Source Code for Module cinfony.opsin

  1  ## Copyright (c) 2011, Noel O'Boyle 
  2  ## All rights reserved. 
  3  ## 
  4  ##  This file is part of Cinfony. 
  5  ##  The contents are covered by the terms of the BSD license 
  6  ##  which is included in the file LICENSE_BSD.txt. 
  7   
  8  """ 
  9  opsin - A Cinfony module for accessing OPSIN from CPython and Jython 
 10   
 11  Global variables: 
 12    opsin - the underlying OPSIN library (uk.ac.cam.ch.wwmm.opsin) 
 13    informats - a dictionary of supported input formats 
 14    outformats - a dictionary of supported output formats 
 15  """ 
 16   
 17  import os 
 18  import sys 
 19   
 20  if sys.platform[:4] == "java": # Jython 
 21      import uk.ac.cam.ch.wwmm.opsin as opsin 
 22  else: # CPython 
 23      import jpype 
 24      if not jpype.isJVMStarted(): 
 25          _jvm = os.environ['JPYPE_JVM'] 
 26          if _jvm[0] == '"': # Handle trailing quotes 
 27              _jvm = _jvm[1:-1] 
 28          _cp = os.environ['CLASSPATH'] 
 29          jpype.startJVM(_jvm, "-Djava.class.path=" + _cp) 
 30      opsin = jpype.JPackage("uk").ac.cam.ch.wwmm.opsin 
 31       
 32  try: 
 33      _nametostruct = opsin.NameToStructure.getInstance() 
 34      _restoinchi = opsin.NameToInchi.convertResultToInChI 
 35  except TypeError: 
 36      raise ImportError("The OPSIN Jar file cannot be found.") 
 37   
 38  informats = {'iupac': 'IUPAC name'} 
 39  """A dictionary of supported input formats""" 
 40  outformats = {'cml': "Chemical Markup Language", 'inchi': "InChI", 
 41                'smi': "SMILES"} 
 42  """A dictionary of supported output formats""" 
 43   
 44 -def readstring(format, string): 
 45      """Read in a molecule from a string. 
 46   
 47      Required parameters: 
 48         format - see the informats variable for a list of available 
 49                  input formats 
 50         string 
 51   
 52      Example: 
 53      >>> input = "propane" 
 54      >>> mymol = readstring("iupac", input) 
 55      """ 
 56      if format!="iupac": 
 57          raise ValueError("%s is not a recognised OPSIN format" % format) 
 58   
 59      result = _nametostruct.parseChemicalName(string) 
 60      if str(result.getStatus()) == "FAILURE": 
 61          raise IOError("Failed to convert '%s' to format '%s'\n%s" % ( 
 62              string, format, result.getMessage())) 
 63   
 64      return Molecule(result) 
 65   
 66       
 67 -class Molecule(object): 
 68      """Represent a opsinjpype Molecule. 
 69   
 70      Required parameters: 
 71         OpsinResult -- the result of using OPSIN to parse an IUPAC string 
 72   
 73      Methods: 
 74         write() 
 75         
 76      The underlying OpsinResult can be accessed using the attribute: 
 77         OpsinResult 
 78      """ 
 79      _cinfony = True 
 80       
 81 -    def __init__(self, OpsinResult): 
 82          if hasattr(OpsinResult, "_cinfony"): 
 83              raise IOError, "An opsin Molecule cannot be created from another Cinfony Molecule" 
 84               
 85          self.OpsinResult = OpsinResult 
 86           
 87 -    def __str__(self): 
 88          return self.write() 
 89      @property 
 90 -    def _exchange(self): 
 91          return (0, self.write("smi")) 
 92 -    def write(self, format="smi", filename=None, overwrite=False): 
 93          """Write the molecule to a file or return a string. 
 94           
 95          Optional parameters: 
 96             format -- see the outformats variable for a list of available 
 97                       output formats (default is "smi") 
 98             filename -- default is None 
 99             overwite -- if the output file already exists, should it 
100                         be overwritten? (default is False) 
101   
102          If a filename is specified, the result is written to a file. 
103          Otherwise, a string is returned containing the result. 
104          """         
105          if format not in outformats: 
106              raise ValueError,"%s is not a recognised OPSIN format" % format 
107           
108          if filename is not None and not overwrite and os.path.isfile(filename): 
109              raise IOError, "%s already exists. Use 'overwrite=True' to overwrite it." % filename 
110   
111          if format == "cml": 
112              result = str(self.OpsinResult.getCml().toXML()) 
113          elif format == "inchi": 
114              result = str(_restoinchi(self.OpsinResult)) 
115          elif format == "smi": 
116              result = str(self.OpsinResult.getSmiles()) 
117   
118          if filename: 
119              outputfile = open(filename, "w") 
120              print >> outputfile, result 
121              outputfile.close() 
122          else: 
123              return result 
124   
125  if __name__=="__main__": #pragma: no cover 
126      mol = readstring("iupac", "propane") 
127      print mol.write("inchi") 
128