using jchem with jython

Jython is an implementation of the high-level, dynamic, object-oriented language Python written in 100% Pure Java, and seamlessly integrated with the Java platform. (See http://www.jython.org/)








This wrapper code was kindly contributed by Daniel McShan at UCHSC:

Code:

import sys sys.path.append("/Users/dan/jchem/lib/jchem.jar") from chemaxon.util import MolHandler from chemaxon.sss.search import StandardizedMolSearch ... def subgraph (A, B):     "Is A a subgraph of B?"     s = StandardizedMolSearch()     Amol = MolHandler(A).getMolecule()     Bmol = MolHandler(B).getMolecule()     s.setQuery(Amol)     s.setTarget(Bmol)     return s.isMatching()

Here is a full jython script that is guaranteed to work:

Code:

#!C:\Programs\jython2.2.1\jython.bat import sys sys.path.append("C:\Program Files\ChemAxon\JChem\lib\jchem.jar") from chemaxon.util import MolHandler from chemaxon.sss.search import StandardizedMolSearch def subgraph (A, B):      "Is A a subgraph of B?"      s = StandardizedMolSearch()      Amol = MolHandler(A).getMolecule()      Bmol = MolHandler(B).getMolecule()      s.setQuery(Amol)      s.setTarget(Bmol)      return s.isMatching() def search_and_print( Q, T):    if subgraph(Q,T):       result = "  found"    else:       result = "  not found"    print "Q:" + Q + " T:" + T + result search_and_print("CCC", "CCCC") search_and_print("CCC", "CC") search_and_print("CCC", "C1CCCCCC1") search_and_print("C[$(CCO)]", "C1CCCCCC1O") search_and_print("C[$(CCN)]", "C1CCCCCC1O") search_and_print("c1ccccc1", "C1=CC=CC=C1")

This is how it can be run, for example:

Quote:

$ C:\Programs\jython2.2.1\jython.bat test_search.jy Q:CCC T:CCCC found Q:CCC T:CC not found Q:CCC T:C1CCCCCC1 found Q:C[$(CCO)] T:C1CCCCCC1O found Q:C[$(CCN)] T:C1CCCCCC1O not found Q:c1ccccc1 T:C1=CC=CC=C1 found