ChemSpiPy.py

import urllib
from xml.etree import ElementTree as ET
import unittest


class ChemSpiderId(str):
    """An class for holding ChemSpider IDs and enabling searches based on them.

    The purpose of the class is to enable a series of bound methods to be easily
    wrapped to provide access to the ChemSpider API in Python. Currently the 
    methods include returning the URL of a png image of the named chemical.
    """

    def __init__(self,csid):
        """Initialize the ChemSpiderId object with a value.

        """

        self.id = ''
        self.image = ''
        self.molwt = ''
        self.mol = ''

        if type(csid) == str and csid.isdigit() == True:
            self.id = csid
            
        elif type(csid) == int:
            self.id = str(csid)

        else:
            raise TypeError('ChemSpiderId needs to be intialised with an int or a str')

    def __string__(self):
        return self.id

    def imageurl(self):
        """ Return the URL of a png image for a specific Chemspider ID.

        The actual ChemSpider API returns the binary of the PNG wrapped in XML. The
        purpose of constructing a URL to the image is to enable easy insertion into
        webservices etc by serving the address for the image rather than the image.
        """

        assert self != '', 'ChemSpiderId not initialised with value'

        if self.image == '':
            baseurl = 'http://www.chemspider.com/'
            url = baseurl + 'ImagesHandler.ashx?id=%s' % self
            self.image = url
            return url

        else:
            return self.image

    def molweight(self):
        """Poll the ChemSpider MS API for average mol wt for a specific Chemspider ID."""

        assert self != '', 'ChemSpiderID not initialised with value'
 
        if self.molwt == '':
            baseurl = 'http://www.chemspider.com/'
            token  = '3a19d00d-874f-4879-adc0-3013dbecbbc9'

            # Construct a search URL and poll Chemspider for the XML result
            searchurl = baseurl + 'MassSpecAPI.asmx/GetExtendedCompoundInfo?CSID=' + self.id + '&token=' + token

            response = urllib.urlopen(searchurl)

            tree = ET.parse(response) #parse the CS XML response
            molwttag = tree.find('{http://www.chemspider.com/}MolecularWeight')
            molecularweight = float(molwttag.text)

            self.molwt = molecularweight
            return molecularweight

    def getMolFile(self):
        """Poll the ChemSpider MS API for the mol descriptor for a specific Chemspider ID."""

        assert self != '', 'ChemSpiderID not initialised with value'

        #if self.molfile == None:
        baseurl = 'http://www.chemspider.com/'
        token  = '3a19d00d-874f-4879-adc0-3013dbecbbc9'

            # Construct a search URL and poll Chemspider for the XML result
        searchurl = baseurl + 'MassSpecAPI.asmx/GetRecordMol?csid=' + self.id + '&calc3d=true&token=' + token

        response = urllib.urlopen(searchurl)
        
        tree = ET.parse(response) #Parse the CS XML response
        moltag = tree.getroot()
        molfiletext = moltag.text

        self.molfile = molfiletext
        return molfiletext 

        #else:
         #   return self.molfile


def simplesearch(query):
    """Returns ChemSpiderId string from a simple search for query.

    SimpleSearch on the Chempspider API provides a list of objects which this
    routine is currently capturing but not returning back. At the moment it 
    simply returns a single object of the type ChemSpiderID
    """

    assert type(query) == str or type(query) == unicode, 'query not a string object'

    baseurl = 'http://www.chemspider.com/'
    token  = '3a19d00d-874f-4879-adc0-3013dbecbbc9'

    # Construct a search URL and poll Chemspider for the XML result
    searchurl = baseurl + 'Search.asmx/SimpleSearch?query=' + query + '&token=' + token

    response = urllib.urlopen(searchurl)

    tree = ET.parse(response) #parse the CS XML response
    elem = tree.getroot()
    csid_tags = elem.getiterator('{http://www.chemspider.com/}int')

    csidlist = []
    for tags in csid_tags:
      csidlist.append(tags.text)
    
    returned_id = ChemSpiderId(csidlist[0])

    return returned_id

########################################
#
# Unit tests
#
########################################

class TestChemSpiPy(unittest.TestCase):
 
    def setUp(self):
        self.testint = 236
        self.teststring = '236'
        self.testquery = 'benzene'
        self.testimageurl = 'http://www.chemspider.com/ImagesHandler.ashx?id=236'
        self.testmolwt = 78.1118
        self.testmol = """241
  -OEChem-10200920453D

  6  6  0     0  0  0  0  0  0999 V2000
   -0.7040   -1.2194   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7040   -1.2194   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4081   -0.0000   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4081    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7040    1.2194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7040    1.2194   -0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  2  0  0  0  0
  4  6  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
"""
 
    def testchemspiderid(self):
        self.assertRaises(TypeError, ChemSpiderId, 1.2)
        self.assertEqual(ChemSpiderId(self.teststring), self.teststring)
        self.assertEqual(ChemSpiderId(self.testint), self.teststring)
        self.assertEqual(ChemSpiderId(self.teststring).imageurl(), self.testimageurl)
        self.assertEqual(ChemSpiderId(self.teststring).molweight(), self.testmolwt)
        self.assertEqual(ChemSpiderId(self.teststring).mol, self.testmol)

 
    def testsimplesearch(self):
        self.assertEqual(simplesearch(self.testquery), self.teststring)
 
 
if __name__ == '__main__':
    unittest.main()