chembl_webresource_client - Usage Examples

Molecule Tutorials - Herong's Tutorial Examples

∟ChEMBL Database - European Molecular Biology Laboratory

∟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;...