[Cdk-devel] minor MDLWriter corrections

[Nina J. <ni...@ac...>]

Hi all,

I am suggesting following minor fixes to MDLWriter class. These does not
affect its general behaviour, but handle a couple of more specific cases. 

1)
Writing a property block of a molecule in SDF file. Properties as obtained
object.getProperties() can be any type, thus 

writer.write((String)sdFields.get(element)) 

gives ClasCastException if the property has type different than String.
Using sdFields.get(element).toString() method should resolve the issue. 


MDLWriter.java 
<code>
    public void writeMolecule(Molecule molecule, boolean[] isVisible) throws
Exception {
    
    .....
    
        //write sdfields, if any
        if(sdFields!=null){
          Set set = sdFields.keySet();
          Iterator iterator = set.iterator();
          while (iterator.hasNext()) {
            Object element = iterator.next();
            //writer.write("> <"+(String)element+">");  
//replace with the line below
            writer.write("> <"+element.toString()+">");
            writer.newLine();
            //writer.write((String)sdFields.get(element)); 
            writer.write(sdFields.get(element).toString());
            writer.newLine();
            writer.newLine();
          }
        }
</code>        


2)
Property block of some SDF files (e.g. at http://ligand.info/)  does not
conform entirely to the specification, lacking the required blank line between
end of property data to the next data header. 

This confuses MDLReader and it reads only the first compound, assuming the
rest of the file as a property data.
I would suggest throwing an exception if $$$$ marker is encountered while
reading the property block.
<code>
 private ChemFile readChemFile(ChemFile chemFile) throws CDKException {
 ....
 			//while ((line = input.readLine()) != null &&
			//       line.trim().length() > 0) {
			while ((line = input.readLine()) != null &&
			       (line.trim().length() > 0)) {	
				if (line.equals("$$$$"))
					throw new CDKException("Expecting data line here, but found end of
molecule!");
</code>					

3)
	Really minor correction, since the second line of an SDF record is generally
ignored ;)
	<code>
	// instead of  writer.write("  CDK\n"); 
        /* From CTX spec
         * This line has the format:
         * IIPPPPPPPPMMDDYYHHmmddSSssssssssssEEEEEEEEEEEERRRRRR
         * (FORTRAN: A2<--A8--><---A10-->A2I2<--F10.5-><---F12.5--><-I6-> )
         * User's first and last initials (l), program name (P), date/time    
  (M/D/Y,H:m), dimensional codes (d), scaling factors (S, s), energy (E) if
modeling program input, internal registry number (R) if input through MDL
form.
         * A blank line can be substituted for line 2.
         */
        
        writer.write("  CDK    ");
        
        writer.write(new SimpleDateFormat("M/d/y,H:m",Locale.US).format(
        		Calendar.getInstance(TimeZone.getDefault()).getTime())
				);
        writer.write('\n');
        </code>



Regards,
Nina

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			Assoc. Prof. Dr. Nina Nikolova-Jeliazkova
       *      *               Institute for Parallel Processing
   *                *         Bulgarian Academy of Sciences
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     http://www.ist.bg        www: http://ambit.acad.bg/nina 	
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