Re: [Jmol-users] Jmol on Maven Central

[Nicolas Vervelle]

Ok,

I've added a comment to request access for you.
https://issues.sonatype.org/browse/OSSRH-3633?focusedCommentId=369327=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-369327

Nico


On Wed, Aug 24, 2016 at 11:12 AM, Spencer Bliven 
wrote:

> I volunteer to push releases to maven central. My OSS username is
> sbliven.
>
> To authorize someone, I believe that it is sufficient to add a comment to
> your OSS project ticket (https://issues.sonatype.org/browse/OSSRH-3633)
> requesting access for the username.
>
> -Spencer
>
> On Tue, Aug 23, 2016 at 10:55 PM, Robert Hanson 
> wrote:
>
>> not aware of any volunteers.
>>
>> On Tue, Aug 23, 2016 at 10:40 AM, Spencer Bliven <
>> spencer.bli...@gmail.com> wrote:
>>
>>> I just wanted to bump this thread. Any chance of getting a new maven
>>> maintainer added soon?
>>>
>>> Cheers,
>>> Spencer
>>>
>>> On Fri, Aug 12, 2016 at 10:19 AM, Spencer Bliven <
>>> spencer.bli...@gmail.com> wrote:
>>>
 So I guess the next step that needs to happen is for Nico to request
 that Mark get added to the OSS ticket. I haven't been an active Jmol
 contributor, but I'd be happy to help with maintaining the maven package if
 you want to add me too (OSS user sbliven).

 -Spencer

 On Thu, Aug 11, 2016 at 11:29 PM, Robert Hanson 
 wrote:

> all checked in.
>
> On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven <
> spencer.bli...@gmail.com> wrote:
>
>> Awesome. BioJava has good mmtf support, so if we can get the new Jmol
>> release into maven then MMTF might be a good exchange format for passing
>> structures to Jmol. We're currently stuck with using PDB and are hurting
>> from the limitations (e.g. on chain identifiers & number of atoms).
>>
>> -Spencer
>>
>> On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson 
>> wrote:
>>
>>> Thanks, Spencer. I am in the process of releasing an important
>>> update for BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE 
>>> files
>>> and the new MMTF format from RCSB (which is FANTASTIC by the way...)
>>>
>>> Bob
>>>
>>> On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven <
>>> spencer.bli...@gmail.com> wrote:
>>>
 Hey,

 I also took a crack at getting the dist-release command to
 complete, since it would be extremely nice to get BioJava using a more
 recent version of Jmol. Using the latest trunk I got all steps to 
 complete
 by modifying tools/jmol-sonatype.xml as you suggest to refer to "${
 Jmol.properties.Jmol.___JmolVersion}" in line 30. This creates the
 build/dist-maven directory as desired.

 Right now only Tomas (plusik) and Nico (nicov) appear to be
 authorized to upload to maven central. It would be great if some 
 additional
 people (e.g. Mark, Bob, perhaps even myself if desired) could get 
 added to
 this. Authorization is granted by adding a user to your OSS
 project ticket (https://issues.sonatype.org/browse/OSSRH-3633).

 Any work towards a maven release is much appreciated. Let me know
 if I can do anything to help with this.

 -Spencer



 On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
 wrote:

> I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
> version number. In Build.xml it is:
>
>    value="${Jmol.properties.Jmol.___JmolVersion}"
> />
>    override = "true"
>   input="${version}"
> regexp='"'
>   replace=""
> global="true"
>   />
>   
>
>
> So you are missing that regex process.
>
>
>
> On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson 
> wrote:
>
>> On 17/05/16 23:15, Robert Hanson wrote:
>> > 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.
>>
>> Sorry for the delay in replying. I have been attempting to use
>> the ant
>> build script, tools/jmol-sonatype.xml, to build some artifacts for
>> deployment to Maven central. Here is my protocol (apologies, I am
>> not
>> that familiar with ant and may have made some basic errors):
>>
>>
>> Preamble
>> -
>> 0) Start with a 64 bit install of Ubuntu 14.04.4
>>
>> 1) Install the following packages
>>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>>
>> 

Re: [Jmol-users] Jmol-users Digest, Vol 123, Issue 4

[Robert Hanson]

It would be great if someone made one.


On Wed, Aug 24, 2016 at 9:48 AM, J. Bays  wrote:

> Well Wavefunction has such a database, but it is not available to
> non-Spartan users, as far as I know.
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Norte Dame, IN
>
> Sent from my iPad
>
> On Aug 24, 2016, at 10:39 AM, Jennifer L. Muzyka <
> jennifer.muz...@centre.edu> wrote:
>
> iSpartan has something like that built into their app rather than
> calculating things on the fly.  I’m not aware of any other database that
> has the information you’re looking for, Bob.
> Jennifer
>
>
>
> Jennifer Muzyka
> H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
> Centre College
> 600 West Walnut Street
> Danville, KY  40422
>
> jennifer.muz...@centre.edu
> http://web.centre.edu/muzyka
> http://organicers.org
>
> 859-238-5413
> fax 859-236-7925
>
>
>
>
>
>
> On Aug 24, 2016, at 10:34 AM, Robert Hanson  wrote:
>
> I mean a database of common organic compounds, with molecular orbitals.
> Spartan files or Gaussian output -- that sort of thing.
> ​
> 
> --
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> 
> --
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> 
> --
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>


-- 
Robert M. Hanson
Larson-Anderson Professor 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-users Digest, Vol 123, Issue 4

[J. Bays]

Well Wavefunction has such a database, but it is not available to
non-Spartan users, as far as I know.

J. Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Norte Dame, IN

Sent from my iPad

On Aug 24, 2016, at 10:39 AM, Jennifer L. Muzyka 
wrote:

iSpartan has something like that built into their app rather than
calculating things on the fly.  I’m not aware of any other database that
has the information you’re looking for, Bob.
Jennifer



Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Aug 24, 2016, at 10:34 AM, Robert Hanson  wrote:

I mean a database of common organic compounds, with molecular orbitals.
Spartan files or Gaussian output -- that sort of thing.
​
--
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Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


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Re: [Jmol-users] Jmol-users Digest, Vol 123, Issue 4

[Dean Johnston]

This is listed on the Wavefunction, Inc. web site (
https://www.wavefun.com/products/databases.html):

Spartan Molecular Database (SMD), a collection of over 150,000 calculated
structures and associated properties of molecules, each obtained from as
many as ten different theoretical models (Hartree-Fock models with 3-21G*,
6-31G* and 6-311+G** basis sets, B3LYP and MP2 models with the 6-31G* and
6-311+G** basis sets, the EDF1 model with the 6-31G* basis set, the G3(MP2)
model and the T1 model)2, as well as a collection of approximately 1,200
small molecules bound to proteins and nucleotides from the PDB. New to the
SMD is the Spartan Infrared Database (SIRD), a collection of approximately
40,000 organic molecules, the infrared spectra of which have been obtained
from the EDF2/6-31G* model2 and which may be searched by matching to an
input (experimental) spectrum.  Current Spartan licenses include access to
a subset of the SMD.  Customers that purchase maintenance are provided with
the full SMD database on DVD ROM.  Licensing and additional information.



Not sure that’s what you’re looking for.

Dean

-
Dean H. Johnston • Professor and Chair • Department of Chemistry
Otterbein University • 1 South Grove St. • Westerville, OH 43081

On August 24, 2016 at 10:40:03 AM, Jennifer L. Muzyka (
jennifer.muz...@centre.edu) wrote:

iSpartan has something like that built into their app rather than
calculating things on the fly.  I’m not aware of any other database that
has the information you’re looking for, Bob.
Jennifer



Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Aug 24, 2016, at 10:34 AM, Robert Hanson  wrote:

I mean a database of common organic compounds, with molecular orbitals.
Spartan files or Gaussian output -- that sort of thing.
​
--
___
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Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users


--

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Re: [Jmol-users] Jmol-users Digest, Vol 123, Issue 4

[Jennifer L. Muzyka]

iSpartan has something like that built into their app rather than calculating 
things on the fly.  I’m not aware of any other database that has the 
information you’re looking for, Bob.
Jennifer



Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY  40422

jennifer.muz...@centre.edu
http://web.centre.edu/muzyka
http://organicers.org

859-238-5413
fax 859-236-7925






On Aug 24, 2016, at 10:34 AM, Robert Hanson 
> wrote:

I mean a database of common organic compounds, with molecular orbitals. Spartan 
files or Gaussian output -- that sort of thing.
​
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol-users Digest, Vol 123, Issue 4

[Robert Hanson]

I mean a database of common organic compounds, with molecular orbitals.
Spartan files or Gaussian output -- that sort of thing.
​
--
___
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Jmol-users Digest, Vol 123, Issue 4

[Jonathan Gutow]

Bob,

Do you mean in the Jmol development files or a more generic system?

The benchmark database at NIST has computational results for some 
molecules using: http://cccbdb.nist.gov/

Or are you interested in the database of basis sets: 
https://bse.pnl.gov/bse/portal

Or something else?

Jonathan

On 8/24/16 4:13 AM, jmol-users-requ...@lists.sourceforge.net wrote:
> Date: Tue, 23 Aug 2016 06:27:43 -0500
> From: Robert Hanson 
> Subject: [Jmol-users] database of Gaussian or other
> To: "jmol-users@lists.sourceforge.net"
>   
> Message-ID:
>   

Re: [Jmol-users] Jmol on Maven Central

[Spencer Bliven]

I volunteer to push releases to maven central. My OSS username is sbliven.

To authorize someone, I believe that it is sufficient to add a comment to
your OSS project ticket (https://issues.sonatype.org/browse/OSSRH-3633)
requesting access for the username.

-Spencer

On Tue, Aug 23, 2016 at 10:55 PM, Robert Hanson  wrote:

> not aware of any volunteers.
>
> On Tue, Aug 23, 2016 at 10:40 AM, Spencer Bliven  > wrote:
>
>> I just wanted to bump this thread. Any chance of getting a new maven
>> maintainer added soon?
>>
>> Cheers,
>> Spencer
>>
>> On Fri, Aug 12, 2016 at 10:19 AM, Spencer Bliven <
>> spencer.bli...@gmail.com> wrote:
>>
>>> So I guess the next step that needs to happen is for Nico to request
>>> that Mark get added to the OSS ticket. I haven't been an active Jmol
>>> contributor, but I'd be happy to help with maintaining the maven package if
>>> you want to add me too (OSS user sbliven).
>>>
>>> -Spencer
>>>
>>> On Thu, Aug 11, 2016 at 11:29 PM, Robert Hanson 
>>> wrote:
>>>
 all checked in.

 On Thu, Aug 11, 2016 at 3:09 AM, Spencer Bliven <
 spencer.bli...@gmail.com> wrote:

> Awesome. BioJava has good mmtf support, so if we can get the new Jmol
> release into maven then MMTF might be a good exchange format for passing
> structures to Jmol. We're currently stuck with using PDB and are hurting
> from the limitations (e.g. on chain identifiers & number of atoms).
>
> -Spencer
>
> On Wed, Aug 10, 2016 at 6:41 PM, Robert Hanson 
> wrote:
>
>> Thanks, Spencer. I am in the process of releasing an important update
>> for BioJava, as a matter of fact -- PyMOL 1.8 dump_binary PSE files and 
>> the
>> new MMTF format from RCSB (which is FANTASTIC by the way...)
>>
>> Bob
>>
>> On Wed, Aug 10, 2016 at 9:25 AM, Spencer Bliven <
>> spencer.bli...@gmail.com> wrote:
>>
>>> Hey,
>>>
>>> I also took a crack at getting the dist-release command to complete,
>>> since it would be extremely nice to get BioJava using a more recent 
>>> version
>>> of Jmol. Using the latest trunk I got all steps to complete by modifying
>>> tools/jmol-sonatype.xml as you suggest to refer to "${Jmol
>>> .properties.Jmol.___JmolVersion}" in line 30. This creates the
>>> build/dist-maven directory as desired.
>>>
>>> Right now only Tomas (plusik) and Nico (nicov) appear to be
>>> authorized to upload to maven central. It would be great if some 
>>> additional
>>> people (e.g. Mark, Bob, perhaps even myself if desired) could get added 
>>> to
>>> this. Authorization is granted by adding a user to your OSS project
>>> ticket (https://issues.sonatype.org/browse/OSSRH-3633).
>>>
>>> Any work towards a maven release is much appreciated. Let me know if
>>> I can do anything to help with this.
>>>
>>> -Spencer
>>>
>>>
>>>
>>> On Sat, Jul 30, 2016 at 4:39 AM, Robert Hanson 
>>> wrote:
>>>
 I'm not sure how ${Jmol.properties.___JmolVersion} would be  the
 version number. In Build.xml it is:

   >>> value="${Jmol.properties.Jmol.___JmolVersion}"
 />
   >>> override = "true"
   input="${version}"
 regexp='"'
   replace=""
 global="true"
   />
   


 So you are missing that regex process.



 On Mon, Jul 25, 2016 at 9:18 AM, Mark Williamson 
 wrote:

> On 17/05/16 23:15, Robert Hanson wrote:
> > 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.
>
> Sorry for the delay in replying. I have been attempting to use the
> ant
> build script, tools/jmol-sonatype.xml, to build some artifacts for
> deployment to Maven central. Here is my protocol (apologies, I am
> not
> that familiar with ant and may have made some basic errors):
>
>
> Preamble
> -
> 0) Start with a 64 bit install of Ubuntu 14.04.4
>
> 1) Install the following packages
>sudo apt-get install mvn libsaxon-java openjdk-7-jdk ant
>
> 2) Create ~/.jmol.build.properties file with contents
>
>
>
> Main
> 
> 1) Obtain the source code and extract
>wget
> http://heanet.dl.sourceforge.net/project/jmol/Jmol/Version%2
> 014.6/Version%2014.6.1/Jmol-14.6.1_2016.07.11-full.tar.gz
>
>tar xfvz Jmol-14.6.1_2016.07.11-full.tar.gz
>cd jmol-14.6.1_2016.07.11