[Jmol-users] Jmol 14.6.0

[Robert Hanson]

Jmol 14.6.0 has been released.

*Download Jmol-14.6.0_2016.05.17-binary.zip (66.2 MB)
*


Full list of new features includes:

Jmol.___JmolVersion="14.6.0_2016.05.17"

new feature: full implementation of OpenSMILES and OpenSMARTS in Jmol

new feature: C13 NMR prediction from
http://www.nmrdb.org/service/jsmol13c?smiles=
 -- although we send MOL file, not SMILES here.
 -- actuated with

   SHOW NMR H1   // H1 1H H or just SHOW NMR all default to this
   SHOW NMR C13  // or C or 13C
   SHOW NMR none // close JSpecView

(this is in the Jmol Application, not the HTML5 application)

new feature: Jmol now implements a way of indicating atropisomer chirality.
 -- measured dihedral angle is clockwise-positive front-to-back, as for
Jmol dihedrals
 -- matching with {*}.find("SMILES","...a^nm-a...") where n and m are 1, 2,
or 3
indicate first, second, or third, respectively, and indicate which
bonds of
the biaryl bond, as written, are to the reference atoms.
 -- for example:

   $ load $biphenol
   $ connect @{@7|@8} @{@1|@2} atropisomer
   $ print {*}.find("SMARTS","c1(O)c1^23-c2c(O)2")

  ({0:13})

  Explained below.

new feature: CONNECT {pair1} {pair2} ATROPISOMER
 -- creates a new bond of type atropisomer (bond chirality in biaryl
systems)
 -- each pair must include the bonded atom and its reference connected atom
 -- example:

   $ load $biphenol
   $ connect @{@7|@8} @{@1|@2} atropisomer
   $ getProperty bondinfo[7].type

   bondinfo[7].type"atropisomer_23"

new feature: BONDORDER ATROPISOMER_nm
  -- not for general use; will be found in state file
  -- for example:

select BONDS ({6});
bondOrder atropisomer_23;

new feature: Jmol SMILES bond atropisomerism ^nm- and ^^nm-
 -- indicates atropisomerism (bond chirality in biaryl systems)
 -- ^ and ^^ for bonds similar to @ and and @@ for atoms
 -- n and m are single-digit bond selectors, generally one of 1, 2, or 3
 -- n = 1/2/3 means "reference atom is first/second/third bonded
 -- ^- and ^^- same as ^22- and ^^22-, respectively
 -- example:

   $ load $biphenol
   $ connect @{@7|@8} @{@1|@2} atropisomer
   $ print {*}.find("SMARTS","c1(O){c1^23-c2}c(O)2")

   ({1 6})

  Here the "^23-" refers to the two carbons with connected oxygen atoms,
because the second
  bond listed for the carbon on the left is to the c1(O) atom, and the
third bond listed for
  the carbon on the right is to the other c(O) atom. Note that bond
numbering includes the
  implicit bond to the atom coming from the atom on its left, which for the
second carbon,
  starts with the atropisomeric bond itself, at least in this case.

 1*23  1*23
 c1(O)c1^23-c2c(O)2



new feature: (JavaScript) Jmol.loadFileFromDialog(jmolApplet0)
 -- asynchronous file loading on demand
 -- can be model file, but can also be script, dssr data - anything
 -- can be a local file or a URL
 -- see dssr.htm
 -- for example:

  Jmol.jmolButton("jmolApplet0",
[function(){Jmol.loadFileFromDialog(jmolApplet0)}],"Open File")

new feature: setting DSSR on the fly:

   model 1 property dssr "1d66.dssr"   // file containing data
   model 1 property dssr @{load("1d66.dssr")} // actual data
   select iloops



new feature: show chemical xxx  where xxx is one of the file types:

 alc cdxml cerius charmm cif cml ctx gjf gromacs hyperchem jme
 maestro mol mol2 sybyl2 mrv pdb sdf sdf3000 sln smiles xyz

   retrieves this information for the currently selected set of atoms
   from the the NCI CACTVS Resolver.

   Note that the PDB writer is nonstandard, and "SDF" no longer returns
   the 2D mol file, only the 3D mol file.

   Can be used as the show() function: x = show("chemical jme")

new feature: print {*}.find("SMILES/hydrogen/") adds hydrogen atoms

feature note: JSME upgraded to JSME_2015-12-06-2


FEATURE CHANGE: Jmol 14.5.4_2016.04.23 by default will implement DSSP 2.0
as described in
Int. J. Mol. Sci. 2014, 15, 7841-7864;
doi:10.3390/ijms15057841
and implemented at http://www.cmbi.ru.nl/dssp.html.
This change only affects helices that have bulges,
indicating them
more appropriately as pi helices rather than alpha
helices.

The original version of DSSP, "DSSP 1.0" will be available
using

calculate structure DSSP 1.0
show DSSP 1.0
load ... filter "DSSP1"

This change is for 14.5 only, not 14.4, which remains DSSP
1.0


new feature: preliminary MMTF reader
  -- MacroMolecular Transmission Format (MMTF, from RTSB)
  -- see https://github.com/rcsb/mmtf/blob/master/spec.md#overview
  -- binary format for file transfer and molecule construction
  -- uses MessagePack binary JSON format
  -- entirely experimental; not for general consumption
  -- biomolecule processing works
  -- DSSP secondary structure is read

 *
 * JmolData RCSB MMTF 

[Jmol-users] JmolApplet.jar

[Robert Hanson]

Two questions:

1. What would you think of dropping JmolApplet.jar from the
distribution?
2. How about JmolAppletSigned.jar?

Could these, perhaps be in a separate zip for download, perhaps
JmolAppletJava.zip?


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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] Jmol on Maven Central

[Robert Hanson]

Will be checking in Jmol 14.6 release as soon as I can. But it's not a
Maven release. Someone else has to do that.

On Tue, May 17, 2016 at 5:57 AM, Spencer Bliven 
wrote:

> We at Biojava are quite interested in getting a more recent version of
> Jmol on maven, so I thought I would bump this thread and offer some
> suggestions.
>
> Authorization is granted by adding a user to your OSS project ticket:
> https://issues.sonatype.org/browse/OSSRH-3633
>
> Right now only Tomas (plusik) and Nico (nicov) appear to be authorized.
>
> I could also help out with this if needed. My username is sbliven.
>
> -Spencer
>
>
> On Sat, Jan 23, 2016 at 5:19 PM, Nicolas Vervelle 
> wrote:
>
>> Hi Mark,
>>
>> On Fri, Jan 22, 2016 at 6:30 PM, Mark Williamson  wrote:
>>
>>> On 31/12/15 13:46, Nicolas Vervelle wrote:
>>> > Hi Mark,
>>> >
>>> > I'm probably the one who deployed the old version a long time ago (or
>>> > Bob, not sure).
>>> > I'm currently way too busy on various matters to keep doing releases
>>> for
>>> > Jmol.
>>> >
>>> > I think having a volunteer to deal with releases on Maven central would
>>> > be very helpful. Anyone interested ?
>>> > There are some ant scripts in Jmol source code to deploy there, but
>>> they
>>> > haven't been used in a very long time.
>>> > So, first thing would be to check if they still work correctly
>>> (probably
>>> > by testing snapshots releases), and then try to find which SVN revision
>>> > should be deployed as a given version.
>>> >
>>> > Nico
>>> >
>>>
>>> Dear Nico,
>>>
>>> Apologies for the delay in responding. Thank you for the reply and
>>> useful information. Egon (offlist) mentioned a script at:
>>>
>>>
>>>
>>> https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/tools/jmol-sonatype.xml
>>>
>>> which I assume is the one that you refer to.
>>>
>>
>> Yes, this is the script that I used to deploy Jmol on Maven central.
>>
>>
>>
>>> I have had experience deploying Maven projects to maven
>>> central(http://search.maven.org/#search|ga|1|oscar4  and
>>> http://search.maven.org/#search|ga|1|fortranformat ), however I think I
>>> can probably grok how the script above works within an ant context.
>>>
>>> I'm happy to try to deploy this, but there is an issue. In order to
>>> deploy to Maven central with GroupId net.sourceforge.jmol, I will
>>> probably need some authorisation from the Maven central admin peeps.
>>> IIRC the person who originally deployed these will receive an email
>>> asking if this is OK.
>>>
>>
>> Yes, no problem for me, I don't remember who has the rights to grant
>> authorisation.
>> If it's me, I will do it when I receive the email.
>>
>>
>>
>>> Secondly, from the tags on the project
>>> (http://sourceforge.net/p/jmol/code/HEAD/tree/tags/) I cannot ascertain
>>> which one I should deploy.
>>>
>>
>> I suggest first trying with snapshots with the current trunk, to check
>> that everything is working correctly.
>>
>> For the version to really deploy, I think you need to see with Bob
>> Hanson, he's the one doing almost all the development on Jmol lately and
>> the one making the releases on sourceforge.
>>
>> Nico
>>
>>
>>
>> --
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>>
>>
>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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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bring their own devices (BYOD) to work are irked by the imposition of MDM
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Re: [Jmol-users] SMILES and SMARTS problems

[Robert Hanson]

forgot one:

On Tue, May 17, 2016 at 11:01 PM, Robert Hanson  wrote:

> The way you would do this is to check the structure using different SMARTS
> codes with different "directives".
>
>
>> 2.b. & 3. Criterion 3: Does the structure contain a ring(set) that meets
>> Criterion 2, and is planar?
>>
>
>
if ({*}.search("/aromaticPlanar/a") {...}  // a flat ring, almost certainly
planar.


>


-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
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Re: [Jmol-users] SMILES and SMARTS problems

[Robert Hanson]

The way you would do this is to check the structure using different SMARTS
codes with different "directives".



On Mon, May 16, 2016 at 5:34 AM, Mike Casey  wrote:

> Hi Bob,
>
>
> From one of your earlier postings I assumed that your algorithm for
> detecting 'strict' aromaticity must be checking the supplied structure
> against a set of criteria (cyclic, uninterrupted pi system, planar, 4n + 2
> electrons), so that it might be possible for the algorithm (optionally) to
> return 'flags' (meets, or does not meet, each criterion) that could then be
> used to generate the appropriate feedback to the learner.  I have now read
> your pdf on how the Jmol SMILES aromaticity algorithm works and, broadly
> speaking, it does seem to function in that manner.  So, following the steps
> listed in your pdf document, and thinking particularly about the STRICT
> directive, would it be possible to create an option for the function to
> return a set of diagnostics, as follows?
>
> 1. Criterion 1: Does the structure contain at least one ring?
>

if ({*}.search("[R]")) {.}// a ring exists

if ({*}.search("[r5,r6]")) {.}// a 5- or 6-membered ring exists



> 2.a., 2.c. (and 4.?) Criterion 2: Does the structure contain a ring(set)
> in which all the ring atoms are involved in the pi system?   (I'm not sure
> what kinds of structures the algorithm is seeking to exclude in Step 4, but
> I think it relates to Criterion 2.)
>

That one I don't have a direct test for. As long as you can restrict this
to 5- and 6-membered rings, perhaps just making sure all ring bonds have
only two or three connections would suffice:

if ({*}.search("[r5;d2,d3]1[$4([r5;d2,d3])]1 ||
[r6;d2,d3]1[$5([r6;d2,d3])]1")) {...} // 5- or 6-membered ring all with 2
or 3 substituents




> 2.b. & 3. Criterion 3: Does the structure contain a ring(set) that meets
> Criterion 2, and is planar?
>



>
> 2.c. & 3. Criterion 4: Does the structure contain a ring(set) that meets
> Criteria 2 & 3, and involves 4n+2 electrons, or 4n electrons?
>
>
if ({*}.search("a")) {...} // an aromatic atom in a planar ring that
satisfies the Hueckel 4n+2 rule

or

if ({*}.search("/open/a")) {...} // an aromatic atom in a planar ring
satisfying a more relaxed Hueckel 4n+2 rule that includes, for example,
unsaturated lactones and lactams such as pyran-2-one and 1H-pyridin-2-one



If you  want to find large-ring aromatic compounds with 18 or more
electrons, you need to use  the  /open/ directive as above, and look for a
ring at least as large as the ring you want.

Bob
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[Jmol-users] Interesting PubChem Error Note

[Otis Rothenberger]

So if PubChem is generating 2d coordinates,  I said why not just try it 
(compound not in PubChem, Jmol SMILES):

http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/SDF?smiles=O[C@H]1CC[C@@]2(C)C3=CC[C@@H]4[C@@H]2CC[C@]5(C)[C@H]6[C@H](C)C[C@H]7[C@@H](C)CC=C.C6C[C@H]54.C7C(C)C.C31_type=3d
 


The PubChem Error Message is interesting:


Status: 501
Code: PUGREST.Unimplemented
Message: Cannot (yet) generate 3D coordinates for structures without an 
existing CID


Stay Tuned…

Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

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Re: [Jmol-users] Interesting PubChem Discovery

[Otis Rothenberger]

You’re going to have to copy/paste that last link!
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

> On May 17, 2016, at 2:12 AM, Otis Rothenberger  wrote:
> 
> http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/PNG?smiles=C/C(C)=C/C(C%5BC@@H%5D(C)%5BC@%5D4(%5BH%5D)%5BC@%5D3(C)%5BC@%5D(%5BH%5D)(%5BC@@%5D1(%5BH%5D)%5BC@@%5D(%5BH%5D)(%5BC@%5D2(C)C(=CC1)C%5BC@@H%5D(O)CC2
>  
> )CC3)CC4)C(C)C

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[Jmol-users] Interesting PubChem Discovery

[Otis Rothenberger]

This really isn’t breaking my promise. It’s just interesting! I looks like 
PubChem will return proper file for these URL’s with ANY legal SMILES. There’s 
probably a size limit, but it worked for some pretty large molecules:

http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/SDF?smiles=C([C@@H](C)Cl)[C@@H](C)Br
 


http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/JSON?smiles=C([C@@H](C)Cl)[C@@H](C)Br

http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/PNG?smiles=C([C@@H](C)Cl)[C@@H](C)Br
 


http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/XML?smiles=C([C@@H](C)Cl)[C@@H](C)Br

Here’s one that’s NOT in PubChem:

http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/PNG?smiles=C/C(C)=C/C(C%5BC@@H%5D(C)%5BC@%5D4(%5BH%5D)%5BC@%5D3(C)%5BC@%5D(%5BH%5D)(%5BC@@%5D1(%5BH%5D)%5BC@@%5D(%5BH%5D)(%5BC@%5D2(C)C(=CC1)C%5BC@@H%5D(O)CC2)CC3)CC4)C(C)C


The SDF is 2D. SDF, XML, and JSON return 2d coordinates, bond annotations 
(stereo), Standard InChI, and OpenEye SMILES, which I think is canonical within 
PubChem. Of course, if the compound is in PubChem, then the full record is 
returned. I mentioned before that to pull data from the JSON you have to go 
through an iteration process. Clearly, the structure of these files can vary 
from compound to compound.

By the way, I purposely put an undeclared chiral carbon in the above structure 
to help me scope out the bond annotations. I think an undeclared stereo bond is 
marked with a 3.

Note that this means that PubChem can be used as an InChI resolver and source 
of canonical SMILES within PubChem.

Otis

--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

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