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# -*- coding: utf-8 -*-
"""
chemspipy.objects
~~~~~~~~~~~~~~~~~
Objects returned by ChemSpiPy API methods.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import warnings
from .utils import memoized_property
class Compound(object):
""" A class for retrieving and caching details about a specific ChemSpider record.
The purpose of this class is to provide access to various parts of the ChemSpider API that return information about
a compound given its ChemSpider ID. Information is loaded lazily when requested, and cached for future access.
"""
def __init__(self, cs, record_id):
"""
:param ChemSpider cs: ``ChemSpider`` session.
:param int|string record_id: Compound record ID.
"""
self._cs = cs
self._record_id = int(record_id)
# TODO: Allow optional initialize with a record-type response from the API (kwarg or class method from_dict?).
def __eq__(self, other):
return isinstance(other, Compound) and self.csid == other.csid
def __repr__(self):
return 'Compound(%r)' % self.csid
def _repr_png_(self):
"""For IPython notebook, display 2D image."""
return self.image
@property
def record_id(self):
"""Compound record ID.
:rtype: int
"""
return self._record_id
@property
def csid(self):
"""ChemSpider ID.
.. deprecated:: 2.0.0
Use :py:attr:`~chemspipy.objects.Compound.record_id` instead.
:rtype: int
"""
warnings.warn('Use record_id instead of csid.', DeprecationWarning)
return self._record_id
@property
def image_url(self):
"""Return the URL of a PNG image of the 2D chemical structure.
:rtype: string
"""
return 'http://www.chemspider.com/ImagesHandler.ashx?id=%s' % self.record_id
@memoized_property
def _details(self):
"""Request compound info and cache the result."""
return self._cs.get_details(self.record_id)
@property
def molecular_formula(self):
"""Return the molecular formula for this Compound.
:rtype: string
"""
return self._details['formula']
@property
def smiles(self):
"""Return the SMILES for this Compound.
:rtype: string
"""
return self._details['smiles']
# TODO: Convert tool to get inchi?
@property
def stdinchi(self):
"""Return the Standard InChI for this Compound.
.. deprecated:: 2.0.0
Use :py:attr:`~chemspipy.objects.Compound.inchi` instead.
:rtype: string
"""
warnings.warn('Use inchi instead of stdinchi.', DeprecationWarning)
return self.inchi
@property
def stdinchikey(self):
"""Return the Standard InChIKey for this Compound.
.. deprecated:: 2.0.0
Use :py:attr:`~chemspipy.objects.Compound.inchikey` instead.
:rtype: string
"""
warnings.warn('Use inchikey instead of stdinchikey.', DeprecationWarning)
return self.inchikey
@property
def inchi(self):
"""Return the InChI for this Compound.
:rtype: string
"""
return self._cs.convert(self.mol_2d, 'Mol', 'InChI')
@property
def inchikey(self):
"""Return the InChIKey for this Compound.
:rtype: string
"""
return self._cs.convert(self.mol_2d, 'Mol', 'InChIKey')
@property
def average_mass(self):
"""Return the average mass of this Compound.
:rtype: float
"""
return self._details['averageMass']
@property
def molecular_weight(self):
"""Return the molecular weight of this Compound.
:rtype: float
"""
return self._details['molecularWeight']
@property
def monoisotopic_mass(self):
"""Return the monoisotopic mass of this Compound.
:rtype: float
"""
return self._details['monoisotopicMass']
@property
def nominal_mass(self):
"""Return the nominal mass of this Compound.
:rtype: float
"""
return self._details['nominalMass']
@property
def common_name(self):
"""Return the common name for this Compound.
:rtype: string
"""
return self._details['commonName']
@memoized_property
def mol_2d(self):
"""Return the MOL file for this Compound with 2D coordinates.
:rtype: string
"""
return self._details['mol2D']
@memoized_property
def mol_3d(self):
"""Return the MOL file for this Compound with 3D coordinates.
:rtype: string
"""
return self._details['mol3D']
@memoized_property
def image(self):
"""Return a 2D depiction of this Compound.
:rtype: bytes
"""
return self._cs.get_image(self.record_id)
@memoized_property
def external_references(self):
"""Return external references for this Compound.
:rtype: list[dict]
"""
return self._cs.get_external_references(self.record_id)
|
