Compound¶
The get_compounds()
function returns a list of Compound
objects. You can also
instantiate a Compound
object directly if you know its CID:
c = pcp.Compound.from_cid(6819)
Dictionary representation¶
Each Compound
has a record
property, which is a dictionary that contains the all the information
about the compound, produced exactly from the JSON response from the PubChem API. All other properties are derived from
this record.
Additionally, each Compound
provides a to_dict()
method that returns PubChemPy’s own dictionary
representation of the Compound data. As well as being more concisely formatted than the raw record
, this method also
takes an optional parameter to filter the list of the desired properties:
>>> c = pcp.Compound.from_cid(962)
>>> c.to_dict(properties=['atoms', 'bonds', 'inchi'])
{'atoms': [{'aid': 1, 'element': 'o', 'x': 2.5369, 'y': -0.155},
{'aid': 2, 'element': 'h', 'x': 3.0739, 'y': 0.155},
{'aid': 3, 'element': 'h', 'x': 2, 'y': 0.155}],
'bonds': [{'aid1': 1, 'aid2': 2, 'order': 'single'},
{'aid1': 1, 'aid2': 3, 'order': 'single'}],
'inchi': u'InChI=1S/H2O/h1H2'}
3D Compounds¶
Many properties are missing from 3D records, and the following properties are only available on 3D records:
volume_3d
multipoles_3d
conformer_rmsd_3d
effective_rotor_count_3d
pharmacophore_features_3d
mmff94_partial_charges_3d
mmff94_energy_3d
conformer_id_3d
shape_selfoverlap_3d
feature_selfoverlap_3d
shape_fingerprint_3d