H])[H])[H]
19855464 Br[H].O(C1=C([H])C2C(C(C(N([H])[H])(C([H])([H])C=2C([H])=C1[H])[H])([H])[H])([H])[H])[H]
20273044 S([O-])(=O)(=O)C([H])([H])[H].O(C1=C([H])C2=C(C(=C(N([H])[H])C(=C2[H])[H])[H])C([H])=C1[H])[H]
20450139 O(C1=C([H])C2C(C(C(N([H])[H])(C([H])([H])C=2C([H])=C1[H])[H])([H])[H])([H])[H])[H].O(C(=O)C(N(C([H])([H])[H])[H])(C(C1C(C(O[H])=O)=C([H])C([H])=C([H])C=1[H])([H])[H])[H])[H]
21144641 Cl[H].O(C1=C([H])C2=C(C(=C(N([H])[H])C(=C2[H])[H])[H])C([H])=C1[H])[H]
22827296 O(C1=C([H])C2C(C(C(N([H])[H])(C([H])([H])C=2C([H])=C1[H])[H])([H])[H])([H])[H])[H].O(C(=O)[C@@H0](N(C([H])([H])[H])[H])(C(C1C(C(O[H])=O)=C([H])C([H])=C([H])C=1[H])([H])[H])[H])[H] |a:28|
44436112 [Br-].O(C1=C([H])C2C(C(C(N([H])[H])(C([H])([H])C=2C([H])=C1[H])[H])([H])[H])([H])[H])[H]

9 rows selected.

Elapsed: 00:00:00.26
SQL> select cid, bingo.smiles(cmol) from pubchem.pccomp where bingo.exact(cmol, 'NC1=CC2=C(C=C1)C=C(O)C=C2', 'ALL')=1;

CID BINGO.SMILES(CMOL)
428605 O(C1=C([H])C2=C(C(=C(N([H])[H])C(=C2[H])[H])[H])C([H])=C1[H])[H]

Elapsed: 00:00:00.23
SQL> select cid, bingo.smiles(cmol) from pubchem.pccomp where bingo.sim(cmol, 'COC(=O)C(O)C1=CC=C(O)C=C1')>0.95;

CID BINGO.SMILES(CMOL)
111357 O(C(=O)C(O[H])(C1=C([H])C([H])=C(O[H])C([H])=C1[H])[H])C(C([H])([H])[H])([H])[H]
111562 O(C(C1=C([H])C([H])=C(O[H])C([H])=C1[H])(C(OC([H])([H])[H])=O)[H])[H]
523496 O(C(C1=C([H])C([H])=C(OC([H])([H])[H])C([H])=C1[H])(C(OC([H])([H])[H])=O)[H])[H]
6931673 O(C(=O)[C@@H0](O[H])(C1=C([H])C([H])=C(O[H])C([H])=C1[H])[H])C(C([H])([H])[H])([H])[H] |a:3|
6931672 O(C(=O)[C@H0](O[H])(C1=C([H])C([H])=C(O[H])C([H])=C1[H])[H])C(C([H])([H])[H])([H])[H] |a:3|
19019488 O(C(C1=C([H])C(O[H])=C([H])C([H])=C1[H])(C(OC([H])([H])[H])=O)[H])[H]

6 rows selected.

Elapsed: 00:00:14.19

[Dmitry Pavlov]

Hello all,

> We have opened a public access to our Oracle server, so everybody
> could try Bingo without installing it. Only a working Oracle client
> is required.

Following up some technical details of our server:

1) Intel(R) Core(TM) i7 CPU 950 @ 3.07GHz
(quad-core, 8 'virtual' cores with Hyper-Threading).

2) 6 GB of memory

3) 1.5 TB of disk space.
PubChem database with Bingo index occupies about 350 GB.

4) OS is Debian GNU/Linux amd64, kernel 2.6.26

5) Oracle memory settings are the following:

Total System Global Area 4175568896 bytes
Fixed Size 2219952 bytes
Variable Size 1526726736 bytes
Database Buffers 2634022912 bytes
Redo Buffers 12599296 bytes

(the most notable is the 'Database Buffers' parameter,
which we increased to 2500M).

With best regards,

Dmitry