aschreyer’s gists

aschreyer / gist:982860

Created May 20, 2011 13:13

Credoscript example

	In [ 1]: from credo.credoscript import *

	# Fetch a structure from a database with the corresponding adaptor
	In [ 2]: s = StructureAdaptor().fetch_by_pdb('3CS9')

	# Database columns are mapped as attributes
	In [ 3]: s.title
	Out[ 3]: 'Human ABL kinase in complex with nilotinib'

	# Relationships with other entities are mapped as attributes as well

aschreyer / openeye-enumerate-tautomers.sql

Created May 20, 2011 14:21

Introduction to the OpenEye PostgreSQL cartridge

	SELECT openeye.enumerate_tautomers('O=C1NN=Cc2cocc12');

	enumerate_tautomers
	---------------------------------------
	'{O=c1[nH]ncc2c1coc2,Oc1nncc2c1coc2}'
	(1 row)

aschreyer / array-intersection.sql

Created May 20, 2011 15:05

Examples of the Eigen PostgreSQL extension

aschreyer / epinephrines.sql

Created May 24, 2011 12:55

Stereochemistry functions in the PostgreSQL OpenEye cartridge

	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 / fuzcav-calpha.sql

Created June 1, 2011 12:16

Binding site similarity search in CREDO using the FuzCav algorithm

	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 / vector3d-angle.sql

Created June 1, 2011 15:50

Eigen Vector3D PostgreSQL extension

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

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

aschreyer / credo-restful-example.py

Created June 1, 2011 15:59

Implementation of RESTful web services for CREDO

	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 / credo-contrib-chemresolver.py

Created June 1, 2011 16:05

Implementing the Chemical Identifier Resolver

	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 / credo-rdkit.py

Created June 1, 2011 16:07

RDKit integration in CREDO

	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 / sql-lingo.sql

Created June 13, 2011 16:41

Using the PostgreSQL pg_trgm extension for chemical similarity searching

	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;

Adrian Schreyer aschreyer