HI Lochana,
The charge column will not be written but the 'M CHG' fields will be.
> M CHG 1 1 -1
> M CHG 1 4 1
This is the correct way to write the charge - the column is ignored if any CHG
field appears in the output.
> M CHGnn8 aaa vvv ...
>
> vvv: -15 to +15. Default of 0 = uncharged atom. When present, this property
> supersedes
> all charge and radical values in the atom block, forcing a 0 charge on all
> atoms not
> listed in an M CHG or M RAD line
If the proprietary program relies on this then it is incorrect and also won't
read anything with a charge < -3 or > +3 which is not writable in the column
(hence why it's superseded).
If you really want this column to be written you can add a patch - which
modifies this line -
https://github.com/cdk/cdk/blob/master/src/main/org/openscience/cdk/io/MDLV2000Writer.java#L417.
Many thanks,
J
On 22 Sep 2013, at 14:21, lochana menikarachchi <[email protected]> wrote:
>
> My biggest concern is the charge column. One of our programs uses a
> proprietary program that relies on this information.
>
> From: John May <[email protected]>
> To: lochana menikarachchi <[email protected]>
> Cc: "[email protected]" <[email protected]>
> Sent: Friday, September 20, 2013 4:11 PM
> Subject: Re: [Cdk-user] Charge and Stereo Columns in SD Files
>
> I can't speak for the charge but the stereo-parity column is read and
> written. This is non-portable and the value is not adjusted for atom
> rearrangements. That is - if you read in a mol file and mess about the atom
> order (add explicit hydrogens) then write it the value will not adjust for
> this and may not be correct.
>
> We have part of a stereo API which can store this information but it needs
> more work to be compatible with mol files and handle this correctly.
> Unfortunately I don't see that being fixed any time soon.
>
>> Some programs rely on information on these
>> columns and it is nice to have SDF in the same format as oechem and Marvin.
>
>
> That is true but officially you're not meant too (see attached image) :-).
> Archaic formats, yay!
>
> <Screen Shot 2013-09-20 at 21.03.04.png>
>
> On 20 Sep 2013, at 20:53, lochana menikarachchi <[email protected]> wrote:
>
>>
>> Was this issue addressed in a later patch?
>>
>> http://www.mail-archive.com/[email protected]/msg02347.html
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