Re: [Jmol-users] problem when selecting smarts [#6]-[#6]

[Robert Hanson]

Terrific. Somehow I never found that myself. We should test a few other
aspects as well. I should note that Jmol will have a different definition of
"aromatic" -- not one based on bonding. Essentially our definition is
"aromatic or antiaromatic" -- ring, all sp2, that's all. That's possible
because we are starting with actual 3D structures generally, not just SMILES
strings.

Bob

-- 
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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Re: [Jmol-users] text box where what happens in the Jmol applet can be read

[Paul Pillot]

To know which residues are selected, you should send the script command "show 
residue" or "show sequence" and parse the response.

Le 19 sept. 2011 à 19:11, Angel Herráez a écrit :

>> So is ScriptCallback the correct way to get the information of the 
>> residues selected and the surfaces rendered?
> 
> I'm not sure. Haven't tested this thoroughly.
> 
> 
> 
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Re: [Jmol-users] text box where what happens in the Jmol applet can be read

[Angel Herráez]

> So is ScriptCallback the correct way to get the information of the 
> residues selected and the surfaces rendered?

I'm not sure. Haven't tested this thoroughly.



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Re: [Jmol-users] text box where what happens in the Jmol applet can be read

[Daniel Carbajo]

So is ScriptCallback the correct way to get the information of the residues
selected and the surfaces rendered?

2011/9/16 Daniel Carbajo 

> I have read the documentation and have played around but can only get the
> information of the measurements with MeasureCallback; I don't seem to be
> able to get the information of residues selected and surfaces rendered...
> the only thing that can give me some information about that is when I use 
> ScriptCallback
> along with *set debugScript TRUE, but it would require substantial
> parsing... is there any easier way?*
>
> El 16 de septiembre de 2011 12:12, Angel Herráez 
> escribió:
>
> You have to read the documentation for callbacks, both in Jmol.js and
>> in the scripting doc.
>> And part may not be fully documented, so you have to test.
>>
>> Measurements are output as messages, so they are there already; you
>> may need to parse the messages for a more descriptive output.
>>
>> Hover is an example, maybe you don't want it.
>>
>>
>>
>>
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>
>
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Re: [Jmol-users] problem when selecting smarts [#6]-[#6]

[Martin Guetlein]

On Mon, Sep 19, 2011 at 5:16 PM, Robert Hanson  wrote:
> That's fixed at http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
> I've also made it so that c=c does not match anything ever, but I'm not 100%
> sure that is correct.

Thanks a lot, I will test it soon.

>
> Q: What is the relationship between Daylight SMARTS and
> http://opentox.informatik.uni-freiburg.de/depict ?
>
> Is that a true implementation of Daylight SMARTS, or is it one (like Jmol)
> that is interpreted from the (somewhat ambiguous) description at the
> Daylight site?
>
> What can you tell us about that site? It looks like it is returning with an
> official Daylight page, but is that same SMILES/SMARTS page available at
> Daylight? I wasn't aware of that.
>
> Looks great, though.
>
> Bob

Its just very simple webservice that wraps the depict match service
(This one: http://www.daylight.com/daycgi_tutorials/depictmatch.cgi ).
The only purpose I built it for, is that I can encode a
smiles-smarts-matching-query to daylight in one URI (and can send it
to a mailing list, for instance).

Best regards,
Martin


>
>
>
> On Mon, Sep 19, 2011 at 7:18 AM, Robert Hanson  wrote:
>>
>> Ah! I see. Right. This is a specific problem to [#n] because those cases
>> are ambiguous in relation to aromaticity. I'm on to it. Thanks.
>>
>>
>> On Mon, Sep 19, 2011 at 2:46 AM, Martin Guetlein
>>  wrote:
>>>
>>> On Mon, Sep 19, 2011 at 3:56 AM, Robert Hanson 
>>> wrote:
>>> >
>>> > Martin,
>>> >
>>> > I'm not catching on. Why isn't 7 atoms correct? There are six C-C bonds
>>> > in the ring and one more C-C bond, 7 atoms total.
>>> >
>>> > $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H]
>>> > $ select smarts("[#6]-[#6]")
>>> > 7 atoms selected
>>> > $ select smarts("[#6][#6]")
>>> > 7 atoms selected
>>> > $ select smarts("[#6]=[#6]")
>>> > 6 atoms selected
>>> >
>>> > Right?
>>> >
>>> > Bob
>>>
>>> I think the aromatic bonds not should be matched. This is how daylight
>>> matches the smarts fragments:
>>>
>>> [#6]-[#6]
>>>
>>> http://opentox.informatik.uni-freiburg.de/depict?data=[H]C%3D1C%28[H]%29%3DC%28[H]%29C%28%3DC%28C%3D1%28[H]%29%29C%28F%29%28F%29F%29S[H]&smarts=[%236]-[%236]
>>>
>>> Best regards,
>>> Martin
>>>
>>>
>>>
>>> >
>>> > On Sun, Sep 18, 2011 at 4:46 PM, Martin Guetlein
>>> >  wrote:
>>> >>
>>> >>
>>> >> On Fri, Sep 16, 2011 at 6:55 PM, Robert Hanson 
>>> >> wrote:
>>> >>>
>>> >>> It's working right for me:
>>> >>>
>>> >>> load $1,3-butadiene
>>> >>> select smarts("[#6]-[#6]")
>>> >>>
>>> >>> 2 atoms selected
>>> >>
>>> >>
>>> >> Thats not what I meant, it makes too many selections:
>>> >>
>>> >> $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H]
>>> >> $ select smarts("[#6]-[#6]")
>>> >> 7 atoms selected
>>> >>
>>> >> Best regards,
>>> >> Martin
>>> >>
>>> >>>
>>> >>>
>>> >>> On Fri, Sep 16, 2011 at 6:25 AM, Martin Guetlein
>>> >>>  wrote:
>>> 
>>>  Hi,
>>> 
>>>  I would like to match the following smarts [#6]-[#6], which is two
>>>  carbon atoms connect with single bond.
>>> 
>>>  The problem: 'select smarts("[#6]-[#6]")' seems to ignore the bond
>>>  type and selects all pairs of carbons, even those who are aromatic.
>>> 
>>>  It is not an aromticity detection problem, as 'select smarts("C-c")
>>>  or smarts("C-C")' works fine (it does _not_ select the aromatic pairs).
>>> 
>>>  (Unfortunately, I cannot just use the last-mentioned expression, my
>>>  smarts strings are created automatically and I have to stick with the
>>>  [#] notation.)
>>> 
>>>  Best regards,
>>>  Martin
>>> 
>>> 
>>> 
>>> 
>>> 
>>>  --
>>>  Dipl-Inf. Martin Gütlein
>>>  Phone:
>>>  +49 (0)761 203 7633 (office)
>>>  +49 (0)177 623 9499 (mobile)
>>>  Email:
>>>  guetl...@informatik.uni-freiburg.de
>>> 
>>> 
>>>  --
>>>  BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
>>>  http://p.sf.net/sfu/rim-devcon-copy2
>>>  ___
>>>  Jmol-users mailing list
>>>  Jmol-users@lists.sourceforge.net
>>>  https://lists.sourceforge.net/lists/listinfo/jmol-users
>>> 
>>> >>>
>>> >>>
>>> >>>
>>> >>> --
>>> >>> 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
>>> >>>
>>> >>>
>>> >>> --
>>> >>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
>>> >>> http://p.sf.net/sfu/rim-devcon-copy2
>>> >>> ___
>>> >>> Jmol

[Jmol-users] Jmol 12.2.RC7 released

[Robert Hanson]

Thanks, Nico, for releasing this. Some bug fixes and new features --
included here for 12.2.RC5 - 12.2.RC7.

bug fixes:

#version=12.2.RC5-RC7

# bug fix: SMILES [#6A] and [#6a] should be distinct
# bug fix: load SMILES should not allow 2D return
# bug fix: load SMILES not saved properly in state
# bug fix: GAUSSIAN reader cannot read MOs when more than 1000 orbitals
# bug fix: load TRAJECTORY does not assign model names
# bug fix: load PACKED SUPERCELL produces red0undant atoms
# bug fix: Crystal reader not handling CONV option properly
# bug fix: AtomSetChooser set up too late -- can override embedded
jmolScript vibration/vector scale commands
# bug fix: CIF reader not reading isotopes such as D and T
# bug fix: imines SMILES may cause null pointer exception
# bug fix: load slab/polymer with PACKED does not work
# bug fix: SOE added to carbohydrate list (L-sorbose in pyranose form; SOL
is the open form, 3AI3.pdb)
# bug fix: QuantumEspresso reader not reading ALAT/A_0 files correctly
# bug fix: deleting of the first model in a set that has load APPEND will
not produce the correct state
# bug fix: deletion of models having atoms with dots can generate
null pointer exception

# bug fix: atomic orbitals should be assigned 0 if |psi| < 1e-7
# bug fix: MO LIST broken
# bug fix: linear combination of MOs broken in 12.1.49
# bug fix: setting DOTS off can cause null pointer exception
# bug fix: measurements, picking not allowed to FIXED atoms
# bug fix: "$phosphorus pentoxide" label %[shape] indicates AX4E not AX4
hybridization on phosphorus
# bug fix: show colorscheme "high"   causes exception
# bug fix: set naviationPeriodic while navigating should disallow unit cell
and standard axes
# bug fix: undocumented "redo" "undo" application-only commands changed to
"redocmd" "undocmd"

new features:

#version=12.2.RC5-RC7

# new feature: CASTEP reader for .md and .geom trajectories
# new feature: load TRAJECTORY now loads vibrations as trajectories
# new feature: preliminary CASTEP .phonon frequency file reader
#  -- preliminary only
#  -- reads q=0 and q#0 points
#  -- use load ... SUPERCELL  to select out a specific q-point
#  -- for example:
#   load c60.phonon {1 1 1} SUPERCELL {2 1 2} # will select for q = (0.5 0
0.5)
#   load c60.phonon -5 {1 1 1} SUPERCELL {2 1 2} # and only mode 5 for q =
(0.5 0 0.5)
#   load c60.phonon -5 {2 2 2} SUPERCELL {-4 1 2} # eight supercells; mode 5
only for q=(-0.25 0 0.5)
# new feature: transparent background PNG images with WRITE PNGT .png
#  -- set ANTIALIASEIMAGES false to avoid slight trim issue
#  -- use an unusual color, such as [x010101] for the background
# new feature: forgotten feature: load ".xxx" [ list of models to load ]
#  -- for example:   load "cyclohexane_movie.xyz" [ 1 6 11 26 ]
# new feature: CRYSTAL reader reads property files for tensor quantities
#  -- displayed as ELLIPSOID
#  -- note that scale is set using ELLIPSOID N  where N is a percent;
default 50; max 100

# new feature: unitcell {xxx yyy scale}
#  -- allows for display of a block of unit cells in 444 555 notation
#  -- cleared by   unitcell {0 0 0}
#  -- where z is negative fills entire (standard) xxx yyy space with unit
cells of size z

# new feature: set minPixelSelRadius
# new feature: UNDO/REDO
#  -- console-only commands same as buttons
#  -- full file reload (saving of full state)
# new feature: undoMove/redoMove
#  -- script commands
#  -- act like CTRL-Z/(CTRL-SHIFT-Z or CTRL-Y)
#  -- just move atoms; no file loading (just atom positions saved)
#  UNDOMOVE/UNDOMOVE 1 # undo last movement
#  UNDOMOVE n  # undo last n movements
#  UNDOMOVE 0/UNDOMOVE ALL  # undo all movements
#  REDOMOVE/REDOMOVE 1 # redo last movement
#  REDOMOVE n  # redo last n movements
#  REDOMOVE 0/REDOMOVE ALL  # redo all movements
#  UNDOMOVE -1 # clear UNDO history
#  REDOMOVE -1 # clear REDO history
#  REDOMOVE -2/UNDOMOVE -2 # clear both histories

# new feature: set isosurfaceKey ON|OFF
#  -- creates a vertical hoverable key on the left
#  -- only the most recent and visible isosurface
#  -- is not exported

-- 
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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Re: [Jmol-users] problem when selecting smarts [#6]-[#6]

[Robert Hanson]

That's fixed at
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zipI've also
made it so that c=c does not match anything ever, but I'm not 100%
sure that is correct.

Q: What is the relationship between Daylight SMARTS and
http://opentox.informatik.uni-freiburg.de/depict?

Is that a true implementation of Daylight SMARTS, or is it one (like Jmol)
that is interpreted from the (somewhat ambiguous) description at the
Daylight site?

What can you tell us about that site? It looks like it is returning with an
official Daylight page, but is that same SMILES/SMARTS page available at
Daylight? I wasn't aware of that.

Looks great, though.

Bob



On Mon, Sep 19, 2011 at 7:18 AM, Robert Hanson  wrote:

> Ah! I see. Right. This is a specific problem to [#n] because those cases
> are ambiguous in relation to aromaticity. I'm on to it. Thanks.
>
>
>
> On Mon, Sep 19, 2011 at 2:46 AM, Martin Guetlein <
> martin.guetl...@googlemail.com> wrote:
>
>> On Mon, Sep 19, 2011 at 3:56 AM, Robert Hanson 
>> wrote:
>> >
>> > Martin,
>> >
>> > I'm not catching on. Why isn't 7 atoms correct? There are six C-C bonds
>> in the ring and one more C-C bond, 7 atoms total.
>> >
>> > $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H]
>> > $ select smarts("[#6]-[#6]")
>> > 7 atoms selected
>> > $ select smarts("[#6][#6]")
>> > 7 atoms selected
>> > $ select smarts("[#6]=[#6]")
>> > 6 atoms selected
>> >
>> > Right?
>> >
>> > Bob
>>
>> I think the aromatic bonds not should be matched. This is how daylight
>> matches the smarts fragments:
>>
>> [#6]-[#6]
>>
>> http://opentox.informatik.uni-freiburg.de/depict?data=[H]C%3D1C%28[H]%29%3DC%28[H]%29C%28%3DC%28C%3D1%28[H]%29%29C%28F%29%28F%29F%29S[H]&smarts=[%236]-[%236]
>>
>> Best regards,
>> Martin
>>
>>
>>
>> >
>> > On Sun, Sep 18, 2011 at 4:46 PM, Martin Guetlein <
>> martin.guetl...@googlemail.com> wrote:
>> >>
>> >>
>> >> On Fri, Sep 16, 2011 at 6:55 PM, Robert Hanson 
>> wrote:
>> >>>
>> >>> It's working right for me:
>> >>>
>> >>> load $1,3-butadiene
>> >>> select smarts("[#6]-[#6]")
>> >>>
>> >>> 2 atoms selected
>> >>
>> >>
>> >> Thats not what I meant, it makes too many selections:
>> >>
>> >> $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H]
>> >> $ select smarts("[#6]-[#6]")
>> >> 7 atoms selected
>> >>
>> >> Best regards,
>> >> Martin
>> >>
>> >>>
>> >>>
>> >>> On Fri, Sep 16, 2011 at 6:25 AM, Martin Guetlein <
>> martin.guetl...@googlemail.com> wrote:
>> 
>>  Hi,
>> 
>>  I would like to match the following smarts [#6]-[#6], which is two
>> carbon atoms connect with single bond.
>> 
>>  The problem: 'select smarts("[#6]-[#6]")' seems to ignore the bond
>> type and selects all pairs of carbons, even those who are aromatic.
>> 
>>  It is not an aromticity detection problem, as 'select smarts("C-c")
>> or smarts("C-C")' works fine (it does _not_ select the aromatic pairs).
>> 
>>  (Unfortunately, I cannot just use the last-mentioned expression, my
>> smarts strings are created automatically and I have to stick with the
>> [#] notation.)
>> 
>>  Best regards,
>>  Martin
>> 
>> 
>> 
>> 
>> 
>>  --
>>  Dipl-Inf. Martin Gütlein
>>  Phone:
>>  +49 (0)761 203 7633 (office)
>>  +49 (0)177 623 9499 (mobile)
>>  Email:
>>  guetl...@informatik.uni-freiburg.de
>> 
>> 
>> --
>>  BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
>>  http://p.sf.net/sfu/rim-devcon-copy2
>>  ___
>>  Jmol-users mailing list
>>  Jmol-users@lists.sourceforge.net
>>  https://lists.sourceforge.net/lists/listinfo/jmol-users
>> 
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> 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
>> >>>
>> >>>
>> --
>> >>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
>> >>> http://p.sf.net/sfu/rim-devcon-copy2
>> >>> ___
>> >>> Jmol-users mailing list
>> >>> Jmol-users@lists.sourceforge.net
>> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> Dipl-Inf. Martin Gütlein
>> >> Phone:
>> >> +49 (0)761 203 7633 (office)
>> >> +49 (0)177 623 9499 (mobile)
>> >> Email:
>> >> guetl...@informatik.uni-freiburg.de
>> >>
>> >>
>> 

Re: [Jmol-users] problem when selecting smarts [#6]-[#6]

[Robert Hanson]

Ah! I see. Right. This is a specific problem to [#n] because those cases are
ambiguous in relation to aromaticity. I'm on to it. Thanks.


On Mon, Sep 19, 2011 at 2:46 AM, Martin Guetlein <
martin.guetl...@googlemail.com> wrote:

> On Mon, Sep 19, 2011 at 3:56 AM, Robert Hanson  wrote:
> >
> > Martin,
> >
> > I'm not catching on. Why isn't 7 atoms correct? There are six C-C bonds
> in the ring and one more C-C bond, 7 atoms total.
> >
> > $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H]
> > $ select smarts("[#6]-[#6]")
> > 7 atoms selected
> > $ select smarts("[#6][#6]")
> > 7 atoms selected
> > $ select smarts("[#6]=[#6]")
> > 6 atoms selected
> >
> > Right?
> >
> > Bob
>
> I think the aromatic bonds not should be matched. This is how daylight
> matches the smarts fragments:
>
> [#6]-[#6]
>
> http://opentox.informatik.uni-freiburg.de/depict?data=[H]C%3D1C%28[H]%29%3DC%28[H]%29C%28%3DC%28C%3D1%28[H]%29%29C%28F%29%28F%29F%29S[H]&smarts=[%236]-[%236]
>
> Best regards,
> Martin
>
>
>
> >
> > On Sun, Sep 18, 2011 at 4:46 PM, Martin Guetlein <
> martin.guetl...@googlemail.com> wrote:
> >>
> >>
> >> On Fri, Sep 16, 2011 at 6:55 PM, Robert Hanson 
> wrote:
> >>>
> >>> It's working right for me:
> >>>
> >>> load $1,3-butadiene
> >>> select smarts("[#6]-[#6]")
> >>>
> >>> 2 atoms selected
> >>
> >>
> >> Thats not what I meant, it makes too many selections:
> >>
> >> $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H]
> >> $ select smarts("[#6]-[#6]")
> >> 7 atoms selected
> >>
> >> Best regards,
> >> Martin
> >>
> >>>
> >>>
> >>> On Fri, Sep 16, 2011 at 6:25 AM, Martin Guetlein <
> martin.guetl...@googlemail.com> wrote:
> 
>  Hi,
> 
>  I would like to match the following smarts [#6]-[#6], which is two
> carbon atoms connect with single bond.
> 
>  The problem: 'select smarts("[#6]-[#6]")' seems to ignore the bond
> type and selects all pairs of carbons, even those who are aromatic.
> 
>  It is not an aromticity detection problem, as 'select smarts("C-c") or
> smarts("C-C")' works fine (it does _not_ select the aromatic pairs).
> 
>  (Unfortunately, I cannot just use the last-mentioned expression, my
> smarts strings are created automatically and I have to stick with the
> [#] notation.)
> 
>  Best regards,
>  Martin
> 
> 
> 
> 
> 
>  --
>  Dipl-Inf. Martin Gütlein
>  Phone:
>  +49 (0)761 203 7633 (office)
>  +49 (0)177 623 9499 (mobile)
>  Email:
>  guetl...@informatik.uni-freiburg.de
> 
> 
> --
>  BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
>  http://p.sf.net/sfu/rim-devcon-copy2
>  ___
>  Jmol-users mailing list
>  Jmol-users@lists.sourceforge.net
>  https://lists.sourceforge.net/lists/listinfo/jmol-users
> 
> >>>
> >>>
> >>>
> >>> --
> >>> 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
> >>>
> >>>
> --
> >>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
> >>> http://p.sf.net/sfu/rim-devcon-copy2
> >>> ___
> >>> Jmol-users mailing list
> >>> Jmol-users@lists.sourceforge.net
> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >>>
> >>
> >>
> >>
> >> --
> >> Dipl-Inf. Martin Gütlein
> >> Phone:
> >> +49 (0)761 203 7633 (office)
> >> +49 (0)177 623 9499 (mobile)
> >> Email:
> >> guetl...@informatik.uni-freiburg.de
> >>
> >>
> --
> >> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
> >> http://p.sf.net/sfu/rim-devcon-copy2
> >> ___
> >> Jmol-users mailing list
> >> Jmol-users@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
> >>
> >
> >
> >
> > --
> > 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
> >
> >
> --
> > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
> > Learn about the latest advances in developing for the
> > BlackBerry® mobile platform with sessions, labs & more.
> > See new tools and technologies. Registe

Re: [Jmol-users] Jmol & Java 7

[Eike Jordan]

Good news for all those folks running JMol under Linux. I just tested
the september release 7u2 build b07 [1] and everything's fine!!!

~eike

[1] http://jdk7.java.net/download.html
[2] http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=7067049

On 07/14/2011 02:23 PM, Robert Hanson wrote:
> thanks, Eike
>
> On Thu, Jul 14, 2011 at 5:00 AM, Eike Jordan  wrote:
>
>> Hi Bob,
>>
>> On 07/13/2011 08:07 PM, Robert Hanson wrote:
>>> Eike,
>>>
>>> OK, then that's your  link to send to both Mozilla and Java. Looks like
>>> there should be enough information there for them to pinpoint  the
>> problem.
>>>
>>>
>>> Can you create that bug report?
>>>
>>
>> Well i did some more testing investigation - the problem is not even
>> confined to
>> Firefox. Opera does not crash but the error message is quite the same and
>> JmolApplet
>> refuses to display.
>>
>> I submitted a bug at http://bugreport.sun.com/ - Java plugin causes
>> Browser crash when
>> display JmolApplet on Linux/Ubuntu
>>
>> "
>> Bug Submit Complete
>> Thank You
>>
>> Thank you for taking the time to provide us with your details.
>>
>> What's Next?
>>
>> We will review your report. Depending upon the completeness of the
>> report and our ability to reproduce the problem, either a new bug will
>> be posted, or we will contact you for further information. You will be
>> notified by email in either case.
>>
>> We will try to process all newly posted bugs in a timely manner, but
>> we make no promises about the amount of time in which a bug will be
>> fixed. If you just reported a bug that could have a major impact on
>> your project, consider using one of the technical support offerings
>> available at Oracle Support.
>> "
>>
>> We'll wait and see! :-)
>>
>> Regards,
>> ~eike
>>
>> --
>> Eike Jordan
>>
>> | FIZ CHEMIE BERLIN
>> | Franklin Str. 11   --,__o
>> | 10587 Berlin  --   _-\_<,
>> |  --   (+)/'(+)
>> | Tel. : 0049-30-39977 214
>>
>>
>>
>> --
>> AppSumo Presents a FREE Video for the SourceForge Community by Eric
>> Ries, the creator of the Lean Startup Methodology on "Lean Startup
>> Secrets Revealed." This video shows you how to validate your ideas,
>> optimize your ideas and identify your business strategy.
>> http://p.sf.net/sfu/appsumosfdev2dev
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
>
>
> --
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
>
>
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

-- 
Eike Jordan  

| FIZ CHEMIE BERLIN
| Franklin Str. 11   --,__o
| 10587 Berlin  --   _-\_<,
|  --   (+)/'(+)
| Tel. : 0049-30-39977 214


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Re: [Jmol-users] problem when selecting smarts [#6]-[#6]

[Egon Willighagen]

On Mon, Sep 19, 2011 at 9:46 AM, Martin Guetlein
 wrote:
> I think the aromatic bonds not should be matched.

I think the '~' bond should match any bond and ':' aromatic bonds, but
'-' is explicit for single bonds...

Egon

-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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Re: [Jmol-users] problem when selecting smarts [#6]-[#6]

[Martin Guetlein]

On Mon, Sep 19, 2011 at 3:56 AM, Robert Hanson  wrote:
>
> Martin,
>
> I'm not catching on. Why isn't 7 atoms correct? There are six C-C bonds in 
> the ring and one more C-C bond, 7 atoms total.
>
> $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H]
> $ select smarts("[#6]-[#6]")
> 7 atoms selected
> $ select smarts("[#6][#6]")
> 7 atoms selected
> $ select smarts("[#6]=[#6]")
> 6 atoms selected
>
> Right?
>
> Bob

I think the aromatic bonds not should be matched. This is how daylight
matches the smarts fragments:

[#6]-[#6]
http://opentox.informatik.uni-freiburg.de/depict?data=[H]C%3D1C%28[H]%29%3DC%28[H]%29C%28%3DC%28C%3D1%28[H]%29%29C%28F%29%28F%29F%29S[H]&smarts=[%236]-[%236]

Best regards,
Martin



>
> On Sun, Sep 18, 2011 at 4:46 PM, Martin Guetlein 
>  wrote:
>>
>>
>> On Fri, Sep 16, 2011 at 6:55 PM, Robert Hanson  wrote:
>>>
>>> It's working right for me:
>>>
>>> load $1,3-butadiene
>>> select smarts("[#6]-[#6]")
>>>
>>> 2 atoms selected
>>
>>
>> Thats not what I meant, it makes too many selections:
>>
>> $ load SMILES [H]C=1C([H])=C([H])C(=C(C=1([H]))C(F)(F)F)S[H]
>> $ select smarts("[#6]-[#6]")
>> 7 atoms selected
>>
>> Best regards,
>> Martin
>>
>>>
>>>
>>> On Fri, Sep 16, 2011 at 6:25 AM, Martin Guetlein 
>>>  wrote:

 Hi,

 I would like to match the following smarts [#6]-[#6], which is two carbon 
 atoms connect with single bond.

 The problem: 'select smarts("[#6]-[#6]")' seems to ignore the bond type 
 and selects all pairs of carbons, even those who are aromatic.

 It is not an aromticity detection problem, as 'select smarts("C-c") or 
 smarts("C-C")' works fine (it does _not_ select the aromatic pairs).

 (Unfortunately, I cannot just use the last-mentioned expression, my smarts 
 strings are created automatically and I have to stick with the 
 [#] notation.)

 Best regards,
 Martin





 --
 Dipl-Inf. Martin Gütlein
 Phone:
 +49 (0)761 203 7633 (office)
 +49 (0)177 623 9499 (mobile)
 Email:
 guetl...@informatik.uni-freiburg.de

 --
 BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
 http://p.sf.net/sfu/rim-devcon-copy2
 ___
 Jmol-users mailing list
 Jmol-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/jmol-users

>>>
>>>
>>>
>>> --
>>> 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
>>>
>>> --
>>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
>>> http://p.sf.net/sfu/rim-devcon-copy2
>>> ___
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>
>>
>>
>> --
>> Dipl-Inf. Martin Gütlein
>> Phone:
>> +49 (0)761 203 7633 (office)
>> +49 (0)177 623 9499 (mobile)
>> Email:
>> guetl...@informatik.uni-freiburg.de
>>
>> --
>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
>> http://p.sf.net/sfu/rim-devcon-copy2
>> ___
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> 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
>
> --
> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
> Learn about the latest advances in developing for the
> BlackBerry® mobile platform with sessions, labs & more.
> See new tools and technologies. Register for BlackBerry® DevCon today!
> http://p.sf.net/sfu/rim-devcon-copy1
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 7633 (office)
+49 (0)177 623 9499 (mobile)
Email:
guetl...@informatik.uni-freiburg.de

--
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