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
> 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
Bob, the doc
http://chemapps.stolaf.edu/jmol/docs/#writemodel
says
"In the case of SPT, a script file containing the coordinates of the model."
How is that? Only the state script is saved (I always thought that was it).
Hi Nico
I have got your changes but now I cannot build Jmol locally; I get these
messages:
Do you have any tips? My local building using Eclipse is not something I trust
much, but it
was working yesterday
[javac] F:\webs\eclipse\Jmol-trunk\Jmol\src\jmol\i18n\GT.java:123:
warning: unmappable
Nico, that looks good (I still have trouble building so don't see it well)
but we should revise the order of languages in the popup menu.
It seems to be alphabetic in the English names, but these are not displayed
when you are on
another language.
So I'd vote for putting the 2-letter (4-letter)
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
Hi Angel,
Building works fine on my computer.
The problems seems to come from the encoding used by Java when you compile
(I had to change GT.java encoding to UTF8).
I've just committed a modification to force using UTF8 when building. Tell
me if it works better.
Nico
2010/12/17 Angel Herráez
>
2010/12/17 Angel Herráez
> Nico, that looks good (I still have trouble building so don't see it well)
> but we should revise the order of languages in the popup menu.
> It seems to be alphabetic in the English names, but these are not displayed
> when you are on
> another language.
>
> So I'd vot
Works great, Nico!
No complains building now.
All languages display well in the menu (I see blocks for those whose fonts I
don't have, but I
guess that's fine)
The addition of language per demand is wonderful addition
I have commited a small fix - English was being displayed only in Spanish. No
Angel,
The menu is broken on my computer with the last fix.
It only shows 4 lines : "null - Català", ..., "null - Deutsch".
Nico
2010/12/17 Angel Herráez
> Works great, Nico!
>
> No complains building now.
> All languages display well in the menu (I see blocks for those whose fonts
> I don't h
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
Nico, those need to be entered in Unicode format, not like that, I think.
Bob
2010/12/17 Angel Herráez
> Hi Nico
>
> I have got your changes but now I cannot build Jmol locally; I get these
> messages:
>
> Do you have any tips? My local building using Eclipse is not something I
> trust much
I see -- Angel, update the full Jmol, not just the src. You need a new
project settings file.
On Fri, Dec 17, 2010 at 4:36 PM, Robert Hanson wrote:
> Nico, those need to be entered in Unicode format, not like that, I think.
>
> Bob
>
> 2010/12/17 Angel Herráez
>
>> Hi Nico
>>
>> I have got yo
Bob,
It's fixed, the problem was only that there was no encoding specified for
the build, so the encoding used was depending on the computer used to build.
I changed the build to force UTF8 encoding.
Nico
On Fri, Dec 17, 2010 at 11:44 PM, Robert Hanson wrote:
> I see -- Angel, update the full
Hi Bob,
Several errors in unit tests.
**
junit.framework.AssertionFailedError: Error returned for
..\Jmol-datafiles\mol\f_socl2b.mol: Error reading file at line 9:
1 2 1
null
for file f_socl2b.mol
type Mol
**
junit.framework.AssertionFailedError: Error returned for
..\Jmol-datafiles\
great, and I just built it without a problem as well.
On Fri, Dec 17, 2010 at 4:46 PM, Nicolas Vervelle wrote:
> Bob,
>
> It's fixed, the problem was only that there was no encoding specified for
> the build, so the encoding used was depending on the computer used to build.
> I changed the build
got it -- and notice that now Jmol automatically converts 2D V3000 files
into 3D. See Jmol-dataFiles/mol/alanine.2D.v3000
On Fri, Dec 17, 2010 at 4:49 PM, Nicolas Vervelle wrote:
> Hi Bob,
>
> Several errors in unit tests.
>
> **
> junit.framework.AssertionFailedError: Error returned for
> ..
If you look in that SPT file, you will see a
DATA "coord set"
block.
2010/12/17 Angel Herráez
> Bob, the doc
> http://chemapps.stolaf.edu/jmol/docs/#writemodel
> says
> "In the case of SPT, a script file containing the coordinates of the
> model."
>
> How is that? Only the state script is
There's just one error left (repeated over and over)
Error: [..\Jmol-datafiles\tests\scripts\run\monster_script.spt] Could not
instantiate shape:org.jmol.shape.Labels - java.lang.NullPointerException
org.jmol.shape.Labels - 75 - initShape
org.jmol.shape.Shape - 114 - initializeShape
org.jmol.viewe
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)
--
Lotusphere 20
(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, 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
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
Interesting. Fixed.
On Fri, Dec 17, 2010 at 5:38 PM, Nicolas Vervelle wrote:
> There's just one error left (repeated over and over)
>
> Error: [..\Jmol-datafiles\tests\scripts\run\monster_script.spt] Could not
> instantiate shape:org.jmol.shape.Labels - java.lang.NullPointerException
> org.jmol.s
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