Miscellaneous¶

Tautomers¶

To get all possible resolved tautomers, use the tautomers parameter:

tautomers = query('warfarin', 'smiles', tautomers=True)

The Molecule object¶

The Molecule class provides an easy way to collect and store various structure representations and properties for a given input:

from cirpy import Molecule

mol = Molecule('N[C@@H](C)C(=O)O')

mol then has the following properties:

mol.stdinchi
mol.stdinchikey
mol.smiles
mol.ficts
mol.ficus
mol.uuuuu
mol.hashisy
mol.sdf
mol.names
mol.iupac_name
mol.cas
mol.image_url               # The url of a GIF image
mol.twirl_url               # The url of a TwirlyMol 3D viewer
mol.mw                      # Molecular weight
mol.formula
mol.h_bond_donor_count
mol.h_bond_acceptor_count
mol.h_bond_center_count
mol.rule_of_5_violation_count
mol.rotor_count
mol.effective_rotor_count
mol.ring_count
mol.ringsys_count

The first time you access each one of these properties, a request is made to the CIR servers. The result is cached, however, so subsequent access is much faster.

Downloading files¶

A convenience function is provided to facilitate downloading the CIR output to a file:

cirpy.download('Aspirin', 'test.sdf', 'sdf')
cirpy.download('Aspirin', 'test.sdf', 'sdf', overwrite=True)

This works in the same way as the resolve function, but also accepts a filename. There is an optional overwrite parameter to specify whether any existing file should be overwritten.

Constructing API URLs¶

Construct API URLs:

>>> cirpy.construct_api_url('Porphyrin', 'smiles')
'http://cactus.nci.nih.gov/chemical/structure/Porphyrin/smiles/xml'

Logging¶

CIRpy can generate logging statements if required. Just set the desired logging level:

import logging
logging.basicConfig(level=logging.DEBUG)

The logger is named ‘cirpy’. There is more information on logging in the Python logging documentation.

Pattern matching¶

Note

It looks like the name_pattern resolver no longer works.

There is an additional name_pattern resolver that allows for Google-like searches. For example:

results = query('Morphine','smiles', ['name_pattern'])

The notation attribute of each Result will show you the name of the match (e.g. “Morphine N-oxide”, “Morphine Sulfate”) and the value attribute will be the representation specified in the query (SMILES in the above example).