Credimus RESTful web service How-to

credimus-json-request.py

import requests

# make sure the headers accept JSON
headers = {'accept': 'application/json'}
response = requests.get('http://marid.bioc.cam.ac.uk/credo/chemcomps/001', headers=headers)

response.status_code # returns 200

credimus-post-file.py

headers = {'accept': 'application/json'}

# the file to upload: web service only looks for the 'file' field
files = {'file': open('003.sdf')}

# post the structure to the resource for doing a USR search against all chemical components
response = requests.post('http://marid.bioc.cam.ac.uk/credo/chemcomps/sim/usr/', 
                         headers=headers, files=files, params={'limit':25})

credo-api-get-contacts.py

response = requests.get('http://marid.bioc.cam.ac.uk/credo/contacts/', headers=headers, 
                        params={'biomolecule_id':56818, 'ligand_id':241717, 'Contact.is_hbond':'t'})

credo-user-structure.py

import requests

# the file to upload: REST resource only looks for the 'structure' field
files = {'structure': open('structure.pdb')}

# post the structure to the resource to identify all contacts and return JSON
# contact search should be restricted with the optional 'pdb_chain_id' and 
# 'res_num' params
response = requests.post('http://marid.bioc.cam.ac.uk/credo/contacts/json', 
                         files=files, params={'title':'foo', 'pdb_chain_id':'B'})

inspecting-the-response.py

# the returned column data
response.json().get('data')
[2, u'001', u'001', None, None, u'[(1S)-1-(3-phenylpropyl)-4-(3-pyridyl)butyl] (2R)-1-[2,2-difluoro-2-(3,4,5-trimethoxyphenyl)acetyl]piperidine-2-carboxylate', u'2001-11-06', u'2011-06-04', u'COc1cc(cc(c1OC)OC)C(C(=O)N2CCCC[C@H]2C(=O)O[C@@H](CCCc3ccccc3)CCCc4cccnc4)(F)F', 624.715, 45, 35, 10, 2, 0.285714, 0, 0, 0, 48, 17, 4, 3, 8, 0, 87.19, 7.258, 0.457143, 1, 0.142935, True, True, False, False, False, False, False, False, False, False, False, True, False]

# the metadata of the response: column names and data types
response.json().get('metadata')
[[u'chem_comp_id', u'INTEGER'], [u'het_id', u'VARCHAR(3)'], [u'three_letter_code', u'VARCHAR(3)'], [u'replaced_by_het_id', u'VARCHAR(8)'], [u'nstd_parent_het_id', u'TEXT'], [u'iupac_name', u'TEXT'], [u'initial_date', u'DATE'], [u'modified_date', u'DATE'], [u'ism', u'TEXT'], [u'mw', u'REAL'], [u'num_hvy_atoms', u'INTEGER'], [u'num_carbons', u'INTEGER'], [u'num_heteroatoms', u'INTEGER'], [u'num_halides', u'INTEGER'], [u'het_carb_ratio', u'REAL'], [u'formal_charge_count', u'INTEGER'], [u'formal_charge_sum', u'INTEGER'], [u'num_chiral_centers', u'INTEGER'], [u'num_bonds', u'INTEGER'], [u'num_rotors', u'INTEGER'], [u'num_ring_systems', u'INTEGER'], [u'num_aro_ring_systems', u'INTEGER'], [u'num_lipinski_hbond_acceptors', u'INTEGER'], [u'num_lipinski_hbond_donors', u'INTEGER'], [u'tpsa', u'REAL'], [u'xlogp', u'REAL'], [u'fraction_csp3', u'REAL'], [u'alerts', u'INTEGER'], [u'qed', u'REAL'], [u'has_std_atoms', u'BOOLEAN'], [u'has_butyl', u'BOOLEAN'], [u'is_solvent', u'BOOLEAN'], [u'is_nat_product', u'BOOLEAN'], [u'is_amino_acid', u'BOOLEAN'], [u'is_nucleotide', u'BOOLEAN'], [u'is_saccharide', u'BOOLEAN'], [u'is_block_buster', u'BOOLEAN'], [u'is_fragment', u'BOOLEAN'], [u'is_drug_like', u'BOOLEAN'], [u'is_lead', u'BOOLEAN'], [u'is_drug', u'BOOLEAN'], [u'is_approved_drug', u'BOOLEAN']]