aschreyer

--
-- PostgreSQL database dump
--

-- Dumped from database version 9.0.4
-- Dumped by pg_dump version 9.0.1
-- Started on 2011-08-12 09:23:17

SET statement_timeout = 0;
SET client_encoding = 'UTF8';

aschreyer

--
-- PostgreSQL database dump
--

-- Dumped from database version 9.0.4
-- Dumped by pg_dump version 9.0.1
-- Started on 2011-07-22 13:30:36

SET statement_timeout = 0;
SET client_encoding = 'UTF8';

aschreyer

SELECT      molregno, s.ism, similarity(s.ism, 'C[NH+](C)CC[C@H](CSc1ccccc1)Nc2ccc(cc2[N+](=O)[O-])S(=O)(=O)NC(=O)c3ccc(cc3)N4CC[NH+](CC4)Cc5ccccc5c6ccc(cc6)Cl') As sim
FROM        chembl.compound_smiles s
WHERE       s.ism % 'C[NH+](C)CC[C@H](CSc1ccccc1)Nc2ccc(cc2[N+](=O)[O-])S(=O)(=O)NC(=O)c3ccc(cc3)N4CC[NH+](CC4)Cc5ccccc5c6ccc(cc6)Cl'
ORDER BY    s.ism <-> 'C[NH+](C)CC[C@H](CSc1ccccc1)Nc2ccc(cc2[N+](=O)[O-])S(=O)(=O)NC(=O)c3ccc(cc3)N4CC[NH+](CC4)Cc5ccccc5c6ccc(cc6)Cl'
LIMIT 20;

aschreyer

from credo.credoscript import *

ca = ChemCompAdaptor()

# GET IMATINIB
sti = ca.fetch_by_het_id('STI')

# GET ALL SIMILAR CHEMICAL COMPONENTS USING CIRCULAR FINGERPRINTS
ca.fetch_all_by_sim(sti.ism, fp='circular')

aschreyer

from credo.credoscript import *
from credo.contrib.chemidresolver import *

ca = ChemCompAdaptor()
rsvr = ChemIdResolver()

# GET THE SDF FILE OF LAPATINIB WITH 3D COORDINATES
molstring = rsvr.get_structure('lapatinib','sdf', get3d=True)

# GET THE USR MOMENTS FOR THE STRUCTURE

aschreyer

import json
from urllib import urlopen

# GET A CHEMICAL COMPONENT
response = urlopen('http://0.0.0.0:8000/credo/rest/chemcomps/sti').read()

# PARSE JSON INTO PYTHON DICTIONARY
sti = json.loads(response)

# COLUMN DATA/ATTRIBUTES ARE CONVERTED TO DICTIONARY KEYS

aschreyer

SELECT degrees('(3,0,0)'::vector3d @ '(5,5,0)'::vector3d) AS angle;

 angle 
-------
    45
(1 row)

aschreyer

SELECT   s.pdb, l.ligand_name, s.title, sq.similarity
FROM     (
         WITH     query AS (SELECT calphafp FROM credo.ligand_fuzcav WHERE ligand_id = 3919) 
         SELECT   f.ligand_id, arrayxi_fuzcavsim_global(query.calphafp, f.calphafp) AS similarity
         FROM     credo.ligand_fuzcav f, query
         WHERE    arrayxi_fuzcavsim_global(query.calphafp, f.calphafp) > 0.17
         ) sq,
         credo.ligands l, credo.biomolecules b, credo.structures s
WHERE    sq.ligand_id = l.ligand_id
         AND l.biomolecule_id = b.biomolecule_id

aschreyer

SELECT  canonical_smiles, openeye.has_undef_stereo(canonical_smiles)
FROM    chembl.compound_structures s
JOIN    chembl.chembl_id_lookup i 
        ON s.molregno = i.entity_id AND i.entity_type = 'COMPOUND'
WHERE   i.chembl_id = 'CHEMBL287587' OR i.chembl_id = 'CHEMBL1437';


       canonical_smiles     | has_undef_stereo 
----------------------------+-----------------------
 'NC[C@H](O)c1ccc(O)c(O)c1' | f

aschreyer

SELECT '{1,2,3,4,5}'::arrayxi & '{5,4,3,2,1}'::arrayxi;
?column?
---------------
 '{0,0,3,0,0}'
(1 row)
 
Time: 0.290 ms