I have a list of parent molecules in SMILES form, and I was running the
SQT against a list of SMARTS queries, to make sure that all my queries
were valid. It works great until it hits Petrichloral. The SMILES and
SMARTS strings parse fine, but there is no more output when the SQT runs
into this query (currently 264/326), so I believe there might be a
possible recursivity problem. There was no CDKException thrown even after
an hour, even though the first 263 queries ran in 15 seconds. Petrichloral
is very symmetric, and daylight's depict.cgi runs the query fine with
31104 matches: apparently (4*3*2)(3*2)^4. I was purposely running a dot
product iteration here so thet's why there is no inner loop. I tried
formatting the SMARTS with and without brackets.
SMILES ------>
ClC(Cl)(Cl)C(O)OCC(COC(O)C(Cl)(Cl)Cl)(COC(O)C(Cl)(Cl)Cl)COC(O)C(Cl)(Cl)Cl
SMARTS ------>
ClC(Cl)(Cl)[CH]([O-,OH,OC])O[CH2]C([CH2]O[CH]([O-,OH,OC])C(Cl)(Cl)Cl)([CH2]O[CH]([O-,OH,OC])C(Cl)(Cl)Cl)[CH2]O[CH]([O-,OH,OC])C(Cl)(Cl)Cl
public static void main(String[] args) throws CDKException,
FileNotFoundException, IOException {
SmilesParser sp=new
SmilesParser(DefaultChemObjectBuilder.getInstance());
ArrayList<String> smarts=new ArrayList();
ArrayList<String> mols=new ArrayList();
String smart=new String();
String mol=new String();
AtomContainerSet acs=new AtomContainerSet();
BufferedReader br1=new BufferedReader(new
FileReader("smarts.txt"));
while ((smart=br1.readLine()) != null){
smarts.add(smart);
}
br1.close();
BufferedReader br2=new BufferedReader(new
FileReader("subStructures.txt"));
while ((mol=br2.readLine()) != null){
mols.add(mol);
acs.addAtomContainer(sp.parseSmiles(mol));
}
br2.close();
BufferedWriter stream= new BufferedWriter(new
FileWriter("deaOut.txt", true));
SMARTSQueryTool sqt=new SMARTSQueryTool("c1ccccc1"); //dummy
string for initialization
for (int ac=0; ac != acs.getAtomContainerCount(); ac++){
sqt.setSmarts(smarts.get(ac));
System.out.println(""+ac); //for debugging purposes
try {
if (sqt.matches(acs.getAtomContainer(ac))){
stream.write(mols.get(ac) + " | " + smarts.get(ac));
stream.newLine();
}
}
catch (CDKException ex){throw new
CDKException(ex.toString());}
}
stream.close();
}
}
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