If it doesn't hurt why not leave it. I will help me to make my program a lot
more open source. Right now I am using marvin because it retains this
information.
________________________________
From: John May <john...@ebi.ac.uk>
To: lochana menikarachchi <locha...@yahoo.com>
Cc: "cdk-user@lists.sourceforge.net" <cdk-user@lists.sourceforge.net>
Sent: Sunday, September 22, 2013 11:25 AM
Subject: Re: [Cdk-user] Charge and Stereo Columns in SD Files
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(hence why it's superseded).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 <locha...@yahoo.com> wrote:
>
>My biggest concern is the charge column. One of our programs uses a
>proprietary program that relies on this information.
>
>
>From:John May <john...@ebi.ac.uk>
>To: lochana menikarachchi <locha...@yahoo.com>
>Cc: "cdk-user@lists.sourceforge.net" <cdk-user@lists.sourceforge.net>
>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 <locha...@yahoo.com> wrote:
>
>
>>
>>Was this issue addressed in a later patch?
>>
>>
>>
>>http://www.mail-archive.com/cdk-user@lists.sourceforge.net/msg02347.html
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