pharmacophore fingerprint

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,

Yuhmei Lin

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?

Regards

Miklos

Dear Miklos,

Thank you for the reply. I have tried command-line, it works. The error only happened in java code.

all the best,

Yuhmei

 

Dear Yuhmei,

 

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?

 

BR

Miklos

Dear Miklos,

Thank you for the help. I created a file object and it works.

I hope you can correct the same code in this page for other users.

http://www.chemaxon.com/jchem/doc/api/chemaxon/descriptors/GenerateMD.html

 

Best regards,

 

Yuhmei

Dear Yuhmei,

Gosh, what a nasty mistake! Thank you for drawing my attention to this problem, we will fix the manual.

Regards

Miklos