Re: [Cdk-user] Adding properties to SDF files

[Kurt W. <kw...@po...>]

On Monday, October 20, 2003, at 03:18  PM, E.L. Willighagen (Egon) 
wrote:

> On Monday 20 October 2003 21:05, Kurt Werle wrote:
>> I have what I hope is a trivial problem: I want to read an SDF file,
>> add some key-values, and write it back out.  The trivial program I've
>> written to do that is at
>> http://shiftmanager.net/~kurt/test.java
>
> Code looks fine, but the problem is that the MDLWriter does not save 
> molecular
> properties at all...

I can accept that (for now :-)

>> It seems to load the molecule, but when it writes it back out, the
>> coordinates are 0'd out, and the property added is not written to 
>> file.
>
> Not sure why that is happening... that should not happen...

Probably worth noting that all the Z values were 0.000 in the original, 
though the X and Y values were not (if I'm reading this damn thing 
right).  In the output file all 3 values were 0.000.

>> Any hints, suggestions, or even "You can't get there from here"
>> appreciated.
>
> You could try the cdk-fileconvertor... which is the sh wrapper around
> org.openscience.cdk.applications.FileConvertor... to convert the SDF 
> into
> CML... by doing
>
> cdk-fileconvertor file.sdf
>
> The CML is more verbose on the content, and might give you an idea 
> what is
> happening...
>
> You could have a look at the sources of the MDLReader and -Writer in 
> the
> org.openscience.cdk.io package... the JavaDoc gives some hints on what 
> it
> reads and doesn't read...

This I will do.

>> NOTE:  I'm a coder - I don't understand 99% of the biochem going on
>> here, nor do I understand SDF file formats.  I just know that CDK
>> doesn't seem to be doing what I expect it to do.
>
> ;)
>
> Will get back to you later this week... if not, remind me...

Thanks.

Kurt
---
kw...@po...
http://www.pobox.com/~kwerle/
Tired of spam? Control your Mailserver (or .forward)? http://tess.sf.net