Dear:
I have sent a mail to egonw, and he suggests me to sent mail to this mailbox. I
have some questions about CDK to consult you. I'm a graduate of lanzhou
university
in China, and we want implement a substructure query by utilizing CDK. Because
the
CDK provide the SMARTS-org.openscience.cdk.smiles.smarts. When i run the example
as following:
public class Test {
public static void main(String[] args) throws CDKException {
SmilesParser sp = new SmilesParser();
AtomContainer atomContainer = (AtomContainer) sp
.parseSmiles("NC5NCNC1C5(NCN1C2OC(C(O)C2(O))C(OP(O)(=O)OP(O)(=O)OP(O)(O)=O)c3c
cc4c(O)cccc4(c3))");
QueryAtomContainer query = SMARTSParser.parse("C1CCCCC1");//or
these
SMILES:("c1ccc2ccccc2(c1)");//("c1ccccc1");
boolean queryMatch = UniversalIsomorphismTester.isSubgraph(
atomContainer, query);
if (queryMatch)
System.out.println("successful");
else
System.out.println("failed");
}
}
an exception occured:
Exception in thread "main" org.openscience.cdk.exception.CDKException: The
string
C1CCCCC1 is not a valid SMARTS string: Encountered "1" at line 1, column 2.
Was expecting one of:
<EOF>
"*" ...
"a" ...
"A" ...
"[" ...
and so on
...
the string of SMILES can not be the int number? but it is everywhere in SMILES.
what should i do? do you have any good ideas?
and the following is Egon's answer of my question, but i still don't know what
to
do:
That's because a SMILES is not always a valid SMARTS... they basically are
two different languages.
thanks a lot!
best regards!
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