Great, then I think we are all set. We will recommend using
write V3000 t.mol
rather than
write t.v3000
and we will not mess with
write t.v3000.mol
How's that? Then it is just the way it is with all the file writing.
write t.mol
and
write V2000 t.mol
are identical now -- V2000 will be the
> and the very latest little fix I just checked in -- there was an extra " 0"
> on the bond records.
Yes, I was just tracking that down that extra zero. That was the origin of the
error DS
Visualizer gives. Now V3000 is loading fine into both
-- Accelrys DS Visualizer 2.0 (3D viewer-editor)
I downloaded the OpenBabel GUI, and it read the V3000 file created using
load =1crn
write V3000 1crn.mol
and the very latest little fix I just checked in -- there was an extra " 0"
on the bond records.
One hitch was that
write 1crn.v3000
didn't work, because apparently OpenBabel requires a spe
2010/12/18 Angel Herráez :
> Thanks, Egon, I had already found that page of yours yesterday.
> But in practical terms I don't know what to make out of it. I haven't got CDK
> installed (and will
> not, since it exceeds my needs and understanding).
OK, point taken. Of course, you can ask on the cd
Thanks, Egon, I had already found that page of yours yesterday.
But in practical terms I don't know what to make out of it. I haven't got CDK
installed (and will
not, since it exceeds my needs and understanding).
Now I'm worried that Bob gets a new laptop and so his development rate will be
dup
Hej Angel,
2010/12/18 Angel Herráez :
> Bob wrote:
>> A satisfying day! After my development laptop died yesterday, that is
>> especially good new.
>
> So you melted it down? ;-D
Would not surprise me either :)
>> Angel, I need you to test those V2000 files to see if they really do load
>> i
Bob wrote:
> A satisfying day! After my development laptop died yesterday, that is
> especially good new.
So you melted it down? ;-D
> Angel, I need you to test those V2000 files to see if they really do load
> into that viewer.
Sure. Later this weekend
I'm trying t find if there is a stan
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
Ah, sure. I missed that. This means you are up late on a Friday night.
Hmm
2010/12/17 Angel Herráez
> (Sorry I sent this to the wrong thread: localizations)
>
> Bob, the month is wrong (zero-based)
> __Jmol-12_11181000533D 1 1.0 0.0 0
> should be
> __Jmol-12_12181000533D
(Sorry I sent this to the wrong thread: localizations)
Bob, the month is wrong (zero-based)
__Jmol-12_11181000533D 1 1.0 0.0 0
should be
__Jmol-12_12181000533D 1 1.0 0.0 0
That's why I added one
1+ c.get(Calendar.MONTH)
Also, I think the position of the decim
Ah, you are too quick for me! I wasn't done.
See latest installment.
-- read/write SDF files (SDF)
-- read/write V2000 files (MOL or V2000)
-- read/write V3000 files (V3000 or atomno > 999 or bondno > 999)
Check it out.
Bob
2010/12/17 Angel Herráez
> Hi Bob,
>
> I've looked at your commit t
Hi Bob,
I've looked at your commit to SVN.
Is there a reason why you want to keep the headers for the MOL export as they
were?
I think we should conform to MDL-Symyx for both SDF and MOL
The only thing different for SDF would be the line
Regards
> Well, we aren't exporting SD files, just MOL files. Let's just
> implement an SDF file writer and do that right rather than faking it.
Bob, you're right, but that's not exactly the situation. I didn't
make myself clear enough.
MOL and SD formats are exactly the same except for the line
Well, we aren't exporting SD files, just MOL files. Let's just implement an
SDF file writer and do that right rather than faking it.
2010/12/16 Angel Herráez
> I have found out that MOL files exported by Jmol, using the "write"
> command, fail to be
> opened in PowerMV, a free SDF viewer.
> So I
I have found out that MOL files exported by Jmol, using the "write" command,
fail to be
opened in PowerMV, a free SDF viewer.
So I've gone into finding the cause, and it is that
1. PowerMV is picky on the MOL/SDF format
2. Jmol exports do not fit the MDL spec in some aspects
So I am working o
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