Molecule Tutorials - Herong's Tutorial Examples - v1.26, by Herong Yang
chembl_webresource_client - Usage Examples
This section provides a tutorial example to install chembl_webresource_client, the Official Python client for accessing ChEMBL API.
With chembl_webresource_client installed, you can try some examples.
1. Get details of a given molecule:
herong$ python3 from chembl_webresource_client.new_client import new_client molecule = new_client.molecule.get('BSYNRYMUTXBXSQ-UHFFFAOYSA-N') print(molecule) {'atc_classifications': ['N02BA01', 'N02BA51', 'N02BA71', 'A01AD05', 'B01AC06'], 'availability_type': '2', 'biotherapeutic': None, 'black_box_warning': '0', 'chebi_par_id': 15365, 'chirality': '2', 'cross_references': [{'xref_id': 'aspirin', 'xref_name': 'aspirin', ...
2. Get the PNG image of the 2D representation of a given molecule and save it to a file. You can open the test.png file in an image viewer to see it.
herong$ python3 from chembl_webresource_client.new_client import new_client image = new_client.image.get('CHEMBL25') file = open("test.png", 'wb') file.write(image) file.close()
3. Search for all approved drugs and get them in JSON format:
herong$ python3 from chembl_webresource_client.new_client import new_client molecule = new_client.molecule approved_drugs = molecule.filter(max_phase=4) print(approved_drugs) [{'atc_classifications': ['C02CA01'], 'availability_type': '1', 'biotherapeutic': None, 'black_box_warning': '0', 'chebi_par_id': 8364, 'chirality': '2', 'cross_references': [{'xref_id': '50104272', 'xref_name': 'SID: 50104272', 'xref_src': 'PubChem'}, {'xref_id': '50100502', 'xref_name': 'SID: 50100502', ...
3. Search for all approved drugs and save them in SDF format:
herong$ python3 from chembl_webresource_client.new_client import new_client molecule = new_client.molecule molecule.set_format('sdf') mols = molecule.filter(max_phase=4) with open('test.sdf', 'wb') as output: for mol in mols: output.write(mol) output.write(b'$$$$\n')
4. Converting to 3D SDF (also called CTAB, Connection Table) from a given 2D SDF file:
from chembl_webresource_client.utils import utils with open('test-3d.sdf', 'w') as output: with open('test.sdf', 'r') as input: mols = input.read().split('$$$$\n') for mol in mols: mol_3D = utils.ctab23D(mol) output.write(mol_3D)
5. Converting SMILES to SDF, then to SVG.
from chembl_webresource_client.utils import utils sdf = utils.smiles2ctab("c1(C=O)cc(OC)c(O)cc1") svg = utils.ctab2svg(sdf) print svg "<?xml version='1.0' encoding='iso-8859-1'?>\n<svg:svg version='1.1' baseProfile='full'\n xmlns:svg='http://www.w3.org/2000/svg'\n xmlns:rdkit='http://www.rdkit.org/xml'\n xmlns:xlink='http://www.w3.org/1999/xlink'\n xml:space='preserve'\nwidth='200px' height='200px' >\n <svg:rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='200' height='200' x='0' y='0'> </svg:rect>\n <svg:path d='M 134.556,74.8299 176.377,82.1956' style='fill:none;fill-rule:evenodd;stroke:#000000;...
Table of Contents
Molecule Names and Identifications
Nucleobase, Nucleoside, Nucleotide, DNA and RNA
►ChEMBL Database - European Molecular Biology Laboratory
Call ChEMBL Data Web Service Directly
ChEMBL Data Resource - molecule
ChEMBL Data Resource - activity
ChEMBL Data Resource - document
ChEMBL Data Resource - chembl_id_lookup
chembl_webresource_client - Python Client
►chembl_webresource_client - Usage Examples
chembl_webresource_client - RetryError Exception
PubChem Database - National Library of Medicine
INSDC (International Nucleotide Sequence Database Collaboration)
HGNC (HUGO Gene Nomenclature Committee)