Dear JChem Technical Support,
I tried to use GenerateMD to add pharmacophore fingerprint to a descriptor set. I used the following code:
PFParameters pfpConfig = new PFParameters( "pharma-frag.xml" );
I got error message 'org.dom4j.DocumentException: Error on line 1 of document : Content is not allow
ed in prolog. Nested exception: Content is not allowed in prolog.'. It seems there is error in XML file. How can I fix it?
I attached the xml and entire error message.
thanks in advance,
Dear Yuhmei Lin,
Did you also try to use the same XML configuration file in the command line of the generatemd batch program?
Sg like this:
generatemd c input.smiles -k PF -c pharma-frag.xml
Does this work or you get the same error message?
Thank you for the reply. I have tried command-line, it works. The error only happened in java code.
all the best,
Oooppps... I overlooked your code line: the API does not provide such method. When you pass a String parameter to the PFParameters() constructor, then it is supposed to be an XML string. File name, even if it refers to an XML file is not allowed. If you wish to load the configuration from an XML file, then the File object has to passed to the constructor.
Does this help?
Gosh, what a nasty mistake! Thank you for drawing my attention to this problem, we will fix the manual.