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.. _misc:
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).
`Read more about pattern matching on the CIR blog`_.
.. _`Python logging documentation`: http://docs.python.org/2/howto/logging.html
.. _`Read more about pattern matching on the CIR blog`: http://cactus.nci.nih.gov/blog/?p=1456
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