A satisfying day! After my development laptop died yesterday, that is
especially good new. Take a look at this:
version=12.1.26_dev
# new feature: write MOL creates V2000 file
# new feature: write SDF creates multi-model SDfile based on models of
selected atoms
# new feature: over-run of SDF, MOL/V2000 reports error
# new feature: write V3000 creates V3000 file; see
http://www.symyx.com/downloads/public/ctfile/ctfile.pdf
Three things are new here:
Write MOL is the same as write V2000 -- writing a correct Molfile in V2000
format and indicating an error if there are more than 999 atoms or bonds. If
atoms are selected from multiple models, the written file is ONE model.
Write SDF is slightly different -- If you have selected atoms that cross
model boundaries -- including trajectories, then this creates a multmodel
SDfile PROVIDED no model goes over 999 atoms or bonds. (If it does, you get
an error.)
Finally, we can now write V3000 files, thus allowing bonding to be indicated
for an unlimited number of atoms and bonds. This is a nice format, because
whatever bonding you have created is preserved (provided it is the sort that
is recognized in a Molfile).
Angel, I need you to test those V2000 files to see if they really do load
into that viewer.
Bob
On Fri, Dec 17, 2010 at 8:40 PM, Robert Hanson <[email protected]> wrote:
> Ah, sure. I missed that. This means you are up late on a Friday night.
> Hmm....
>
> 2010/12/17 Angel Herráez <[email protected]>
>
>> (Sorry I sent this to the wrong thread: localizations)
>>
>> Bob, the month is wrong (zero-based)
>> __Jmol-12_11181000533D 1 1.00000 0.00000 0
>> should be
>> __Jmol-12_12181000533D 1 1.00000 0.00000 0
>>
>> That's why I added one
>> 1+ c.get(Calendar.MONTH)
>>
>>
>> Also, I think the position of the decimal point in XYZ for MOL2000 and
>> SDF is wrong by one
>>
>> xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmm...
>> 2.03475 -1.57247 -0.91833 C 0 0 0 0 0 0
>>
>>
>> V3000 support is a great thing! (not that I need it :-)
>>
>>
>>
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>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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