Re: [Avogadro-devel] Version 1.1 Enhancements

[Marcus D. Hanwell]

On Tue, Apr 19, 2011 at 11:34 AM, Geoffrey Hutchison geo...@pitt.edu wrote:
 I started a webpage for the 1.1 release, listing new features. I know it's 
 incomplete -- since we've been working on this ever since branching for 1.0, 
 please add any new functionality to the page:
 http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0

I actually have a binary built too, for 1.1.0 as of last night. I
could put it in SF.net in the beta area I added. I think 1.0.2 is
about ready as I have not heard anything back. I have been
streamlining the build process so that new releases should not be such
a big deal.

I would like to get back into a habit of making releases every 3
months. With the 1.1 line of development I think that is reasonable,
marking them as beta so that people know there are some features which
have yet to stabilize.

Marcus

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[Avogadro-devel] Avogadro 1.0.2 tagged

[Marcus D. Hanwell]

Hi,

As promised, I created the 1.0.2 tag for Avogadro. I have uploaded
source tarballs, and a Windows installer without Python support. I am
not quite sure how we make the Mac drag and drop installer, and so
didn't do that (although I have a build that works fine locally in an
app. I was out for the evening, but I think it would be great to get
an announcement out over the weekend (preferably once we have a Mac
binary too).

https://sourceforge.net/projects/avogadro/files/avogadro/1.0.2/

Still working out some issues with my new Windows box and scheduled
tasks, but I hope to get nightly binaries built there soon too.

Thanks,

Marcus

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Re: [Avogadro-devel] Avogadro 1.0.2, 1.0.3 on Monday and then onto the 1.1 series

[Marcus D. Hanwell]

On Sun, Apr 24, 2011 at 10:15 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
 As I already announced, Avogadro 1.0.2 was tagged, and released with a
 new Windows package.

 Oh, before I forget, are there wiki pages for the releases? We'll also need 
 to bump the file for the update-checker -- perhaps on Tuesday.

Yes, they are in the normal places,

http://avogadro.openmolecules.net/wiki/Avogadro_1.0.2
http://avogadro.openmolecules.net/wiki/Avogadro_1.0.3

Thanks,

Marcus

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Re: [Avogadro-devel] Building Avogadro on OpenBSD

[Marcus D. Hanwell]

On Tue, Sep 20, 2011 at 10:43 AM, David Lonie lonieda...@gmail.com wrote:
 Hi Anthony,

 Run make VERBOSE=1, and look at the gcc/g++ commands that are being
 executed to see what include dirs (-I/include/path) are being
 searched.

 HTH,
 Dave

 On Sun, Sep 18, 2011 at 12:54 PM, Anthony J. Bentley
 anthonyjbent...@gmail.com wrote:
 Hi,

 I am attempting to build Avogadro on OpenBSD 5.0. During the compile,
 I get this error:

 In file included from /usr/local/include/X11/qt4/QtOpenGL/QGLWidget:1,
                 from
 /usr/ports/pobj/avogadro-1.0.3/avogadro-1.0.3/libavogadro/src/glwidget.h:35,
                 from
 /usr/ports/pobj/avogadro-1.0.3/avogadro-1.0.3/libavogadro/src/camera.cpp:26:
 /usr/local/include/X11/qt4/QtOpenGL/qgl.h:77:20: error: GL/gl.h: No
 such file or directory
 /usr/local/include/X11/qt4/QtOpenGL/qgl.h:79:23: error: GL/glu.h: No
 such file or directory

 It looks like it is not finding the GL headers, which are located at
 /usr/X11R6/include/GL/gl.h and /usr/X11R6/include/GL/glu.h.

I suspect we missed a call to include_directories somewhere, I will take a look.

Marcus

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Re: [Avogadro-devel] Insert Crystal feature vs. File-Import

[Marcus D. Hanwell]

On Mon, Nov 7, 2011 at 12:53 PM, David Lonie lonieda...@gmail.com wrote:
 On Mon, Nov 7, 2011 at 12:12 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 I posted an insert crystal feature to give Avogadro a crystal library of 
 common structures, much like the molecular fragment database.

 I'm now re-thinking the UI aspect of this. Right now, the patch adds a 
 command to Build-Insert-Crystal right below the molecular fragments.

 In some sense, that isn't consistent because we add molecular fragments to 
 grow a molecule. The crystal library mostly replaces the current system.

 So I'm wondering if we should add a command under File-Import to read from 
 the crystal library? Should I do the same thing for the molecular fragment 
 database? This would save a few clicks for people looking to do simulations 
 on common molecules: instead of creating a new file, and inserting a 
 fragment, they can also import the molecule directly. The dialog box would 
 look identical, but it would be a different (more intuitive) way to find it?

 I would like this feature -- I usually just want to replace the
 current molecule with a fragment, and the import menu sounds like a
 good home for this functionality. I also agree that inserting a
 crystal into an existing crystal doesn't make a whole lot of sense ;-)

I concur - I think import would be a great spot for this as crystals
do seem to need to mostly take over rather than be inserted.

Marcus

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Re: [Avogadro-devel] Avogadro OSX Port Question

[Marcus D. Hanwell]

On Mon, Nov 7, 2011 at 12:04 AM, Eric Jang ericjang2...@gmail.com wrote:
 Hello,
 I am wondering if anybody has gotten compilation of Avogadro to work using
 XCode? I would like to study the program by stepping through the code and
 learning how to do it using XCode would really help. To my knowledge
 Avogadro was compiled using CMake but I am unfamiliar with debugging in
 CMake...
 I am using XCode 3.2.1 on OSX 10.6.8

Hi,

CMake has multiple generators, including an XCode generator. This is
part of the reason that CMake was chosen - it can generate MS Visual
Studio solution files, XCode projects, etc. You can run cmake-gui and
point it at the source and build trees, click configure and choose
XCode.

I never got on with XCode, and so can't help you much after that. I
also know that the latest version of XCode made some major changes and
likely doesn't work yet. I use Qt Creator and the CodeBlocks generator
on Linux and Mac all the time.

Marcus

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Re: [Avogadro-devel] Bug in Avogadros CMake-System?

[Marcus D. Hanwell]

On Wed, Nov 23, 2011 at 8:07 AM, Carsten Niehaus cnieh...@gmx.de wrote:
 Hey,

 I just got this request

 https://git.reviewboard.kde.org/r/103209/#review8407

 I cannot say anything about it, it is beyond me :)

Hi,

I need to recover my password to access reviewboard...but the fix is a
bad one. We do not use the Qt imported target stuff explicitly as far
as I know. I will have to dig into this, but I never ported Avogadro
to use it, perhaps this is a distro patch?

Marcus

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Re: [Avogadro-devel] Crashing bug report -- MoleculeDocument?

[Marcus D. Hanwell]

On Fri, Dec 16, 2011 at 11:48 AM, David Lonie lonieda...@gmail.com wrote:
 Any thoughts or opinions? This would be a large scale change, and I'm
 not sure what version something like this should be slotted for. But
 as evidenced by the bug report, we are turning away a lot of potential
 users with a negative experience and this is a major area that needs
 improvement.

We are spinning up our effort on Avogadro 2, and I honestly want to
focus our effort on that for large scale changes like this. Being able
to build up a real delta is something Geoff and I sketched out, and I
think it is the right way to go. I would like to release 1.1 to expose
much of the new functionality, but I think there are also several
other issues causing crashes.

Having a better testing framework, and actually writing tests will
help us avoid many of these issues. Infrastructure is coming online as
part of our work to facilitate this - I will try to post more about
the early MolCore work we have been doing that shows off some of this
infrastructure.

Marcus

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Re: [Avogadro-devel] Gerrit branches

[Marcus D. Hanwell]

On Wed, Dec 21, 2011 at 5:11 PM, David Lonie lonieda...@gmail.com wrote:
 On Wed, Dec 21, 2011 at 4:25 PM, Marcus D. Hanwell
 marcus.hanw...@kitware.com wrote:
 You can look at our test deployment here,

 http://reviewtest.source.kitware.com:81

 This is also where we have been testing out the build testing scripts
 for early MolCore development.

 That looks very nice, I like the new topic and navigation features in
 the header. So MolCore patches sent here will automatically run the
 gtests? Will that work with Avogadro's CTest system when the main
 gerrit instance is upgraded?

It should, once I have figured out how to ensure all of Avogadro's
dependencies are met. So there is still the challenge of ensuring the
tested Avogadro can find everything it needs, and I think I have that
largely figured out using a superbuild approach to built the bulk of
the dependencies.

Going to the Qt developer days gave me a few new ideas on the best
ways to use Gerrit - their instance is up and running now too. I also
verified Avogadro master builds with the recently released Qt 4.8.

Marcus

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Re: [Avogadro-devel] zlib cmake error building avogadro-squared on ubuntu

[Marcus D. Hanwell]

Hi Jens,

On Wed, Jan 4, 2012 at 9:31 AM, Jens linuck...@gmail.com wrote:
 Hey Marcus!

 Many thanks for that.

 I was using cmake 2.8.0. I downloaded the latest version (2.8.7) from
 the website and built it from source and it then worked fine.

 Maybe the required cmake version for avogadro-squared should be bumped
 to stop prevent anyone else hitting this?

Agreed - I will try to figure out which version added support for MD5
and bump it to that.

Marcus

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[Avogadro-devel] Gerrit updates and replication to other locations

[Marcus D. Hanwell]

Hi,

I wanted to let you all know that Gerrit was upgraded recently, it
appears that there were a few teething issues with the replication
process after this update. These are now resolved, and all new changes
should be replicated automatically. You should review code, and once
it is approved and verified it can be submitted. You should only
submit topics, and that will create an appropriate merge commit, which
will be pushed to replicated locations (normally within minutes).

For the remaining commits, they can also be submitted as commits and
merge commits should appear as expected. No one should be pushing
directly to master anymore, if you have problems please let me know so
that I can get them resolved.

Marcus

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Re: [Avogadro-devel] Gerrit updates and replication to other locations

[Marcus D. Hanwell]

On Sun, Jan 22, 2012 at 2:54 PM, Geoff Hutchison
ge...@geoffhutchison.net wrote:
 submit topics, and that will create an appropriate merge commit, which
 will be pushed to replicated locations (normally within minutes).

 So does that mean that we should review a whole topic branch and then submit 
 the tip of the branch?

 I'm looking at things like:
 http://review.source.kitware.com/#/c/3549/

That is an individual change, and until we work through all of these
they should be submitted when they are approved (as I did) and they
will be merged correctly. I was referring to things like,

http://review.source.kitware.com/#/t/9/

This is a topic which has one commit, reviewing the individual commits
and then submitting the entire topic from this page once the topic is
ready to be merged. Open topics can be found by going to All - Topics
- Open on the top navigation bar. A topic has a list of all commits
that are part of the topic, and you can extend topics (add new
commits) or drop commits from topics (causing individual changes to be
marked as abandoned).

The testing scripts I have will test the topic tips, and I will be
bringing dashboard resources online to automate this testing of the
topic tips soon with Kyle and Dave Cole's help. Let me know if
anything is unclear, I will finish up the wiki pages explaining how
all of this works and provide pointers there too.

Marcus

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Re: [Avogadro-devel] compile error on Debian testing...

[Marcus D. Hanwell]

On Sun, Feb 5, 2012 at 2:33 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 Hi Egon,

 On Sat, Feb 4, 2012 at 2:08 PM, Egon Willighagen
 egon.willigha...@gmail.com wrote:
 Hi all,

 I started of today looking into Gerrit for the CDK, and found that
 Avogadro was using it already... good opportunity for me to try the
 user side of Gerrit...

 Thanks for the patch ;-)

 I set up a development environment and made a git clone, etc,
 following your wiki page, and found a trivial patch.

 But, I also found that things do not compile on my Debian testing
 machine... I ran sudo apt-get build-deps avogadro, and cmake was fine
 with what it found.

 Yet, when running 'make -j1' I get:

 snip

 I have libboost-python 1.46 ...

 Suggestions?

 You could disable the Python wrapping, run cmake-gui . in the build
 directory and remove the tick from ENABLE_PYTHON. I am just taking a
 look at this to check (I have Boost 1.48 here) and have a failure on.

 [  1%] Generating moc_pythonengine_p.cxx
 usr/include/boost/type_traits/detail/has_binary_operator.hp:50: Parse
 error at BOOST_JOIN

 This was on my todo, as I think there is a change in Boost behavior
 and interaction with Qt's MOC that is causing issues. Let me see what
 I can do, I think it was an Arch developer who pointed this out and we
 just haven't had time to dig into it.

See,

http://review.source.kitware.com/4169

for a possible fix, this works around some issues in Boost 1.48/MOC
interaction, and also fixes up the fragment wrapping a little for some
issues that crept in late last year I think. I will take a better look
at the properties for fragment later, it would be great to know if
this allows you to compile Avogadro master (+ this patch) on your
system.

Thanks,

Marcus

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Re: [Avogadro-devel] Change in avogadro[master]: Compilation fixes for Python wrapping.

[Marcus D. Hanwell]

On Mon, Feb 6, 2012 at 7:38 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
 HI devs,

 On Sun, Feb 5, 2012 at 9:02 PM, Marcus D. Hanwell (Code Review)
 rev...@kitware.com wrote:
 I'd like you to do a code review.  Please visit

    http://review.source.kitware.com/4169

 to review the following change.

 OK, I left my review comment... how does a reviewer sign off the
 patch, using Gerrit?

The +1 is enough (and I was emailed). There are different access
levels (the +2 code review and +1 verified) which we keep to a core
group who is able to merge new patches. This definitely needs fixing
before our release, I need to get my head back into Boost Python to
fix it properly.

Thanks,

Marcus

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Re: [Avogadro-devel] Gerrit / Google OpenID issues?

[Marcus D. Hanwell]

On Tue, Feb 7, 2012 at 3:57 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 I'm trying to review / approve some patches on Gerrit and I'm having a weird 
 issue signing in with my Google OpenID. I consistently get

 The server could not process your request.

 But there's no additional information. Any ideas?

It seems to be working for me with either of me Google IDs, are you
clicking on the Sign in with Google ID link? The auto remember stuff
seems to have occasional glitches, but I haven't seen the Google link
in the signin dialog fail.

Marcus

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[Avogadro-devel] Compile failures on the dashboard

[Marcus D. Hanwell]

Hi,

I think it would be great to get a 1.1.0 release out sometime in the
near future. I was looking at a couple of compilation failures on the
dashboards, and have addressed some of them here,

http://review.source.kitware.com/#/t/36/

Albert just submitted a patch I merged to address something introduced
by the terachem input deck generator. The Mac dashboard looks similar,
with a fix in the code I submitted. I was going to revisit the extra
attributes being removed from the fragment wrapping, but I think the
rest of that patch is ready to go in.

Are there other outstanding problems that need to be resolved? I need
to take a look at the Windows submission as it is reporting a
conflict, it would be good to get some new binaries out for Windows.

Marcus

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[Avogadro-devel] OpenQube, Avogadro and Eigen 3

[Marcus D. Hanwell]

Hi,

I wanted to let the list know that I just uploaded a patch porting
OpenQube to use Eigen 3. Avogadro maintains a snapshot of it, and can
optionally build against the system installed version. In the new work
we are doing we want to use Eigen 3, and that was the motivation for
porting to the newer Eigen. If there are updates that Avogadro wants
before it moves to Eigen 3 I could just backport them. With a little
more work we could add some #ifdefs, but I largely wanted to see how
well this worked and avoid the complication of having to test any
Eigen change twice (once with Eigen 2, and again with Eigen 3).

The change is here,

http://review.source.kitware.com/#/c/4260/

I was not proposing to go through Avogadro and change everything, but
for Avogadro 2 my intent is to depend on Eigen 3. After talking with
Benoit, it seems that basic structures such as the vectors could
probably be passed between APIs using Eigen 2 or Eigen 3 but I am not
sure how much testing that has received.

Thoughts?

Marcus

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Re: [Avogadro-devel] Compile failures on the dashboard

[Marcus D. Hanwell]

On Tue, Feb 14, 2012 at 9:08 AM, David Lonie lonieda...@gmail.com wrote:
 On Mon, Feb 13, 2012 at 4:16 PM, Marcus D. Hanwell
 marcus.hanw...@kitware.com wrote:
 I think it would be great to get a 1.1.0 release out sometime in the
 near future. I was looking at a couple of compilation failures on the
 dashboards, and have addressed some of them here,

 http://review.source.kitware.com/#/t/36/

 Albert just submitted a patch I merged to address something introduced
 by the terachem input deck generator. The Mac dashboard looks similar,
 with a fix in the code I submitted. I was going to revisit the extra
 attributes being removed from the fragment wrapping, but I think the
 rest of that patch is ready to go in.

 Are there other outstanding problems that need to be resolved? I need
 to take a look at the Windows submission as it is reporting a
 conflict, it would be good to get some new binaries out for Windows.

 I have a topic branch I'd like to merge in before the next release:

 http://review.source.kitware.com/#/t/66/

Sounds reasonable - I was just taking a look at this topic. I was
hoping to work through all of the commits, and decide if they should
be merged, abandoned or fixed up and merged.

 It modifies how the initial viewpoint is set for crystals and
 orthographic projections.

 It's also about time for bug-fixing weekend to catch up on the
 tracker. Does anyone have time for this in the near future, e.g.
 pre-release? I might be able to find a few hours this weekend to work
 on this.

I am traveling this weekend unfortunately, but will try to make some
time before I leave. I have been going through a few of the open bugs
as and when I have had time.

 There was also a post about adding a submit backtrace on crash
 feature -- this may be a good project to focus on, too.

Agreed, but I would rather not delay a release for it. I think we are
well overdue. It would be good for us to make more regular releases
and get feedback. I keep showing off Avogadro, and having people ask
why they can't use feature x, and it is because we haven't made a
1.1.0 release with binaries. I need to get back on the Windows
packaging too, which could do with being rewritten but at least needs
a little patching up. That would allow for the easy creation of
nightly binaries on Windows at least.

Last I checked, Windows was still the one with the largest user base,
and the most need for testing as it has more crashers lurking than the
other two platforms.

Marcus

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Re: [Avogadro-devel] Questions about Avogadro

[Marcus D. Hanwell]

On Sun, Feb 19, 2012 at 3:44 PM, Donald Ephraim Curtis
dcur...@milkbox.net wrote:
 Hey guys, long time mailing the list.

 So the other day I built Avogadro from scratch, starting off by downloading 
 the latest Eigen and OpenBabel from code repositories.  I built both 
 successfully but had problems building Avogadro I originally chalked it up to 
 being Eigen3 instead of Eigen2.

Still using Eigen2.

 But then when I went back to Eigen2 and used the latest development version 
 of OpenBabel, I still had problems building.

 So then I went back to the latest releases for OpenBabel and Eigen2 and 
 everything built nicely…. BUT…

I am not tracking OB head, but any Eigen2 release should work just
fine. Geoff would know better on OB.

 I notice there were a lot of crashes on my end.  I don't know offhand what 
 they relate to, but I have to guess it's the development version of Avogadro 
 that is having the problems.  Because I downloaded the latest Avo release and 
 things actually ran pretty smooth.

 In the end my major questions are:

 1) is anyone working on migrating things to Eigen2?

We are already on Eigen2.

 2) How does the 1.0 branch relate to the master branch?

1.0 forked when we released 1.0, it contains bug fixes and backports.
Master is what will be 1.1, if you look back in the mailing list a few
threads we are working on stabilizing master for a 1.1 release.

 3) Who is the guy that put together the Mac build stuff.  It is very nice – 
 and maybe part of cmake ? – but it's pretty cool.  Though, I'd like to know 
 more about how I should do development from a Mac.  Should I be opening 
 Avogadro.app that is in my build directory or should I be running the 
 executable that is in Avogadro.app/Contents/MacOS?

I did a lot of the build bundle stuff, when I did it the code only
worked on Macs. It has actually been generalized since, and will work
on Windows, Mac and Linux. Geoff does the Mac packaging (or at least
has done all of the previous Mac packages). I did some work getting
Mac builds to work out of the build tree, so you should be able to run
the app in the build tree. Opening Avogadro.app, or directly executing
the exe inside should both work.

If you have trouble you can always try a make install to see if it is
a build tree issue. I do some development on the Mac and don't see
lots of crashes, I haven't tried with Lion yet, but that should work.

 4) Am I missing a lot of documentation somewhere.  The only thing I could 
 find were my older docs about building the development version and some docs 
 about building on Mac OSX which seemed to leave a bit to the imagination.

There are docs on the wiki we wrote, and they should be up to date.

http://avogadro.openmolecules.net/wiki/Building:Development_Version

 Thanks.

 Also, is anyone planning to put up a Google Summer of Code for this project?  
 I am wanting to put something together with a Chemistry prof here but I'm not 
 sure what Google looks for.  Is adding features that are relevant to 
 education a big enough pull?

We talked about this, but haven't done anything yet. We do need to get
moving, I would like to establish how we want to apply.

Marcus

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Re: [Avogadro-devel] python boost unresolved overloaded function type

[Marcus D. Hanwell]

On Mon, Feb 27, 2012 at 2:23 PM, Gary Kedziora gkedzi...@gmail.com wrote:
 I have having trouble compiling ~/libavogadro/src/python/fragment.cpp.
  The issue appears to be that the python boost template function
 arguments can not be resolved when there is a constant and non
 constant version.  Here is the make output for an example:

snip

 This has to do with initializing the name property of the Fragment
 class for Python.  In ~/libavogadro/src/fragment.h, we have

      inline QString name() { return m_name; }
      inline const QString  name() const { return m_name; }

 It seems that in situations where there are not const member functions
 (or other const qualifies), this works ok.  I have run across this
 type of problem with C++ the distant past, but don't remember much
 about it.  Anyway, what solution would be acceptable for the Avogadro
 developers?

You don't mention what version you are building, this should be fixed
in master as far as I am aware. If doing a git pull does not fix the
issue can you let me know what commit you are on (git show from the
source directory).

Thanks,

Marcus

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Re: [Avogadro-devel] Python SIP module

[Marcus D. Hanwell]

Hi Gary,

On Thu, Mar 1, 2012 at 10:56 AM, Gary Kedziora gkedzi...@gmail.com wrote:
 On Tue, Feb 28, 2012 at 3:03 PM, Gary Kedziora gkedzi...@gmail.com wrote:
 Hi,

 cmake/modules/PythonDeps.cmake is having trouble finding SIP on my
 system.  The sip.h on my system is in a nonstandard place.  I have a
 work around, but it is not fully tested yet.  I made my own
 FindSIP.cmake that is called from PythonDeps.cmake.  It both finds
 sip.h and tests that the sip module loads in Python.  It works through
 completion of cmake.  I haven't found out if the build requires and
 finds the sip.h yet though due to other problems with building.  I
 definitely found this problem in the master and in Geoff's
 pettt-master branch.  I'm waiting to see if the build works to know if
 the cmake changes work.


 This was in a version of Geoff's with that was merged to the  master.
 I checked the master also, and it had a construct that was not general
 enough  for the SIP portion of PythonDeps.cmake.

 I got it to build with some modification to cmake files.  I modified
 ~/cmake/modules/PythonDeps.cmake by calling find_package(SIP).  In
 FindSIP.cmake the main thing is that I have

    find_path(SIP_INCLUDE_DIR NAMES sip.h
     PATHS
     ${INCLUDE_INSTALL_DIR}
     ${CMAKE_INCLUDE_DIR}
     PATH_SUFFIXES SIP
    )

 Should probably include other directories in there as well.  And
 finally, in ~/libavogadro/src/python/CMakeLists.txt I add
 ${SIP_INCLUDE_DIR} to the include_directories() function.

 Let me know if I should provide further details and the  best way to do that.

How did you install SIP over there? The suggested modifications seem
reasonable, and I would love to reproduce the failure (and ensure the
fix works here). You can provide a patch through Gerrit if you would
like to, or supply me with a little extra information and I can work
on getting a patch ready for master. I would like to get this in
before the 1.1.0 release.

Thanks,

Marcus

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Re: [Avogadro-devel] How to turn off graphics?

[Marcus D. Hanwell]

On Tue, Mar 13, 2012 at 12:26 PM, David Lonie lonieda...@gmail.com wrote:
 Hi Divya,

 On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divne...@umail.iu.edu 
 wrote:
 I need avogadro to perform minimization and some other operations on
 proteins.

 I'm not sure how you would perform any operations without the GUI, as
 there is no real command line interface to Avogadro. I think your best
 bet is to use the openbabel utilities. For instance, obminimize will
 perform a geometry relaxation using the same forcefield
 implementations that Avogadro uses:

 http://openbabel.org/wiki/Obminimize

 There are quite a few others that may help with the other tasks you need:

 http://openbabel.org/wiki/Guides

 Another option that I use with our remote clusters is to forward an X
 connection over SSH by using the -X or -Y options to ssh. This will
 launch the avogadro GUI on your workstation, even though it's actually
 running on the remote cluster.

I would agree with David here. There are several command line
components that have things like the underlying forcefields used in
the GUI, Python bindings can make it easy to script them too. We never
developed a powerful command line mode for Avogadro, because
everything is in a library I think our efforts would be best focused
in developing a command line frontend if it was useful, rather than
trying to make the gui do both.

I am having trouble understanding how you are using Avogadro in a
non-graphical context.

Marcus

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Re: [Avogadro-devel] Problem with Gerrit

[Marcus D. Hanwell]

Hi Tim,

On Sun, Mar 18, 2012 at 11:45 AM, Tim Vandermeersch
tim.vandermeer...@gmail.com wrote:
 Hi,

 I pushed a patch to gerrit but it doesn't show up on the webpage. When
 I try to push it again it says there is no Change-Id so I think the
 patch was uploaded correctly. Any ideas what might have gone wrong?

Since we switched to topic based review we need to have a Change-Id
line as the final line in the commit message (I have been looking at
whether we can relax that). The setup for development script contains
instructions for downloading the local hook that will add that
automatically for you,

http://avogadro.openmolecules.net/wiki/Working_with_Gerrit

You can add the line to your last commit by running git commit
--amend, if you downloaded the local hook it will simply append it for
you once you save and close.

Let me know if you are still having trouble - I would like to automate
the local hook stuff soon to make this simpler.

Marcus

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[Avogadro-devel] Avogadro 1.1.0 rc next week

[Marcus D. Hanwell]

Hi,

Geoff and I were chatting on IRC - the 1.1.0 release is well overdue.
I was going over patches this morning. I would like to ask anyone who
has pending patches they would like in the 1.1.0_rc1 to get them
submitted to Gerrit ASAP. I will make a tag early next week (depending
on feedback) and we will aim to get some binaries out.

There are some great new features in master, and we should make sure
more people see them. I would also like to put some time into finding
bugs causing segfaults in master, but they can come after the first
rc.

Thanks,

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.0 rc next week

[Marcus D. Hanwell]

On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
 We were just talking about this. I will make a tag/tarball now and
 let's start testing this out.

 Any chance I can put in the minor changes David requested for the slab 
 builder?

Is that the topic on Gerrit? I can take a look and test it out/merge
it. I am currently trying to track an issue with an empty, new
Avogadro window. The molecules I draw do not show up, but if I load a
molecule then that is displayed and I can edit it. Can others
reproduce this?

Thanks,

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.0 rc next week

[Marcus D. Hanwell]

On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
 ge...@geoffhutchison.net wrote:
 We were just talking about this. I will make a tag/tarball now and
 let's start testing this out.

 Any chance I can put in the minor changes David requested for the slab 
 builder?

 Is that the topic on Gerrit? I can take a look and test it out/merge
 it. I am currently trying to track an issue with an empty, new
 Avogadro window. The molecules I draw do not show up, but if I load a
 molecule then that is displayed and I can edit it. Can others
 reproduce this?

I fixed the initial camera issue, and will test the slab builder
extension now briefly. I was going to grab some lunch and tag/create
tarballs etc after lunch for rc1. Please let me know if you spot any
other issues.

Thanks,

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.0 rc next week

[Marcus D. Hanwell]

Marcus D. Hanwell, Ph.D.
RD Engineer, Kitware Inc.
(518) 881-4937


On Wed, May 2, 2012 at 12:17 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 On Wed, May 2, 2012 at 11:47 AM, Marcus D. Hanwell
 marcus.hanw...@kitware.com wrote:
 On Wed, May 2, 2012 at 11:42 AM, Geoffrey Hutchison
 ge...@geoffhutchison.net wrote:
 We were just talking about this. I will make a tag/tarball now and
 let's start testing this out.

 Any chance I can put in the minor changes David requested for the slab 
 builder?

 Is that the topic on Gerrit? I can take a look and test it out/merge
 it. I am currently trying to track an issue with an empty, new
 Avogadro window. The molecules I draw do not show up, but if I load a
 molecule then that is displayed and I can edit it. Can others
 reproduce this?

 I fixed the initial camera issue, and will test the slab builder
 extension now briefly. I was going to grab some lunch and tag/create
 tarballs etc after lunch for rc1. Please let me know if you spot any
 other issues.

Please find the Avogadro 1.1.0_rc1 tarballs on SourceForge,

https://sourceforge.net/projects/avogadro/files/avogadro-beta/1.1.0_rc1/

This is built from bb1002da (the current tip of master). Please test
this and let us know of any issues. I would like to clear up any
remaining issues and get an rc2 out next week. I will see about making
some binaries early next week, any help with this would certainly be
appreciated!

There are some awesome new features in 1.1, and it is past time we
showed them off to the wider community. There are still some crashers
and other bugs that have crept in, so let's please spend some time
ironing these issues out.

I will be away for most of the weekend, but back for Monday to push on
the 1.1.0 release. This is a beta series which should culminate in a
1.2.0 release once master has stabilized. Remember we already broke
ABI after 1.0, the distro maintainers will need to be aware of this
when packaging.

Thanks and May the 4th be with you ;-)

Marcus

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Re: [Avogadro-devel] Bugfix installing avogadro-squared

[Marcus D. Hanwell]

On Wed, May 16, 2012 at 5:28 AM, Anders Steen Christensen
ande...@nano.ku.dk wrote:
 Hey boys

 Avogadro-squared wouldn't compile because the zlib tarball from zlib.net was
 no longer there. Here's a patch.

Hi,

Sorry I missed this, I will get that applied and update the submodules
while I am at it later.

Thanks!

Marcus

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Re: [Avogadro-devel] [ avogadro-Bugs-3530795 ] File-Import-Insert Crystal segfaults

[Marcus D. Hanwell]

On Wed, May 30, 2012 at 10:52 AM, Michael Banck mba...@gmx.net wrote:
 On Wed, May 30, 2012 at 10:40:31AM -0400, Geoffrey Hutchison wrote:
 I think both things are important -- disable the menu item when no
 files are available. My concern about the source tree is knowing where
 that is. I'm not sure I want to compile-in the source directory.
 Should I know that it was compiled by /home/mbanck/avogadro/... ?

 I guess it wouldn't hurt, so long as it is just a fall-back that is
 used if the data directory is not available and the source tree is
 present, but it should not be exposed to GUI in any way otherwise.

We do this for the plugins etc already. I would like to find a way to
remove some of the burden from the developer of the plugin. We might
just want to add one function that gives a prefix for data directories
that can have a second entry for the build tree. We would have one
place to disable that second entry then for distros etc if they were
concerned about searching additional paths.

Marcus

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Re: [Avogadro-devel] Cottrell Scholar's Meeting

[Marcus D. Hanwell]

On Wed, Aug 8, 2012 at 3:08 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 Before I forget, a few weeks ago, I gave a demo at the Cottrell Scholar's 
 meeting -- an award given to non-tenured university faculty with strength in 
 research and education.

 Avogadro was mentioned quite prominently:
 http://www.huffingtonpost.com/james-m-gentile/leading-scholareducators-_b_1683028.html

 Several of the faculty were extremely impressed, with one saying he told 50 
 of his colleagues to download and use it!

Congratulations on the award Geoff, we shared the link you posted in a
few other places. This is great exposure for Avogadro. While you were
at that meeting I was at PNNL at the second semantic physical science
meeting discussing how we might work with NWChem and others in the
community.

These are interesting times, I am excited about what the future holds!

Marcus

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[Avogadro-devel] Avogadro paper published in provisional form

[Marcus D. Hanwell]

Hi,

In case anyone missed it, I am very pleased to announce that the
Avogadro paper was published in provisional form today,

http://www.jcheminf.com/content/4/1/17

It was a long time in the making, thanks to everyone who contributed
to the paper and to Avogadro. It is open access, so anyone can access
the paper as they can the software. I would like to thank Peter
Murray-Rust and the Semantic Physical Science meeting for taking the
paper into the series and for his support in getting the manuscript
published.

Several of us will be at the ACS meeting next week, so the timing is
great. Lots to do before the meeting.

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.0 tagging

[Marcus D. Hanwell]

On Tue, Sep 4, 2012 at 11:49 AM, Geoff Hutchison
ge...@geoffhutchison.net wrote:
 I think we are more than ready to release once we have the Mac
 package. This is the first in the beta series to stabilize for a 1.2.0
 release. I would like to get some of the pending changes on Gerrit
 merged (and have a few things queued I would like to add) once we have
 this release out.

 I can spin a Mac package tomorrow -- unfortunately, due to the holiday, and 
 some prior commitments, I can't do that today.

 Thanks Marcus for all the hard work on finalizing the release. It will be 
 great to get it out there and show people what we've been working on!

That sounds great, I figured with the holidays things might be hectic.
I pushed the tag to the repository and the other files are all in
staging on SourceForge (you should be able to see them and upload the
Mac package).

Thanks,

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.0 tagging

[Marcus D. Hanwell]

On Tue, Sep 4, 2012 at 1:10 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 On Tue, Sep 4, 2012 at 11:49 AM, Geoff Hutchison
 ge...@geoffhutchison.net wrote:
 I think we are more than ready to release once we have the Mac
 package. This is the first in the beta series to stabilize for a 1.2.0
 release. I would like to get some of the pending changes on Gerrit
 merged (and have a few things queued I would like to add) once we have
 this release out.

 I can spin a Mac package tomorrow -- unfortunately, due to the holiday, and 
 some prior commitments, I can't do that today.

 Thanks Marcus for all the hard work on finalizing the release. It will be 
 great to get it out there and show people what we've been working on!

 That sounds great, I figured with the holidays things might be hectic.
 I pushed the tag to the repository and the other files are all in
 staging on SourceForge (you should be able to see them and upload the
 Mac package).

Hi Geoff,

Did you get chance to create some Mac binaries? I would like to get an
announcement together in the next few days. I noticed that SourceForge
unveiled the staged binaries/tarballs (only holds them for three
days), and we are seeing quite a few downloads.

For those interested in trying out the latest Avogadro that is great,
nearly 300 downloads yesterday. I am inclined to leave the files
as-is, once the Mac binary is added I would like to add a news item
and update the main page etc.

Thanks,

Marcus

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[Avogadro-devel] Avogadro 1.1.0 Released

[Marcus D. Hanwell]

We are very proud to announce the availability of Avogadro 1.1.0.

Avogadro is a free, open source, cross-platform molecular editor
designed for flexible use in computational chemistry, molecular
modeling, bioinformatics, materials science, and related areas.
Packages are available for Windows, Linux and Mac OS X. The source
code source is available under the GNU GPLv2.

What does Avogadro do?
* We've tried to make the best, most intuitive builder, including
common fragments, downloading directly from PDB or PubChem, and
peptide sequences
* Innovative auto-optimize tool which allows you to continue to
build and modify, during molecular mechanics optimization
* Interfaces to many common computational packages
* Designed to help both educational users and advanced research
* Plugins that allow Avogadro to be extended and customized
* Well defined public API, library and Python bindings for development
* Embedded Python interpreter
* Translations available in 19+ languages

Download: https://sourceforge.net/projects/avogadro/files/avogadro/1.1.0

What's New? See the Release Notes:
http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0

For more information: http://avogadro.openmolecules.net/wiki/

If you use Avogadro please check out the recently published Avogadro
paper, and consider citing it: http://www.jcheminf.com/content/4/1/17

This is a community project and we couldn't have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. Particular
thanks go to all the translators.

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Re: [Avogadro-devel] Upgrading SourceForge for Avogadro

[Marcus D. Hanwell]

On Wed, Sep 12, 2012 at 1:32 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 One thing we should consider with the release of 1.1.0 is to upgrade Avogadro 
 to the new SourceForge version:
 https://sourceforge.net/p/upgrade?search=avogadro

 I think the improved tracker would be great for handling many of the new bug 
 fixes, enhancements we're likely to get!

I am no fan of the current trackers, and so would be interested in
seeing how much better then new one is. I think we should switch, and
was tempted to do it. Do you want to flip the switch?

Marcus

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Re: [Avogadro-devel] Avogadro Paper Accesses

[Marcus D. Hanwell]

On Fri, Sep 14, 2012 at 10:35 AM, Geoffrey Hutchison geo...@pitt.eduwrote:

 I'll admit I've been very intrigued by the # of accesses statistic from J.
 Cheminf. I wish more journals showed this -- it's a very interesting way of
 measuring impact of particular articles.

 Thanks to Noel O'Boyle's recent blog post:

 http://baoilleach.blogspot.com/2012/09/plotting-accesses-on-axis-part-ii.html

 I've been able to finish up the graph of the first 30 days of the Avogadro
 paper (which is now #1 for the last 30 days and #19 for the last year). Not
 surprisingly, there was an exponential fall-off over the first few days,
 but we seem to be in the noisy long-tail now.

 Hi Geoff,

Thanks for collecting the numbers, I had started but missed too many days.
I noticed we had more than 3,000 accesses in the first 30 days too, but
didn't get the exact number - it is a shame they don't offer a details page
with more numbers.

Marcus
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Re: [Avogadro-devel] 300,000 Downloads

[Marcus D. Hanwell]

On Sun, Jan 27, 2013 at 1:33 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 I was pulling up statistics on Avogadro for an NSF proposal, and saw that we 
 finally broke the 300,000 download mark! In 2012, there were ~100,000 
 downloads alone.

 http://sourceforge.net/projects/avogadro/files/avogadro/stats/timeline?dates=2001-01-01+to+2013-01-26

 Incidentally, the usage is profoundly international. There are now 26 
 localizations with 50% coverage, including Vietnamese, Malay, and Indonesian.
 https://translations.launchpad.net/avogadro

That is awesome news, I saw we were getting close when I looked around
the new year. I just made a blog post and the Avogadro paper is also
the most viewed paper in the Journal of Cheminformatics over the last
year, and it is at number 10 all time I think.

http://blog.cryos.org/archives/262-Avogadro-Paper-Published-Open-Access.html

Showing 12 citations on Google Scholar too.

Marcus

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Re: [Avogadro-devel] Regarding request for suggestion.

[Marcus D. Hanwell]

On Sun, Feb 24, 2013 at 11:41 PM, Sujit Tangadpalliwar
sujit_tangadpalli...@persistent.co.in wrote:
 I am using your software
 Avogadro since a month as it having multiple functionality like
 visualization, molecule editor, optimization structure conversion etc. and
 it quite easy and user friendly. I want to use Avogadro in my project. I am
 trying to connect Avogadro with my Perl script but I am unable to find Perl
 module for this connection please guide me regarding my query.

 Hope for guidance to go my project smoothly in right direction.

I am not sure how you want to integrate Avogadro into a Perl script,
we have no Perl integration that I am aware of. You can call Avogadro
from the command line, if you want scripting then Python would be a
better way to go. We have wrapped the majority of our API in Python,
although most of the installers do not have the feature enabled by
default.

You would have to give us a little more detail on what you are trying
to accomplish to help any further.

Thanks,

Marcus

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Re: [Avogadro-devel] painter

[Marcus D. Hanwell]

On Fri, Mar 1, 2013 at 1:31 PM, Marc-André Dubois ma.dub...@me.com wrote:
 Hi everyone,
   I would like to draw a sphere in the molecule render area
 of avogadro. I simply tried to test this command:

  gl-painter()-drawSphere(center,13.0);

 where gl is my GLWidget, but I received: GLPainter not active. Is there
 something I don't understand? Thanks guys,

You must make these calls when the GL context is valid. The easiest
way is to write an Engine and do it in one of the virtual render calls
in the method. See the Van der Waals plugin for example. This ensures
the render call happens at the appropriate moment when the GL context
is current.

Marcus

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[Avogadro-devel] Contributor approval for 3-clause BSD relicensing (YOUR ACTION NEEDED)

[Marcus D. Hanwell]

Hi,

We have talked about this offline, and at times on the list. As many
of you already know we are working on a rewrite of Avogadro, and we
are preparing to make an initial alpha release. It features many great
new features, but does not yet have feature parity with Avogadro 1.x.
Avogadro 2 is a rewrite and re-architecture of Avogadro using a
simpler, more liberal 3-clause BSD license. A lot of the API has
changed, and we invite community participation. For some background to
the project please see,

http://wiki.openchemistry.org/
http://www.slideshare.net/cryos/the-open-chemistry-project

You can see the latest version make use of obabel command line tools
for file translation, geometry optimization, and other pieces using a
qprocess to manage execution. We are also looking at using this
approach to run Python and Java in a more loosely coupled form, and we
have ported most of the input generators to use a much simpler
scripting framework where the addition of scripts can add new
generators to the GUI using pure Python, or other languages.

To that end, we would like to know which of our Avogadro contributors
agree to relicensing their contributions under the 3-clause BSD
license, linked below,

http://opensource.org/licenses/BSD-3-Clause

If you contributed code to Avogadro, please reply to this email with
either one of the following statements (adapted from the Eigen
relicensing effort led by Benoit),

  Yes, I agree to have all the code that I contributed to Avogadro
relicensed to the 3-clause BSD license.

or

  No, I do not agree.

Anything other than the above Yes sentence will mean No. Without
your agreement we will make no attempt to port your contribution to
Avogadro 2's code base, we would also love input from our contributors
on Avogadro 2, and have made every attempt to address many of the
shortcomings we perceived in Avogadro.

Thanks,

Marcus

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[Avogadro-devel] Avogadro relicensing agreement update

[Marcus D. Hanwell]

Hi,

Just a quick update from the replies I have received as far as
agreement to relicensing goes. Those who have replied positively (one
or two off-list, hopefully they will follow up with on list soon),

Marcus D. Hanwell
Casper Steinmann
David Lonie
Geoffrey Hutchison
Jens Thomas
Matthew Kennedy
Tim Vandermeersch
Eric Brown
Albert DeFusco
James Bunt
Jordan Mantha
Simon Ochsenreither
Gary Kedziora
Naomi Fox
Egon Willighagen

Those who have yet to reply,

Konstantin Tokarev
Donald Ephraim Curtis
Michael Banck
Jogvan Magnus Olsen
Benoit Jacob
Carsten Niehaus
Raimondas Galvelis
Ross Braithwaite
Shahzad Ali
Kristof Bal
Reinis Danne

Thanks to everyone who got back to me already, I will see if I can
follow up on a few of these in the next few days along with analyzing
the amount of code affected if some do not respond. As we get further
down the list there are less lines that were changed with the bottom
five all being less than 250 lines changed.

Marcus

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Re: [Avogadro-devel] Contributor approval for 3-clause BSD relicensing (YOUR ACTION NEEDED)

[Marcus D. Hanwell]

On Mon, Mar 18, 2013 at 11:30 AM, Benoit Jacob jacob.benoi...@gmail.com wrote:
 Dear Avogadro developers,


 Yes, I agree to have all the code that I contributed to Avogadro
 relicensed to the 3-clause BSD license.

 Also, I would suggest moving to Eigen 3 if you haven't already: it is now
 MPL2-licenced, which is closer to the 3-clause BSD license than Eigen2's
 licensing options are.

Thanks, you may have recognized the relicensing email text which I
modeled on your emails ;-) Avogadro 2 is already using Eigen 3, and
there is possibly a patch to do most of this a contributor sent to me
recently - I need to take a look at it and assess the impact of it.

Thanks,

Marcus

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Re: [Avogadro-devel] [Avogadro-Translations] Avogadro in Spanish for Windows

[Marcus D. Hanwell]

On Fri, Apr 5, 2013 at 2:47 PM, Louis Ricard
louis.ric...@polytechnique.edu wrote:
 Hi all,

 This is a recurrent problem for Windows users: Windows does not know i18n
 and, consequently, only english menus are available.
 Since the Windows version is not compiled with internationalization support,
 there are two solutions :
 1) compile the .po files from Launchpad: they will not correspond to those
 of the current Avogadro binaries, requires Qt deveopment
 tools installed;
 2) obtain the .qm files from a friend using a Mac or Linux (same version, 32
 or 64 bits) and install them under
 C:\Program Files\Avogadro\share\avogadro\i18n.

 If not other solution exists, this should be mentioned in the FAQS.

We should add this to the release notes, I used to make the copy when
making a Windows release but think I forgot the last few times. I will
try to do this for the next release, we never got the tools to work in
the build system on Windows correctly but I can always revisit that
too.

Thanks for reporting this, an FAQ entry would be reasonable but I will
try to improve the Windows i18n support in the next bug fix release.

Marcus

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[Avogadro-devel] First Avogadro 2 beta release

[Marcus D. Hanwell]

Hi,

I wanted to let people on these lists know that we just made our first
beta release of Avogadro 2, along with MoleQueue and MongoChem. Please
see the blog post here,

http://blog.cryos.org/archives/265-First-Open-Chemistry-Beta-Release.html

We have created binary installers for Windows and Mac OS X, along with
regular source releases,

http://www.openchemistry.org/OpenChemistry/resources/software.html

These are not feature complete, and we intend to make regular releases
as new features land in master. There are several exciting new
features, along with some missing pieces that will be brought back as
we can get to them. I will work on making a screen cast highlighting
how the three applications can be used together soon, and discussing
some of the new features in more detail.

We have automated as much of the testing and release process as
possible, and will continue to streamline things. Binaries are
uploaded nightly to the dashboards for Windows and Mac, and API
documentation is updated nightly,

http://cdash.openchemistry.org/
http://doc.openchemistry.org/avogadrolibs/api/

Avogadro 2 also uses a different binary name, and library names,
meaning that there should be no problems in installing Avogadro 1 and
2 on the same system in the same prefixes. There is lots more to do
before, so I will get back to it, but I hope you will check out what
we have been working on. I will see if I can get some more of the
features you have grown to expect back in Avogadro 2.

Thanks,

Marcus

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Re: [Avogadro-devel] First Avogadro 2 beta release

[Marcus D. Hanwell]

On Fri, Apr 12, 2013 at 9:29 AM, David Lonie david.lo...@kitware.com wrote:
 Hi Jens,

 On Fri, Apr 12, 2013 at 5:00 AM, Jens linuck...@gmail.com wrote:
 Really great to hear that avogadro2 is now on the scene and I'm excited to
 see how it develops in the future.

 It's already looking very impressive - I read in some pretty big molecules
 and the performance and responsiveness was incredibly snappy.

 Great to hear the positive feedback! Out of curiousity, just how big
 were your molecules?

 Where's the place to log bug reports while it's still in the initial testing
 phase? I found one (see below) but it wasn't immediately obvious on the
 openchemistry website where the tracker was.

 We have a bug tracker up here:

 http://projects.openchemistry.org/

 I'll add a link on the openchemistry wiki and see about adding one to
 www.openchemistry.org.

The main site already has a link (Resources, Bug Tracker), we can
certainly get links on the wiki too. The Doxygen links there too, but
let's work on making it as obvious as possible.

 As for the bug:

 draw C atom, click Extensions - Open Babel - Add Hydrogens:

 Command-line output:

 OBProcess::executeObabel: Running
 /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel -icml
 -ocml -h
 /Volumes/Avogadro2-0.5.0-Darwin/Avogadro2.app/Contents/MacOS/obabel
 stderr:
  ==
 *** Open Babel Error  in RegisterOptionParam
   The number of parameters needed by option t in The LPMD file format.
 differs from an earlier registration.
 0 molecules converted
 
 Bad CML:  

 I noticed this odd behavior in obabel and brought it up on
 openbabel-devel a little while ago, see
 http://forums.openbabel.org/obabel-h-bug-while-adding-hydrogens-td4655976.html.
 This is a feature, not a bug from their perspective.

 We plan to implement our own add-hydrogens routine (and maybe even our
 own remove-hydrogens, if I can figure that out ;-) ). I've filed a
 bug for this here:

 http://projects.openchemistry.org/issues/169

There seem to be a few bugs on the Mac with obabel and CML too, so I
am afraid geometry optimization looks a little dicey. I think there
are some simple workarounds we can implement there to improve things
in the next release.

Thanks for the feedback Jens. I think ensuring anyone can have
Avogadro 1 and 2 installed should make it easier to try out the new
stuff without having to give up Avogadro 1.

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.0 Released

[Marcus D. Hanwell]

On Fri, Apr 26, 2013 at 11:13 AM, Michael Banck mba...@debian.org wrote:
 Hi,

 On Wed, Sep 12, 2012 at 02:07:21PM -0400, Marcus D. Hanwell wrote:
 We are very proud to announce the availability of Avogadro 1.1.0.

 [...]

 Download: https://sourceforge.net/projects/avogadro/files/avogadro/1.1.0

 What's New? See the Release Notes:
 http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0

 The release notes mention that this is a Beta release and that a 1.2.0
 release is forthcoming.  Is this still the case, or was this changed
 later on and 1.1.0 is a stable public release?

 If not, what is the timeline for a 1.2.0 release?

There were a lot of changes made in 1.1.0, and new stability issues
have cropped up since we made the release. I think we should make a
1.1.1 release addressing some of the stability issues if possible. Is
there a distro freeze date pressing?

Thanks,

Marcus

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Re: [Avogadro-devel] Packmol, Symmol and other Fortran through Webapps

[Marcus D. Hanwell]

On Fri, May 24, 2013 at 4:49 AM, Jens linuck...@gmail.com wrote:

 On 23 May 2013 18:15, Geoffrey Hutchison geo...@pitt.edu wrote:

 I've been silent on the lists, since I'm hard at work getting tenure (the
 package gets submitted in early August).

 But I had a brainstorm about some of the features we've discussed, like
 Packmol -- which is a Fortran code. While we can supply binaries and detect
 if the program is available at run-time, it might be nice to offer some of
 these programs as web applications as well.

 Right now, we offer integration with PubChem, the NIH resolver (also for
 compound naming) and a few other web services.

 But it'd be pretty easy to offer a web app that runs Packmol. A similar
 Fortran program which might be useful is symmol, which detects point group
 symmetry and can symmetrize molecules.

 To be clear, these programs are already available, and I'd suggest making
 the webapp interface layer available as open source (probably BSD-license).
 I'm just thinking that for many users and for development purposes, a webapp
 would be useful (i.e., no need to get a Fortran compiler for Windows or
 Mac).

 Thoughts?

 I think that sounds like a really good idea.

 I've always thought that it would be great to work towards a kind of
 eco-system of tools with Avogadro sitting in the middle and providing the
 interface to all of them and creating a really powerful modelling
 environment - something a bit like CCP4 have (http://www.ccp4.ac.uk/).

 There are so many helpful tools out there, but many aren't known about or
 difficult to integrate together. Avogadro could provide that glue and make
 them easy to use too.

 I don't know whether that would work best as a distributed software bundle,
 or as something that calls on webapps, but then there's no reason why a
 mixture of both wouldn't work.

One of the things we have been looking at is looser integration of
components using MoleQueue and separate processes, but more recently
we have been exploring easy ways to make and expose RESTful APIs that
allow you to query data sources or run external codes. At the core it
is just a simple RESTful API that returns results as JSON and one or
two other things. We have been experimenting with using Python as the
glue language on the server, and don't have anything worth exposing
yet but this might be one approach.

I totally agree on using a combination of the two, there are some new
developments in CMake for example that make it easier to use gfortran
from MinGW with Visual Studio for the C/C++ code.

Thanks,

Marcus

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[Avogadro-devel] CML, NWChem, FoX, Avogadro paper

[Marcus D. Hanwell]

Hi,

I wanted to point out our paper (part of the same special issue as the
Avogadro paper) was released recently. It discusses the use of CML
produced by NWChem using FoX and visualized in Avogadro.

www.jcheminf.com/content/5/1/25

We should hopefully see releases of NWChem soon that can output this
CML, and I will clean up the code and get it merged in soon too. This
has been part of an ongoing collaboration looking at how we can
improve the quality of the data coming out of computational codes, and
it is intended to be complimentary to log file parsing/other file
parsing we have been working on for years.

In other news, I just noticed that the Avogadro paper has hit 50
citations on Google Scholar already. Great to see so many from the
community citing it and using Avogadro.

Thanks,

Marcus

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Re: [Avogadro-devel] Unable to configure OS X installation directory away from /Applications/Avogadro.app...

[Marcus D. Hanwell]

On Mon, Sep 2, 2013 at 1:33 AM, Christian Herbig c.her...@me.com wrote:
 I sincerely hope this is a question that can easily be answered, but I cannot 
 at all figure out how to change the final installation directory from 
 /Applications/Avogadro.app to /Applications/MacPorts/Avogadro.app.  I have 
 tried multiple permutations on -DCMAKE_INSTALL_PREFIX= , yet nothing seems to 
 change the final configuration from:

 set(Avogadro_INSTALL_PREFIX  /Applications/Avogadro.app/Contents)
 set(Avogadro_INCLUDE_DIRS/Applications/Avogadro.app/Contents/include)
 set(Avogadro_LIBRARY_DIRS/Applications/Avogadro.app/Contents/lib)
 set(Avogadro_LIB_SUFFIX  )
 set(Avogadro_PLUGIN_DIR  
 /Applications/Avogadro.app/Contents/lib/avogadro/1_1)
 set(Avogadro_BIN_DIRS“/Applications/Avogadro.app/Contents/bin)

 To be specific, I need to be able to do something like 
 -DCMAKE_INSTALL_PREFIX=${destroot}${applications_dir}

On the Mac we ended up hard wiring more than we perhaps should have to
make the default case work. I am not sure you can easily modify this
without modifying some of the CMake code, it is indeed a bug in the
way we wrote out CMakeLists.txt file. I have a lot of that figured out
now in newer build systems. I will see if I can find time to go back
and apply it to Avogadro 1, but I am not sure when I will have time.

Marcus

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Re: [Avogadro-devel] Eigen3 Support

[Marcus D. Hanwell]

Hi Geoff,

On Mon, Sep 30, 2013 at 8:17 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 I had a little time to fiddle this afternoon and I've push a patch to Gerrit 
 that allows building against Eigen3 using the support mode. This means that 
 Eigen3's API is not yet supported in Avogadro 1.1.x and that the ABI may 
 break.

The ABI does break, the Eigen vector classes changed some template
arguments for Vector3d defines for example, I hit this when porting
some of the QM code.

 I think this is a good thing -- it allows building against either Eigen 2 or 
 Eigen 3 (long requested). Considering Avogadro 1.x is something of an 
 evolutionary dead-end, I think there isn't really much motivation to migrate 
 all the code in the v1.x codebase. Such migration can occur as code is 
 migrated to 2.x.

 Thoughts?
 http://review.source.kitware.com/#/c/12868/

Most of the migration is relatively simple, I took a quick look and
the only change I would suggest is configuring the Eigen definition so
that users of the Avogadro API don't need to duplicate this define (or
would it work if they did not). Great to see it was so easy - I had
been meaning to take a look.

Marcus

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[Avogadro-devel] Avogadro 2 0.7.0 Released

[Marcus D. Hanwell]

We are very proud to announce the availability of Avogadro 2 0.7.0.

Avogadro 2 is a free, open source, cross-platform molecular editor
designed for flexible use in computational chemistry, molecular
modeling, bioinformatics, materials science, and related areas.
Packages are available for Windows, Linux and Mac OS X. The source
code source is available under the 3-clause BSD license.

Avogadro 2 is a rewrite of Avogadro, and still lacks features present
in Avogadro 1. Both packages can be installed on the same system, and
so it is possible to try the latest without losing access to the
previous version. We will be making occasional releases of Avogadro
1.x too, along with migrating functionality to Avogadro 2. We value
your feedback, and hope that you will find the improvements made in
version 2 useful.

What does Avogadro 2 do?
* We've tried to make the best, most intuitive builder
* Interfaces to many common computational packages
* Designed to help both educational users and advanced research
* Plugins that allow it to be extended and customized
* Can be extended with simple Python scripts for file IO and input generation
* Well defined public API, libraries and modular design

Download: https://sourceforge.net/projects/avogadro/files/avogadro2/0.7.0/

What's new? See the Release Notes: http://wiki.openchemistry.org/Avogadro2_0.7.0

For more information: http://wiki.openchemistry.org/Avogadro

If you use Avogadro or Avogadro 2, please check out the recently
published Avogadro paper, and consider citing it:
http://www.jcheminf.com/content/4/1/17

This is a community project and we couldn't have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. We
acknowledge that the development of Avogadro 2 has been funded by a US
Army SBIR with the Engineering Research Development Center under
contract (W912HZ-12-C-0005) at Kitware, Inc.

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[Avogadro-devel] Avogadro 1.1.1 Released

[Marcus D. Hanwell]

We are very proud to announce the availability of Avogadro 1.1.1.

Avogadro is a free, open source, cross-platform molecular editor
designed for flexible use in computational chemistry, molecular
modeling, bioinformatics, materials science, and related areas.
Packages are available for Windows, Linux and Mac OS X. The source
code source is available under the GNU GPLv2.

What does Avogadro do?
We've tried to make the best, most intuitive builder, including
common fragments, downloading directly from PDB or PubChem, and
peptide sequences
Innovative auto-optimize tool which allows you to continue to build
and modify, during molecular mechanics optimization
Interfaces to many common computational packages
Designed to help both educational users and advanced research
Plugins that allow Avogadro to be extended and customized
Well defined public API, library and Python bindings for development
Embedded Python interpreter
Translations available in 19+ languages

Download: https://sourceforge.net/projects/avogadro/files/avogadro/1.1.1

What's New? See the Release Notes:
http://avogadro.openmolecules.net/wiki/Avogadro_1.1.1

For more information: http://avogadro.openmolecules.net/wiki/

If you use Avogadro please check out the recently published Avogadro
paper, and consider citing it: http://www.jcheminf.com/content/4/1/17

This is a community project and we couldn't have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. Particular
thanks go to all the translators.

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Re: [Avogadro-devel] Avogadro Low Resolution Icon in Arch Linux

[Marcus D. Hanwell]

On Mon, Dec 23, 2013 at 2:19 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 I can take a look at this, and will see if I can improve it. The report 
 doesn't reference what version you are referring to, but I presume 1.1.1?

 We have both a 512x512 icon and an SVG version, so this shouldn’t be too hard 
 to fix.

 https://github.com/cryos/avogadro/blob/master/avogadro/src/icons/avogadro.png
 https://raw.github.com/cryos/avogadro/master/avogadro/src/icons/avogadro.svg

 Or in the source tree, these are avogadro/src/icons/avogadro.*

 Does the .desktop file just need some patching? (Sorry, I’ve never used Arch.)

Yeah, I use Arch everyday for development so I don't mind patching this.

Marcus

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Re: [Avogadro-devel] Avogadro Low Resolution Icon in Arch Linux

[Marcus D. Hanwell]

On Mon, Dec 23, 2013 at 2:41 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 On Mon, Dec 23, 2013 at 2:19 PM, Geoffrey Hutchison
 geoff.hutchi...@gmail.com wrote:
 I can take a look at this, and will see if I can improve it. The report 
 doesn't reference what version you are referring to, but I presume 1.1.1?

 We have both a 512x512 icon and an SVG version, so this shouldn’t be too 
 hard to fix.

 https://github.com/cryos/avogadro/blob/master/avogadro/src/icons/avogadro.png
 https://raw.github.com/cryos/avogadro/master/avogadro/src/icons/avogadro.svg

 Or in the source tree, these are avogadro/src/icons/avogadro.*

 Does the .desktop file just need some patching? (Sorry, I’ve never used 
 Arch.)

 Yeah, I use Arch everyday for development so I don't mind patching this.

Just to be clear, the .desktop file will of course affect all Linux
systems, but I don't think this will be an issue.

Marcus

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Re: [Avogadro-devel] Building Avogadro2 w/o MoleQueue on Arch Linux-64bit

[Marcus D. Hanwell]

On Sun, Dec 29, 2013 at 5:12 AM, Mark Lee m...@markelee.com wrote:
 Salutations!

 I have been trying to build Avogadro2 (to test it out) on my Arch Linux
 64 bit system. However, while building avogadrolibs-0.7.2; I get the
 following error from CMake:

snip

 Is there a way to disable the building of MoleQueue?

Not at this time, but that shouldn't be too hard to achieve. I will
try to make sure it can be done for the next release, I'm afraid this
one slipped through (and it only needs a tiny client library we could
consider simply bundling).

Marcus

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Re: [Avogadro-devel] avogadro 1.1.1: Building with Eigen3 fails

[Marcus D. Hanwell]

On Tue, Dec 31, 2013 at 8:55 AM, Daniel Leidert daniel.leid...@wgdd.de wrote:

 Hi there,

 I'm speaking as part of the Debian package maintainers of avogadro. The
 latest release 1.1.1 fails to build with Eigen3. The reason is, that
 Eigen2 is still required, e.g. in
 libavogadro/src/extensions/surfaces/openqube/CMakeLists.txt. Also
 cmake/modules/AvogadroUse.cmake requires Eigen2. So it is not possible
 to build with Eigen3 only and the build fails. Is this some kind of
 intentional result or a bug?

 I'm attaching the build log.

It is a bug, Geoff submitted a patch to enable building with Eigen 3
for 1.1.1 (this is very new, and not well-tested - thanks for the
feedback). We can work on a fix for 1.1.2 (a few other things have
come up too), I will try and find some time to look into this further
unless Geoff gets to it first.

Marcus

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Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting

[Marcus D. Hanwell]

On Tue, Feb 4, 2014 at 5:39 AM, Jure Varlec jure.var...@ki.si wrote:
  Also, I had to add an include path for Eigen to  fix building, do I have
  to make a separate branch for that single commit?
 I'm not sure why that (adding an Eigen include path) would be necessary.
 That should be covered by CMake. Why don't you comment on your problems
 with Eigen and we'll see if it can be fixed outside of a patch.

 Well, CMake finds both Eigen2 and Eigen3, but build fails with 'fatal error:
 Eigen/Core: No such file or directory' unless I patch it with

 diff --git a/libavogadro/src/colors/CMakeLists.txt
 b/libavogadro/src/colors/CMakeLists.txt
 index a967516..c0836a8 100644
 --- a/libavogadro/src/colors/CMakeLists.txt
 +++ b/libavogadro/src/colors/CMakeLists.txt
 @@ -6,7 +6,7 @@ ADD_DEFINITIONS(-DQT_SHARED)

  set(DESTINATION_DIR ${Avogadro_PLUGIN_INSTALL_DIR}/colors)

 -include_directories(${CMAKE_CURRENT_BINARY_DIR})
 +include_directories(${CMAKE_CURRENT_BINARY_DIR} ${EIGEN_INCLUDE_DIR})

  set(LINK_LIBS avogadro)
  set(PLUGIN_LABEL colors)

Are you building with Eigen 2 or 3? I just looked at master, and
libavogadro/src/CMakeLists.txt adds it to the include directories, the
same is not true for Eigen 3. There are still a number of rough edges
with the Eigen 3 support, we should take a pass at getting that to
build consistently. A lot of people (myself included) have Eigen
installed and can miss this.

I also don't see anything that defines EIGEN_INCLUDE_DIR, both
variants have the major version number. Hope that helps.

Marcus

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Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting

[Marcus D. Hanwell]

On Tue, Feb 4, 2014 at 10:45 AM, Jure Varlec jure.var...@ki.si wrote:
 On Tuesday 04 of February 2014 09:56:01 Marcus D. Hanwell wrote:
 Are you building with Eigen 2 or 3? I just looked at master, and
 libavogadro/src/CMakeLists.txt adds it to the include directories, the
 same is not true for Eigen 3. There are still a number of rough edges
 with the Eigen 3 support, we should take a pass at getting that to
 build consistently. A lot of people (myself included) have Eigen
 installed and can miss this.

 I also don't see anything that defines EIGEN_INCLUDE_DIR, both
 variants have the major version number. Hope that helps.

 I'm building with both. Although Eigen is a header-only library, I'm running
 Gentoo so both versions need to be installed as build-time dependencies of
 various packages, they are at /usr/include/eigen{2,3}

 Actually, when I touched one of CMakeLists and caused a reconfiguration, the
 problem popped out elsewhere, then disappeared later. It seems that, starting
 with an empty build directory, I have to run CMake twice, then it builds
 successfully. This behaviour seems to be consistent.

It is, I will see if I can reproduce. I don't even see where
EIGEN_INCLUDE_DIR would get defined, and how it would solve any
problem. A git grep for it in the source tree turns up nothing, and we
should consistently choose Eigen 2 or 3 - mixing the two would not end
well.

Thanks for your feedback, I will try to dig a little deeper when I
have some time and see if we can clean things up a little more.

Marcus

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Re: [Avogadro-devel] Avogadro 1.1.x and Linux Distributions

[Marcus D. Hanwell]

On Fri, Aug 29, 2014 at 6:58 PM, Michael Banck mba...@debian.org wrote:
 Hi,

 On Fri, Aug 29, 2014 at 04:51:49PM -0400, Geoffrey Hutchison wrote:
  Any progress on this?  The Debian freeze is approaching in a couple of
  months, so I it would be nice to include Avogadro-1.2.0 into the next
  version.

 I think we should probably fix as many bugs as possible and push out
 1.1.x as 1.2, even though it'll be missing a few features. Is there a
 date for the freeze? When do you want something?

 The hard freeze is early November, but early October would be
 appreciated to leave some time for integration etc.

Sounds like something we could work towards.

 The relative quiet is that Marcus came to visit Pittsburgh and we've
 been assembling a hit list to get as many things ready for an
 Avogadro v2 release. The new rendering architecture is a huge
 improvement, but day-to-day usability needs a bit of work.

 If avogadro2 is out by then, I can see about getting it packaged, but it
 might be premature to replace avogadro1 with it for the Debian release.

Avogadro 2 is totally compatible with being installed in the same
prefix as Avogadro 1, would it be reasonable to package it as as well
as Avogadro 1 rather than replacing? The executable is avogadro2, the
libraries have different names, share directory etc.

Just a thought, if not then I am fine with holding off but I think it
would be nice to consider. Thanks for pushing us on this - it would be
great to get what we can in before the freeze.

Marcus

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Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

[Marcus D. Hanwell]

Hi Geoff,

Sorry, crazy travel schedule, so didn't get this finished as soon as I
had hoped. I am working on some changes to make the conversion much
simpler, and to alleviate the UI issue. As I said at the time -
totally agree, and not pushing to keep the current UI. I think it was
a necessary step as I fleshed it out, but hope to make this much
smoother.

I think any of the edit functionality can convert to an editable
molecule, they use implicitly shared arrays and so the copy cost is
minimal with only the coordinates triggering a real copy when the
forcefield kicks in. I would love to see what you are thinking for the
auto-optimize, I just spent a few days at Daresbury Lab last week
talking about some of these features (along with QMMM, how we might
define regions, residues, etc).

Let me see what I can get done on the weekend to make it clearer, and
sketch out what I thought would work. Happy to iterate on this, and
yes it is better to put more of these discussions on the mailing list.
Measurement is a tool that I think we make work with edit and view
molecules to be honest - so no need to switch at all.

Marcus

On Wed, Sep 3, 2014 at 10:44 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 Hi Marcus,

 I wanted to follow-up about an off-list discussion with Avogadro v2. Between 
 v0.7, and the current git master (0.8?) there's now a clear UI division 
 between edit and view molecules.

 Can you outline some of the real reasons for this behind the scenes, 
 particularly on the UI side? I think this is currently a usability nightmare 
 and I'd like to make sure we can work past this or write up conversion code 
 that allows tools, extensions, etc. to convert back and forth.

 My big use-case concern is the Auto Optimize tool, which I'm trying to design 
 for Avogadro v2's very different architecture. For example, let's say a user 
 wants to set a measurement between two atoms (view). Then they switch to the 
 Auto Optimize tool (edit) and start pushing atoms around.

 In Avogadro v1, this wasn't a problem. The measurements would update while 
 the optimization occurred in a different thread.

 How can this work in Avogadro v2?

 Thanks,
 -Geoff

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Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

[Marcus D. Hanwell]

So the weekend resulted in no code being written, mostly ended up
having to fix some stuff in the house I was behind on due to all the
travel :-/ I did manage to get Windows reinstalled on the machine I
was using to create binaries (it suffered a hard drive failure a month
or two back - new, bigger hard drive too). I will have some time to
actually work on this in the coming days though, apologies on the
delay - I hadn't factored in spending so much time on real life
stuff...

Marcus

On Thu, Sep 4, 2014 at 9:31 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 Hi Geoff,

 Sorry, crazy travel schedule, so didn't get this finished as soon as I
 had hoped. I am working on some changes to make the conversion much
 simpler, and to alleviate the UI issue. As I said at the time -
 totally agree, and not pushing to keep the current UI. I think it was
 a necessary step as I fleshed it out, but hope to make this much
 smoother.

 I think any of the edit functionality can convert to an editable
 molecule, they use implicitly shared arrays and so the copy cost is
 minimal with only the coordinates triggering a real copy when the
 forcefield kicks in. I would love to see what you are thinking for the
 auto-optimize, I just spent a few days at Daresbury Lab last week
 talking about some of these features (along with QMMM, how we might
 define regions, residues, etc).

 Let me see what I can get done on the weekend to make it clearer, and
 sketch out what I thought would work. Happy to iterate on this, and
 yes it is better to put more of these discussions on the mailing list.
 Measurement is a tool that I think we make work with edit and view
 molecules to be honest - so no need to switch at all.

 Marcus

 On Wed, Sep 3, 2014 at 10:44 PM, Geoffrey Hutchison
 geoff.hutchi...@gmail.com wrote:
 Hi Marcus,

 I wanted to follow-up about an off-list discussion with Avogadro v2. Between 
 v0.7, and the current git master (0.8?) there's now a clear UI division 
 between edit and view molecules.

 Can you outline some of the real reasons for this behind the scenes, 
 particularly on the UI side? I think this is currently a usability nightmare 
 and I'd like to make sure we can work past this or write up conversion code 
 that allows tools, extensions, etc. to convert back and forth.

 My big use-case concern is the Auto Optimize tool, which I'm trying to 
 design for Avogadro v2's very different architecture. For example, let's say 
 a user wants to set a measurement between two atoms (view). Then they switch 
 to the Auto Optimize tool (edit) and start pushing atoms around.

 In Avogadro v1, this wasn't a problem. The measurements would update while 
 the optimization occurred in a different thread.

 How can this work in Avogadro v2?

 Thanks,
 -Geoff

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Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

[Marcus D. Hanwell]

On Mon, Sep 8, 2014 at 10:14 AM, Defusco III, Albert A defu...@pitt.edu wrote:
 Good morning,

 Let me add a bit to this discussion as well. I've been working on the 
 crystallography extension in Avogadro2 and I find it exceeding difficult to 
 use the CrystalTools while editing or creating molecules.

 1. It takes several clicks in and out of view mode along with renaming the 
 molecule before the Crystal QT plugin recognizes that there is even a 
 molecule present. From what I can tell in edit mode the following check 
 returns false for a new molecule.

 crystal.cpp:
 if (m_molecule)

 2. Once a unit cell has been added it is not visible in edit mode. The 
 following appears to return false.

 3. Crystal operations, like filling a unit cell, show nothing in edit mode. 
 They appear to work and the output is present once the user changes to view 
 mode.

 All of these operations just worked in the 0.7 release and it didn't care if 
 the user had selected an edit tool or a view tool. One of the great features 
 of Avogadro is that the molecule was always editable and the programmer 
 didn't have to make many, or even any, special considerations when writing 
 tools.

Like I said, please give me a little time to finish it up, perhaps I
committed the feature too soon. Many of these issues are rendering
artifacts, along with some issues around certain editing features not
being ported to use the right structure. I am not pushing to keep it
this way, but like I said when I was over in Pittsburgh this can be
made intuitive with a little more work - I will see if I can get that
finished up soon so that things are easier, and we can make a release.

Thanks for your patience, I am thankfully done with travel for a
while, and should be able to focus on finishing this up. Major
advantages are a scalable undo/redo (with some rough edges
admittedly), and I honestly think it will be worth it to reduce
confusion about properties that are simply no longer valid after
editing. In the UI the difference between editing and viewing should
be fluid, but I hope to create a much clearer model in the API so that
we focus on doing one or the other well in most cases.

If by some chance it doesn't work out I can back out some of the changes.

Marcus

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Re: [Avogadro-devel] Discourse / Forum Interface

[Marcus D. Hanwell]

On Tue, Oct 7, 2014 at 12:46 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 I've been looking around at web forums, since I see a lot of current 
 undergrads and grad students (i.e., users) don't use e-mail much (much less 
 mailing lists).

 There are multiple packages and I'm open to suggestions. One that seems to 
 pop up a lot recently is Discourse (http://www.discourse.org) which looks 
 pretty slick. The feature set is nice, plus multi-language support 
 (http://v1.discourse.org/about/)

 The one caveat is that I don't have anywhere to host it (i.e., it uses 
 Postgres, .. Docker). They recommend Digital Ocean, for an extra $10/month..

 I know Ubuntu uses Discourse. Any feedback? Advantages or disadvantages?

I have played with Discourse, and it looks pretty nice but I haven't
really used it seriously in any sense. I wouldn't object to giving it
a try, but don't have anywhere I could host it right now either.

Marcus

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Re: [Avogadro-devel] Switching to GitHub pull requests for review/merge?

[Marcus D. Hanwell]

On Mon, Oct 6, 2014 at 10:34 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
 Hi,

 Would there be any objections to switching to GitHub pull requests for
 development? The Kitware instance of Gerrit will be upgraded at some
 point, removing the topic branch functionality. Gerrit feels a little
 heavy/clunky, and I feel like GitHub has come a long way since we made
 the switch to Gerrit.

Geoff gave me a +10 off-list, I will work on clearing the Gerrit
backlog, planning to move to GitHub pull requests unless I hear
objections. We are looking at a project called GitLab for several
Kitware projects that are considering moving from Gerrit (they are
also considering GitHub). This may be interesting, but it effectively
mirrors much of the functionality of GitHub.

Thanks,

Marcus

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Re: [Avogadro-devel] Migrating Wiki to GitHub Pages

[Marcus D. Hanwell]

On Thu, Oct 16, 2014 at 4:33 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
 Hi everyone,

 Despite the low level of action, I’ve been spending a lot of time *thinking*
 about Avogadro and the future. There are quite a few exciting things,
 although it may take a while before they fully appear.

 One thing I can talk about is pushing for tutorials and manuals.

 The University of Pittsburgh is putting money and student-power towards
 improving tutorials and manuals for Avogadro. We’re converting from a
 proprietary program to Avogadro over the next two years. So we’ll be putting
 up workflows, learning exercises, etc.

 One thing I'm considering is moving away from MediaWiki. It's insecure and
 spammy. The whole point was to let people easily edit the pages, and that
 doesn't work now.

 I'm open to suggestions, but I'd like to suggest GitHub pages. These are
 generated from a repo, so it's easy to add a pull request to modify them,
 translate, etc. As static pages, they're easier to package and distribute
 too.

 One catch is converting from MediaWiki to Jekyll, so if someone can help
 with that, eg parsing the XML dump, please let me know.

 Thoughts? Better alternatives?

This sounds good to me, I think being able to issue pull requests
would be useful along with easier packaging, offline editing.

Marcus

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Re: [Avogadro-devel] Migrating Wiki to GitHub Pages

[Marcus D. Hanwell]

I turned on wiki and issues for the repo if that helps. The GitHub
wikis are backed by git, and have editing facilities built in, so that
might be the easiest (I haven't used the GitHub wikis much, but
willing to give it a try).

Marcus

On Fri, Oct 17, 2014 at 1:47 PM, Patrick Fuller patrickful...@gmail.com wrote:
 To reiterate what Ian said, I think that pandoc + maybe a shell script will
 get you most of the way there. If you have the XML, you can try (untested):

 pandoc -f mediawiki -t markdown file.xml

 (f is “from”, t is “to) I also just tried parsing a URL directly and it’s
 not bad. This works decently well:

 pandoc -f html -t markdown http://avogadro.cc/wiki/Tutorials:Getting_started

 Regarding Jekyll / Liquid, I don’t think the AvogadroChem.github.io approach
 is the way to go. There’s a little wiki button to the right of any github
 repo (ex. d3’s wiki). My vote is to start with an official avogadro git repo
 (https://github.com/cryos/avogadro maybe?), git clone
 cryos/avogadro.wiki.git, dump in pandoc markdown, and then review the
 contents.

 Regards,
 Pat


 On Fri, Oct 17, 2014 at 12:30 PM, Geoffrey Hutchison
 geoff.hutchi...@gmail.com wrote:

 OK, a first pass is here:

 https://github.com/AvogadroChem/AvogadroChem.github.io
 e.g.

 https://github.com/AvogadroChem/AvogadroChem.github.io/blob/master/features.md

 This includes all the images I could grab, although I'm sure there are
 errors. It's not a functioning site yet, but if someone has worked with
 Jekyll or GitHub Pages before, please send me an e-mail so we can get
 something up and running.

 Also, thanks to those who wrote off-list about educational use. I might
 start a separate e-mail list for that, but I think we can coordinate to get
 some really nice exercises up for everyone to use.

 -Geoff

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Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

[Marcus D. Hanwell]

On Thu, Dec 11, 2014 at 4:14 PM, Defusco III, Albert A defu...@pitt.edu wrote:
 Hi guys,

 Would good project be to re-wire Avogadro to use cclib instead of relying on 
 the quantumio in Avogadro2? I'm very much in favor of adding visualization 
 capabilities for QuantumEspresso and CP2K.

You don't need to rewire, the Open Babel plugin reuses all of the
readers/writers advertised. That pattern could be used to reuse the
cclib readers/writers, offering the option of what reader to use if
there is more than one. I think it would be great to add that
capability.

Marcus

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Re: [Avogadro-devel] Google Summer of Code

[Marcus D. Hanwell]

On Mon, Dec 8, 2014 at 3:00 PM, Michael Banck mba...@gmx.net wrote:
 On Mon, Dec 08, 2014 at 10:53:50AM -0500, Geoffrey Hutchison wrote:
 The deadline for applying to be a mentoring organization for Google
 Summer of Code is fast approaching.

 I'm not sure precisely where to hang our hat (e.g., Avogadro alone,
 general open-source chemistry like Blue Obelisk, or through another
 group like the University of Pittsburgh) but I'd really like to see
 Avogadro apply and get a student or three funded again.

 Personally, I'd like to see more interoperability between the
 open-source chemistry apps, including avogadro, openbabel and cclib
 growing support for open source quantum chemistry packages like PSI4,
 NWchem, CP2K, Quantum ESPRESSO (Avogadro might support a few already),
 and I'd probably be willing to mentor.  However, I did think that Blue
 Obelisk might be the better umbrella organization for that.  In general,
 if there is enough good proposals etc. I'd say Blue Obelisk might have
 a better shot at being accepted as Avogadro alone.  On the other hand,
 if nobody else is pushing this...

I would vote for Blue Obelisk, but it has been hard in previous years
to get any momentum around it. I would be interested in mentoring, it
is hard to tell what Google is looking for and so I think we would
have a shot as Avogadro or Blue Obelisk - they certainly accept a
number. We could also talk to KDE, and see about doing it in their
umbrella as we did in previous years.

Marcus

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Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

[Marcus D. Hanwell]

On Thu, Dec 11, 2014 at 11:36 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 I think Albert was talking about a glue layer for quantum io, not for
 regular input. Regular input is probably best handled through Open Babel,
 since that already handles bond perception, typing, etc.

 Right now, Avogadro v1 and v2 have separate code for reading basis set and
 MO information from various formats. Instead, such information (which is
 only performed when computing orbitals, etc) could be handled through a
 python call and cclib parsing.

It sounds like you think of these things as exclusive, and I don't see
why they should be. Maybe we just need to chat, and flesh out what is
meant a little more. If what was done for Open Babel is considered a
glue layer for regular input, then what I meant in my reply was
that it sounded like a great idea and that we even have a template for
such a layer.

We could certainly expand what can be brought in by such a layer, but
I have some motivation to keep some of the other IO work present as it
is demonstrably much more efficient than going through Open Babel for
regular input for example. We can certainly tweak defaults, so the
richest approach would be offered automatically.

Marcus

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Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

[Marcus D. Hanwell]

Albert,

I think CML will continue to be very much a first class citizen too.
JSON feels much easier to change/augment, and Python support for JSON
is very good - it would be great to add it, but I don't think it is
critical. We could add some simple Python glue too, the format is
super-simple. With Open Babel we ended up using CML, MDL and XYZ to
get data into Avogadro 2.

Marcus

On Thu, Dec 18, 2014 at 9:59 AM, Defusco III, Albert A defu...@pitt.edu wrote:
 Hi Karol,

 It looks Avogadro2 will be using Chemical JSON whenever possible to transfer 
 data. Do you think this would be possible with cclib?

 http://wiki.openchemistry.org/Chemical_JSON



 Albert



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 412-648-3094
 http://www.pitt.edu/~defusco
 http://www.sam.pitt.edu

 On Dec 17, 2014, at 11:22 PM, Karol Langner karol.lang...@gmail.com wrote:

 One of the things I want to do soon is give cclib the ability to output CML. 
 That would be an easy way to communicate between programs in a standard 
 format.

 Karol

 On Fri, Dec 12, 2014 at 12:33 PM, Geoffrey Hutchison 
 geoff.hutchi...@gmail.com wrote:
  It sounds like you think of these things as exclusive, and I don't see
  why they should be.

 The current state of the code is 
 https://github.com/OpenChemistry/avogadrolibs/tree/master/avogadro/quantumio

 That is, these things are *separate* from “regular” IO. Reading files and 
 finding quantum data are currently in different parts of the code.

 Now, one may question whether “regular” and quantum IO *should* be separate. 
 But I’m not talking about throwing away existing code - I believe Albert was 
 saying that rather than adding X new implementations to 
 avogadrolibs/avogadro/quantumio, it would be helpful to have an interface to 
 cclib for parsing quantum data.

  is demonstrably much more efficient than going through Open Babel for
  regular input for example. We can certainly tweak defaults, so the

 I certainly wasn’t talking about changing the current pattern for regular 
 IO, although I’d certainly suggest that the interface could merge “import” 
 and “open” commands. In the case of CML or other formats that Avogadro 
 directly handles, preference can go to the internal implementation, and 
 other formats could be handled through Open Babel.

 I’d be happy to make that change.

 I thought the discussion was about Summer of Code projects, and certainly 
 improving quantum IO would be great. (Adding features to read and visualize 
 other “cube” formats would be nice too.)

 -Geoff


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[Avogadro-devel] Editing, viewing, and making things more fluid again

[Marcus D. Hanwell]

Hi,

So I slacked off a lot over the Christmas break, but have been working
on a few patches and thinking about the overall data architecture in
the Avogadro 2 application. We spent quite a while thinking about the
design, and I looked at a lot of what went well and not so well in
Avogadro 1. I thought now might be a good time to explain some of
those decisions (after a little prompting from Geoff), and
improvements I am working on to improve the (unfortunately)
non-intuitive interaction in the current application.

Overly general mega-classes were a source of many
bugs/crashes/inefficiencies in Avogadro. Several design decisions work
to improve that situation in Avogadro 2, including the use of
copy-on-write arrays, storing most molecular data in these arrays, use
of proxy classes for atom/bond/other lightweight objects, and
specializing an editable molecule with scalable undo/redo support,
signals, slots, etc.

If we have a specialized editable molecule we can focus on only the
things that can/should be editable. We can add the necessary
infrastructure to support scalable undo/redo - i.e. record
addition/removal of an atom rather than make many copies of the entire
molecule before and after an edit. The signals fired for each change,
along with the undo/redo objects created, do not scale when adding
millions of atoms though, and so having a view-focused molecule offers
a more scalable option for I/O.

Using copy-on-write arrays also offers very efficient copying from
each molecule type - these arrays do not copy any underlying data
unless a non-const method is called. So reading into a view molecule,
copying to an editable molecule, deleting the view molecule, and
editing the editable actually only ever creates one copy of the bulk
of the data - the array will only be duplicated if a non-const method
is called and its internal reference count is greater than 1.

What doesn't work at all well is the edit/view GL widget, and the
tough/hard line between editing a molecule/viewing it. I am working on
merging the two widgets together, and reflecting the fluidity of
moving between the two types in the interface so that it will be far
less/barely noticeable that you went from viewing to editing a
structure. I had hoped to get this merged sooner, I think I am pretty
close to having it resolved now.

I have also been experimenting with templating more of the algorithms,
like hydrogen addition/removal, bond perception, etc. This would make
it easy to use a command-line version with no undo/redo support (or Qt
dependency), and build the same algorithm using the editable molecule.
An added benefit would be the potential reuse by any other
library/application using its own molecule class if they implement an
adaptor that offers the expected API. I would love to avoid forcing
everyone into virtuals and using the same base class/API.

For the render widgets I was also hoping to move to the new OpenGL
classes added in Qt 5.4 soon. This email got very long, and I haven't
necessarily covered everything but would be happy to talk more on
IRC/Skype/Hangouts/on this thread. If this generates a lot of
additional work we should talk, and one thing I was never all that
sold on was not having a common base class for the view/edit molecule
- I have been weighing up if that would make things simpler/easier.

I was hoping to start posting more details/discussions as things have
become very quiet. I really want to get a new release out, but have
been delaying until the edit/view problems are resolved, and apologize
for the delays in getting this sorted - last year was pretty tough and
featured very little spare time. This year is looking much better, and
I really want to get this right while maintaining the speed and
efficiency improvements made.

Sincerely,

Marcus

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Re: [Avogadro-devel] Editing, viewing, and making things more fluid again

[Marcus D. Hanwell]

On Tue, Jan 6, 2015 at 12:03 PM, Michael Banck mba...@gmx.net wrote:
 On Tue, Jan 06, 2015 at 11:05:15AM -0500, Marcus D. Hanwell wrote:
 What doesn't work at all well is the edit/view GL widget, and the
 tough/hard line between editing a molecule/viewing it. I am working on
 merging the two widgets together, and reflecting the fluidity of
 moving between the two types in the interface so that it will be far
 less/barely noticeable that you went from viewing to editing a
 structure. I had hoped to get this merged sooner, I think I am pretty
 close to having it resolved now.

 Are you talking about how the user should do this with respect to mouse
 button-drag and modifier keys?  If so, it would be interesting to this
 disucss this, but I have no idea how it does (not) work currently, how
 it was supposed to work, and how you plan to fix it, based on your
 information above.

Referring to the need to close the edit widget, open the view widget,
or vice-versa. That will go away, and the switch between the two modes
will be pretty seamless. It is currently quite painful, but should be
fixed up soon.

 For the render widgets I was also hoping to move to the new OpenGL
 classes added in Qt 5.4 soon.

 Any good reason for doing this?  Is any major distribution shipping Qt
 5.4 already?

Yes, that is where I was hesitating... I may see if the API is close
enough that we can detect the version and use the latest when
available. I know how irritating it can be to require the latest
release of a major library. QGLWidget is deprecated, the OpenGL
variants already have more features and will be supported going
forward.

Marcus

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Re: [Avogadro-devel] Google Summer of Code

[Marcus D. Hanwell]

Hi,

To update the list, we were not selected this year. I got feedback
from Google which was very positive and encouraged us to apply again
next year. They only accepted 137 organizations this year (down from a
high of 190 last year). We had some great ideas, and we will continue
to work on links with other open source chemistry projects to put
together an even stronger proposal next year.

Thanks for everyone's interest, disappointed we didn't make it this
year but encouraged to try again next year. Working on some patches
and hopefully a release soon...more threads on that soon.

Marcus

On Wed, Dec 17, 2014 at 11:18 PM, Karol Langner karol.lang...@gmail.com wrote:
 Hi guys,

 I would definitely be happy to help out from the cclib side of things. I
 don't think I would manage the time to mentor, but could help generally
 organize things as well. I have been trying to make some time to get into
 Avogadro and openbabel, and this would be a good pretext.

 I have participated in GSOC in the past (as a student), in a project
 unrelated to chemistry.

 Cheers,
 Karol


 On Fri, Dec 12, 2014 at 12:41 PM, Geoffrey Hutchison
 geoff.hutchi...@gmail.com wrote:

 Here are some of the questions for mentoring organizations. I would hope
 that KDE and/or VTK/Kitware could vouch for us as an organization?



 In addition to anything else your organization would like to submit a
 proposal, Google will be asking (at least) the following questions as part
 of the proposal process:

 • Describe your organization.
 • Why is your organization applying to participate in Google
 Summer of Code 2015? What do you hope to gain by participating?
 • Has your organization participated in past Google Summer of
 Codes? (yes/no)
 • If you answered “yes” to the question above, please summarize
 your involvement and the successes and challenges of your participation.
 Please also list your pass/fail rate for each year.
 • If your organization has not previously participated in Google
 Summer of Code, have you applied in the past? If so, for what year(s)?
 • What Open Source Initiative approved license(s) does your
 project use?
 • What is the URL for your Ideas list? This is the most important
 part of your proposal. Please make sure we can access it and it is complete
 when you submit this proposal. “Placeholder” or inaccessible ideas pages
 will be grounds for an automatic rejection for participation in Google
 Summer of Code2015.
 • What is the main development mailing list for your organization?
 • What is the main IRC channel for your organization?
 • Who will be your backup organization administrator?
 • What criteria did you use to select the mentors? Please be as
 specific as possible.
 • What is your plan for dealing with disappearing students? Please
 be as specific as possible.
 • What is your plan for dealing with disappearing mentors? Please
 be as specific as possible.
 • What steps will you take to encourage students to interact with
 your project's community before, during and after the program?
 • Are you a new organization who has a Googler or other
 organization to vouch for you? If so, please list their name(s) here.
 • Are you an established or larger organization who would like to
 vouch for a new organization applying this year? If so, please list their
 name(s) here.
 • What will you do to encourage that your accepted students stick
 with the project afterGoogle Summer of Code concludes?

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Re: [Avogadro-devel] Getting Avo2 to release

[Marcus D. Hanwell]

On Thu, Jun 4, 2015 at 4:07 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 Selection and residues, along with some rendering features seem most 
 critical to me (we have stick but it has a rendering bug I need to dig into).

 I'd put selection slightly above residues because I think it's critical for 
 copy/paste/clear and moving fragments. (Which I guess also means that 
 inserting fragments is a needed piece.) Indeed, I think selection affects a 
 *lot* of tools and extensions, so that's my preference.

Agreed - wasn't really ranking, but selection is certainly more
critical than residues. I really don't think we are that far apart,
and value the input on priorities. If others have feelings it would be
great to have them.

I will do selection first, but would like to follow that quite quickly
with fragments, residues, monomers, etc.

Marcus

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Re: [Avogadro-devel] subclass QColumnView

[Marcus D. Hanwell]

On Wed, Jun 3, 2015 at 10:55 AM, Defusco III, Albert A defu...@pitt.edu wrote:
 Hi everyone,

 I am nearing completion of my space group dialog. You can see the current 
 state on GitHub

 https://github.com/AlbertDeFusco/avogadrolibs/tree/spg-rw

 The next thing I need to do is remove the final preview widget from my 
 QColumnView. I believe I can subclass it as follows in spacegroupdialog.cpp.

 class spgColumnView : public QColumnView
 {
   public:
 spgColumnView(QWidget* p) : QColumnView(p) {}
 QAbstractItemView * createColumn ( const QModelIndex  index )
 {
   Avogadro::QtPlugins::SpaceGroupItem *thisItem = 
 static_castAvogadro::QtPlugins::SpaceGroupItem*(index.internalPointer());
   QAbstractItemView *view = 0;
   if(thisItem-childCount() == 0)
 return view;
   else
 return QColumnView::createColumn(index);
 }
 };

 I then change QColumnView to spgColumnView in spacegroupdialog.ui. When I try 
 to build it I get the following error.

 /Users/albert/Development/oc-clean/build/avogadrolibs/avogadro/qtplugins/crystal/ui_spacegroupdialog.h:26:10:
  fatal error: 'spgcolumnview.h' file not found
 #include spgcolumnview.h
  ^
It looks like you are using the wrong include, should be  as this is
a local header, not  for system headers. The compiler will then
search the same directory automatically, as it knows that is the most
likely/default location.

 I was using the FileComboBox class, which is a subclass of QComboBox, in 
 qtplugins/clientserver as an example. Is there something I have to do in 
 CMake to get this to build? I tried setting SKIP_AUTOMOC to true for these 
 source files, but it didn’t seem to work.

You don't want to skip automoc.

Marcus

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Re: [Avogadro-devel] Require C++11/dropping Boost fallback

[Marcus D. Hanwell]

On Wed, Jun 3, 2015 at 6:50 PM, Michael Banck mba...@debian.org wrote:
 On Wed, Jun 03, 2015 at 01:20:01PM -0400, Geoffrey Hutchison wrote:
  Debian stable (jessie) ahs GCC 4.8 and 4.9, but it got released very
  recently and many are still on oldstable (wheezy) with GCC 4.7.

 I guess your impression agrees with Marcus - that probably everything
 we would use soon is fine and we can target anything supported by GCC
 4.7.x.

 As far as important Debian/Ubuntu releases are concerned, yes, (if 4.7
 really implements all the features), RHEL/CentOS/SL 6 might be an
 important target as well (or not, dunno), and AFAIK it only ships GCC
 4.4 (but might have some C++ features backpatched).

Closing the loop on this, I feel pretty comfortable in bumping this. I
think tagging before making a hard dependency on C++11 features would
be good in case people wanted that, but see no reason not to start
using modern C++ functionality.

Compiler support seems reasonable, building new compilers on older
machines is also possible, I know Ubuntu 12.04 still has a few years
of support left and that may present some issues but there is already
a new LTS people can move to (I think they get five years).

Marcus

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Re: [Avogadro-devel] Volume Rendering

[Marcus D. Hanwell]

On Thu, Jun 11, 2015 at 1:12 PM, Barry Moore moore0...@gmail.com wrote:
 Dear All,

 I recently saw Volume Rendering in the Getting Avo2 to release email and
 wanted to start some discussion. I recently exposed the Gaussian Cube file
 type to render MOs (pull request was submitted, including an example to
 avogadrodata) and I had some ideas for improvements:

 1) Is there a good place to submit improvements (not issues), and possibly
 rank the importance of such an improvement? I would like to help with
 important issues instead of just issues I am particularly interested in.

In the issue tracker, but tag them as enhancements. Bugs should be
tagged as bugs.

 2) Instead of Set background color in View tab, it might be better to
 have a Color Preferences where one could set many different colors
 (including opacity etc).

Sounds reasonable.

 3) Alignment tool, click two atoms, align to some axis (for exporting images
 mainly)

I had been meaning to port this from Avogadro 1 - it is a simple tool
I wrote for similar purposes (including QM with electric fields).

 4) I have suggested this to Marcus previously, but exporting graphics in
 vector formats for publications. The PNG images generated currently are
 lackluster. I dug into this a little, but I lack experience with Qt and the
 concepts were a bit over my head at the moment (working on that!).

Vector graphics is tougher, I would like to finish off some of my work
on bringing back POV-Ray/ray tracing export. For a scene of any
complexity even when you export the vector it can often be too much
for the rendering engine in Adobe Reader for example. After having
done this in Avogadro, and seen results from VTK I would say you are
best off rasterizing the 3D and exporting text, lines, etc.

We are pretty focused on getting some essentials finished up, as per
Geoff's post, but if you have time and want to develop some of these
features I would be interested in what you come up with.

Best,

Marcus

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Re: [Avogadro-devel] Getting Avo2 to release

[Marcus D. Hanwell]

On Wed, May 27, 2015 at 3:55 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 Thoughts? Concerns? Something I've missed?

 Oh, I forgot color schemes and custom colors. My feeling is that can fall to 
 nice to have for v2.1?

I have some time this next couple of weeks to take a stab at some
pieces. I think the critical and nice to have may vary a little
depending on person. I will make a new release soon (0.8) as I would
like to get more people testing stuff. Selection and residues, along
with some rendering features seem most critical to me (we have stick
but it has a rendering bug I need to dig into). I would like to expose
the transfer function editor from VTK, and finish off the volume
rendering piece but would put that firmly in nice to have.

This has languished more than I would like, so apologies from me for
not having as much time as I had hoped. There are some great features
in there, but UI polish is needed to make it more accessible. It is
orders of magnitude faster loading initial data, and rendering it, for
large systems, but the interface is missing some key pieces (some
already fixed) which led to me delaying 0.8.

I think your list is a good yard stick, and just like with 1.0 we will
possibly wait too long, but know it when we see it. I had hoped to
have it a year ago, and am determined to make it happen. I think a
test run on Qt 5 deployment will be valuable (it was working for me on
Mac and Windows when I tried it last time.

I am blown away by over 600,000 downloads since our first release of
Avogadro, and over 400 citations of our paper. I want to get some
momentum going again, and hope we have even more ideas to put into a
Google Summer of Code proposal next year.

Best,

Marcus

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Re: [Avogadro-devel] Avogadro2 Extensions Priorities

[Marcus D. Hanwell]

On Thu, May 21, 2015 at 3:43 PM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
 I'd like to ask about Avogadro2 extensions and priorities.

 In Avogadro 1, plugins were loaded in alphabetical order (sorted by the 
 filesystem) and then the extension provided an ordered list of commands. This 
 meant that the extension basically was responsible for building out a menu 
 in-order. (I'm thinking for example of the Molecular Mechanics submenu.)

They were sorted by the 'usefulness', which was global for that
plugin. That allowed us to go beyond simple alphabetical sorting, but
only offered one global 'usefulness' per extension, and modulated the
position of all entries provided.

 In Avogadro v2, it's *very* hard to do this. Menu items are sorted 
 alphabetically and/or by priority. But since *nothing* has priority set right 
 now, things jump to the top.

I don't think it is very hard to do it, but maybe we failed to add the
right prorities. The intent was to order things with priority, and
fallback to alphabetical. We could add a convenience to increment
priority by 1 for each action if that is desired.

 I'm thinking for example of cut/copy/paste.

 Every OS has standardized on the order of cut-copy-paste. Of course this 
 isn't in alphabetical order.

 So right now, in Avogadro v2, you get Copy - Cut - Paste.

I can fix that, it was something we missed (and I admit that I tend to
use the keyboard shortcuts).

 I'm happy to patch the behavior (and revert back to Avogadro v1 strategy of 
 each plugin providing an ordered list). Was there a reason for this design?

It was a desire to go beyond some of the hardwired separators, so
every 100 a separator would be interted, and the menu items from
multiple plugins can be blended together/put in the same section, or
separated sections.

The menus need to be tidied, and maybe the menu ordering code needs
some refinement, but I would like to keep the additional flexibility.
I found it limiting in v1, hence the work to build something a little
more flexible, may be the API needs a bit more work (I would hate to
scrap it though as I think it has some real value).

We could simply call a second virtual, ordered, and usefulness, if we
wanted to offer a more global method as was done before. This could be
mapped into the new ordering by applying the number, and incrementing
each action by 1.

Marcus

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Re: [Avogadro-devel] Symmetry element rendering

[Marcus D. Hanwell]

On Wed, Aug 19, 2015 at 11:26 AM, Marcus Johansson mcode...@gmail.com wrote:

 Hi

 Was wondering if anyone has some input on rendering symmetry elements in 
 Avogadro v2. There is a need for “disc” (mirror plane) and “vector” (rotation 
 axis) geometries as well as alpha in order to make things look good. Im 
 currently using the “cylinder” and “sphere” geometries, but as you can see 
 they are not well suited for the job.

For some of the other display types we added factories to create
triangle geometry. Many things can be represented by triangle meshes,
we made the special cases for spheres because we were using impostors
and cylinders because there are lots of them and might want to use
impostors in the future.

It would be great to consider what primitives might be missing, and
either add factories that simply create meshes, or boost them to new
primitive types if that makes more sense. I also need to dig into an
issue with text rendering on Windows where it appears to be causing
crashes in the latest release.

It would be great to get symmetry elements in Avogadro 2, thanks for
working on this!

Thanks,

Marcus

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Re: [Avogadro-devel] Build Avogadro in Windows from source. MinGW or MSVC?

[Marcus D. Hanwell]

On Mon, Nov 16, 2015 at 7:13 AM, Carlos Salgado
 wrote:
> Dear all,
>
> I am trying to build the developer version of Avogadro in Windows, but I am
> not sure if I have to use MSVC or MinGW, and the corresponding version of
> Qt. I have build it in UNIX with ccmake-2.8.11 and it works like a charm. I
> have introduced modifications to the Gaussian calculation interface, for
> example. Avogadro is a very nice project.
>
> Could sombody, please, tell me which version of Qt in windows to use, and if
> I need to build it using MinGW or MSVC? I would really appreciate it.
>
I have been building Avogadro 1.1.x on Windows with MSVC 2008, and I
think 2010 more recently, using the latest Qt 4.8 binaries at the
time. That should work, my hard drive failed on that machine so I need
to get this spun up again. For Avogadro 2 I use Qt (5.3 I think last
time, want to try with 5.5) using MSVC 2010.

They both have superbuilds that can make it easier to get all of the
dependencies, or you can get them for yourself.

Hope that helps.

Marcus

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Re: [Avogadro-devel] New Avogadro Manual

[Marcus D. Hanwell]

On Mon, Aug 31, 2015 at 4:51 PM, Geoffrey Hutchison
 wrote:
> Thanks to support from the University of Pittsburgh Department of Chemistry, 
> there is a new manual for Avogadro:
> http://ghutchis.gitbooks.io/avogadro/
>
> You can find the images and Markdown on GitHub, of course, which should make 
> it fairly easy to edit, patch, and/or translate into other languages:
> https://github.com/avogadro/manual
>
That is great, thanks for putting this together!

Marcus

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Re: [Avogadro-devel] [Openchemistry-developers] avogadrolibs UHF calculation representation

[Marcus D. Hanwell]

Adding Avogadro developers list to CC, this is probably most appropriate there.

On Mon, Sep 14, 2015 at 9:14 AM, Bryce Anderson
 wrote:
> First of all I should state my motivations: what I want is proper plotting
> of UHF wave functions including being able to select the spin and get the
> correct HOMO/LUMO if that is a 'automatic' feature. If things go well, I'd
> like to see support for more interesting features (not necessarily UHF
> related) such as Charge Decomposition Analysis (CDA) and visualizing the
> results of TD-DFT calculations, but those are distant future dreams.

Sounds great.
>
> The current state of avogadrolibs master branch on GitHub (currently at
> commit 65141530f6831c6364b71230512097b9d1de95ae) has poor support for
> unrestricted (UHF) calculations. My concerns are the lack of plotting
> features for UHF (the plotting interface is completely unaware of UHF) and
> the partial/broken parsing of quantum output. Functions like `lumo()` are
> completely unaware of UHF and can return incorrect results in UHF
> calculations.

It has some beginnings, but it honestly has no exposed support for any
open shell calculations at this point. There is some API that Albert
added, and we have bounced some ideas around, but it was not completed
and no user interface elements are present so that a user could
visualize the beta MOs.
>
> I have made a PR that is a work in progress, #38 on Github, that more or
> less addresses my concerns. Part of it is removing default arguments for
> many of the functions that have a different meaning for RHF and UHF
> calculations which turns out to be controversial.
> A few examples of functions that drop defaults are
>
> `virtual unsigned int molecularOrbitalCount(ElectronType type) = 0;`
> `unsigned int electronCount(ElectronType type);`
> in the `BasisSet` class.
>
Not controversial, but we have already thought about some of this and
I think there are better solutions in this case. We also have some
conventions used in the API, and I would like to keep things as
consistent as possible. I think we could verify correctness with some
additional asserts that can be triggered at runtime based upon the
input type for example.

>  Less controversial (I assume) is correcting a few of the quantumio parsers
> (I believe they are corrected: I don't have first hand experience with many
> of the packages that generate the results in the avogadrodata repository, if
> the examples exists at all) to either emit the UHF information they already
> parsed or to actually parse it. I doubt they are complete but I believe they
> are moving in the right direction. They really need examples and testing for
> both RHF and UHF calculations.

Agreed, building up examples of both types, and improving verification
of results would be extremely useful for us all. I would really like
to add the capability to display this class of calculations, and am
more actively working on this part of the code now as I have a project
to develop improved integration with NWChem output too.
>
> I have brought up some suggestions as to refining the type model to drop
> some of the features from `BasisSet` that are are not actually basis set
> related. I think the current representation would be more aptly named
> `WaveFunction`. I have made an initial attempt to separate the concepts of
> 'wave function' and 'basis set' but the combinations of Rhf/Uhf with STO/GTO
> make that abstraction very repetitive at best. The idea was to create a new
> type `WaveFunction` that contains a basis, the energies and coefficients. It
> would have subtypes `RhfWaveFunction` and `UhfWaveFunction`. The problem is
> that setting the MO coefficients for STO and GTO would require further type
> refinement to classes `StoRhfWaveFunction` etc. or shifting the point of
> representation duplication to an even less desirable position. Ultimately,
> I'm inclined to abandon this effort unless someone has a good suggestion
> about how to avoid the excessive duplication.

I remember Albert and I going down a similar path, and becoming
concerned about duplication and questioning if it was worth it. I
would love to focus on a minimum viable product in terms of user
interface for open shell, and how we expose that in an intuitive way
in the graphical interface. We could then look at what API is missing
- and you pointed out several bits in the calculation of the cubes for
example.

These classes have undergone some refactoring already, where the data
structure is now (mostly at least) separate from the algorithms that
act upon them. As a first step do we literally just need a drop down
for alpha/beta when the calculation is open shell for example?

Thanks for looking at this, and providing examples.

Best wishes,

Marcus

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Re: [Avogadro-devel] Discourse and Translations

[Marcus D. Hanwell]

On Fri, Jan 1, 2016 at 1:06 PM, Geoffrey Hutchison
 wrote:
> Happy New Year!
>
> I'm looking into forum options (e.g., Discourse vs. Biostar). Seems like both 
> can import mbox archives, so I think a key question would be setting up the 
> Docker instance for Discourse, which can be deployed to Digital Ocean easily. 
> So I sent a message to Digital Ocean asking if they have deals for open 
> source projects - my current web host doesn't support Docker.

We talked about Discourse at a session during the GSoC mentor summit
last year, and it sounds like a number of communities have had great
results. From what they said you can use it as a mailing list
replacement if desired, but it has a number of options that they made
use of. I was hoping to look into this more soon as it sounds like it
is maturing really well.
>
> I'm also curious about an alternative to Launchpad for translations. Bazaar 
> doesn't support submodules, so the automatic git import-and-export is broken 
> for v.1.x (and also for v2).
>
> Two alternatives are Transifex (https://www.transifex.com) and Pootle 
> (http://pootle.translatehouse.org)
>
> Both are open source and used by different projects (Discourse is translated 
> using Transifex):
> http://www.worddelights.com/blog/gnome-outreach-program-for-women/translation-management-tools-transifex-pootle-and-launchpad-a-comparison-of-features
> * Transifex: Fedora, Tor, VLC
> * Pootle: LXDE, LibreOffice
>
> I'd be open to other suggestions - particularly if they natively support Qt's 
> .ts files (Launchpad still doesn't.)
>
Yeah, it would be great to look at translations for v2, although we
don't really need to worry about submodule support for v2. The libs
and app repositories have no submodules, they are within the
openchemistry superbuild repo that gathers them. I personally prefer
that method, it keeps third party code in a higher level module, that
looks more like system libraries. Still, very much open to looking at
new approaches for translation.

Happy New Year.

Best,

Marcus

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Re: [Avogadro-devel] Avo2 - Downloading from GitHub

[Marcus D. Hanwell]

On Thu, Jun 9, 2016 at 1:57 PM, Geoffrey Hutchison
 wrote:
>> I wonder if we might either use the GitHub APIs
>
> We can definitely use the GitHub API via HTTP. The catch is this ties us to 
> GitHub a bit more, while using Git directly makes it easier to point at 
> multiple repositories.
>
> It's pretty easy to walk the JSON from the API, e.g.
> https://api.github.com/repos/cryos/avogadro/contents/crystals?ref=master

It also makes it pretty easy to add other RESTful endpoints, and they
can be backed by whatever people choose. Calling git or other tools
from the command line would let us clone/update without committing
entirely to git.

I feel like expanding out interaction with RESTful services is a good
general direction, GitHub provides one endpoint but it is not the only
one.

My $0.02 on it...

Marcus

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Re: [Avogadro-devel] Avo2 - Downloading from GitHub

[Marcus D. Hanwell]

On Thu, Jun 9, 2016 at 1:25 PM, Geoffrey Hutchison
 wrote:
>> GNU Octave can download and compile its C++ packages automatically.
>> Perhaps it can serve as an example?
>
> My concern is this requires a C++ compiler from the end-user. On Mac and 
> Windows in particular, that’s not very common.
>
> Moreover, while we've offered nice C++ APIs for Avo1, I think the pool of 
> Python programmers is greater in science than those who know C++.
> (Indeed, the APIs in Avo2 could probably be ported to other languages too - 
> we're mostly running scripts as separate processes.)
>
Yes, my vision was to go beyond prescribing the language they wrote
extensions in. Python is a great start, but anything is acceptable as
they execute in their own process.

I wonder if we might either use the GitHub APIs, or simply call the
git command line to clone/update. This is what Qt Creator does, and we
would simply need to ask the user to install git/point us at it. We
call obabel like that too.

Marcus

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Re: [Avogadro-devel] avogadro-super custom targets?

[Marcus D. Hanwell]

Hi Geoff,

On Wed, May 25, 2016 at 2:51 PM, Geoffrey Hutchison  wrote:
> Hi Marcus,
>
> There was a request for an “uninstall” target for openbabel. So I added one.
>
> Now, the avogadro-super build fails because there are duplicate custom 
> targets..
>
> Any suggestions to resolve this?
>
You would need to use avogadro-squared, which uses the more modern
approach of external projects. Then each project has its own build
tree, and so you don't have the issue of duplicate targets. Otherwise
I don't think it is possible to resolve in an old-style combining all
projects in one CMake project approach as you cannot have duplicate
target names.

Marcus

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Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Marcus D. Hanwell]

On Fri, May 27, 2016 at 11:22 AM, Marcus D. Hanwell
<marcus.hanw...@kitware.com> wrote:
> On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison
> <geoff.hutchi...@gmail.com> wrote:
>>> I thought that ideally HydrogenTools would operate on the RWMolecule,
>>> but RWMolecule is now a lightweight class. There is not currently a
>>> way to get the Atom from an RWAtom, but the code would be very simple
>>> so if we want to add it we can.
>>
So I was just taking another look, and I think all you need assuming
you have the QtGui::Molecule, and the Atom object you want to access:

RWAtom rwAtom = molecule->undoMolecule()->atom(atom.index());

If you have an example where that doesn't seem to work I can take a
better look. The call to undoMolecule on molecule is cheap, no object
creation/destruction, and the rwAtom object creation should also be
really cheap. There is also atomByUniqueId if you want it, but the
index version should be faster and safe in the context you want it.

Marcus

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Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

[Marcus D. Hanwell]

On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison
 wrote:
>> I thought that ideally HydrogenTools would operate on the RWMolecule,
>> but RWMolecule is now a lightweight class. There is not currently a
>> way to get the Atom from an RWAtom, but the code would be very simple
>> so if we want to add it we can.
>
> Just a follow-up.. Can you point me in the direction here?
>
Sorry, I knew I owed you something. I will take a look at it, too much travel...

Marcus

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Re: [Avogadro-devel] Avogadrolibs Roadmap

[Marcus D. Hanwell]

On Wed, Jun 15, 2016 at 3:44 PM, Geoffrey Hutchison
 wrote:
>
> - Are there general or specific “loose threads” in the code? It seems like 
> there are some needs for batch undo/redo in RWMolecule, for example.

I would like to investigate grouping commands, and naming them.
Batches/larger commands would be good for efficiency, and achieve much
the same. I could see both being useful.
>
> - You mentioned implementing selections.. where should selections "live"? 
> Does the molecule track this? Does the widget? For example, should selections 
> be a special type of molecular fragment?

I was working on making some additions to molecule, and think that is
a natural place. I could see some argument for attaching them to
widgets, but would prefer to keep it simple for now.
>
> - Implementing fragments and residues.. this seems like it needs to live in 
> both Molecule and RWMolecule with the current class scheme. How do changes to 
> fragments coalesce? For example, does there need to be a mechanism to 
> invalidate a residue name when an edit occurs?

Nothing really lives in RWMolecule, it simply references data in
Molecule, and provides undo/redo functionality. Anything in RWMolecule
that is not in Molecule should be to facilitate undo/redo. Those are
my thoughts at least, and by layering RWMolecule on Molecule it allows
much of the cost for undo/redo to live in that class too.
>
> - Rendering options? Right now, there's no way to change atom sizes or bond 
> sizes.. where would this code live?

I would say the view configuration, in much the same way it did in
Avogadro 1. The ball and stick plugin features a configuration widget,
and offers multiple bonds/hydrogen visibility as two options. I meant
to go back and add bond/atom radius multipliers - it shouldn't be too
hard.
>
> - Settings in general.. Do we need to go add QSettings read/write to plugins 
> like in Avo1? How should this work with the Python scripts like input 
> generators?

QSettings is a good question - is that still supported as the Qt
community was talking about deprecating the INI file stuff, and
QSettings I thought. I would love to wrap more of this in JSON, and
have a JSON settings file, along with JSON data files. This could then
be passed to Python even, or combined. That is a good question on
persistent settings and input generators - I hadn't looked into that.
>
> - How / when will volume rendering show up? (i.e., what's the barrier for 
> that to be possible?)

VTK changed quite a bit, I would like to resurrect it. I know know the
code to edit the color maps much better too, and so could add the user
interface for it more easily than back then. This was the big missing
piece. I will see if I can take a look at where that is on the weekend
- it was crashing which is why I removed the option, but I really want
to get it back in there.

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Re: [Avogadro-devel] Windows Build for v1.2

[Marcus D. Hanwell]

Hi Geoff,

On Wed, Jan 13, 2016 at 2:21 PM, Geoffrey Hutchison
 wrote:
> Hi Marcus,
>
> My undergrad this term is working on a Windows build (using VS 2015). He's 
> had some problems with variable length array declarations and with linking.

Some of the topics merged were big, this has been a common theme when
getting Windows builds.
>
> I'd like to get a v1.2 build finalized - do you still have the CDash build 
> bot for Windows on v1.x master?
>
I can take a look at resurrecting the builder, that machine had its
hard drive die so I would need to add it back in.

> Assuming we can get everything built, I'd like to add a crash reporter to the 
> Windows build to debug some of the hard-to-understand random crashes people 
> mention. While Breakpad is used in lots of apps (e.g., Mozilla, Chrome, 
> Mendeley) getting the server running might be tricky.
>
> https://en.wikipedia.org/wiki/Crash_reporter
>
> Crashrpt / Crashfix Server (now completely open source under BSD)
> * http://crashrpt.sourceforge.net
> * http://crashfix.sourceforge.net
>
> Breakpad / Server (multiple forks at this point)
> * https://github.com/Mendeley/breakpad
> * https://github.com/atom/mini-breakpad-server
> * https://github.com/mozilla/socorro
>
Totally in favor, thanks for the extra info. Who is going to work on
that? Sounds like things have improved.

Marcus

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Re: [Avogadro-devel] Avogadro v2 Roadmap

[Marcus D. Hanwell]

On Wed, Mar 16, 2016 at 4:01 PM, Geoffrey Hutchison
 wrote:
> Since there's more interest in pushing for an Avogadro v2 "full" release in 
> 2016 (e.g., fall?) I wanted to start a roadmap.
> http://wiki.openchemistry.org/Avogadro_Roadmap
>
> The text came from some discussions that Marcus and I had previously, and was 
> hosted on GitHub, but no one actually edited it. :-)
>
> The roadmap will obviously be influenced by potential Summer of Code projects 
> (and progress) and some people contributing here at Pitt.
>
> Thoughts? Missing pieces? Better ways to host the list?
>
I think the wiki is fine for now, and it is good to get something up
in a generally accessible spot. I will be spending some time getting
the selection working, and have some basics working now.

My focus is going to be on carving out enough time to make progress on
missing features that prevent people from using Avogadro 2 over one,
but I am sure I will continue to be distracted by shiny things and
other work.

I tagged and released 0.9.0, I will put out a general announcement. It
was delayed a fair bit by packaging issues. Now that Qt 5.6.0 is out I
would like to get an updated release built against that, and hopefully
at least have selection working in it.

Best,

Marcus

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Re: [Avogadro-devel] Hello GSoC-2016

[Marcus D. Hanwell]

On Mon, Mar 14, 2016 at 10:01 AM, Reinis Danne  wrote:
> Two questions came up (Python binding project).
>
> 1. Is it ok to relay on C++11 compiler? A search showed that
> there was this discussion before and it was decided that it is ok
> to rely on the presence of C++11 compiler. But in the same time
> I saw some recent commits specifically removing reliance on C++11
> features (e.g., auto).

I think C++11 will be OK, when we removed them we hadn't decided to
make C++11 a hard requirement. I think we have good agreement now, but
I need to update the dependencies for Windows at least to build with a
more recent Visual Studio with C++11 support, several of the current
dependencies do not build.
>
> 2. Is tight integration with QML a strict requirement for the
> chosen solution? As far as I can see QML is not used in the
> current codebase. I'm interested in a solution which currently
> doesn't have QML support (might get added sometime later).
>
I don't think it is, personally I would rather see Python support over
QML, but see value in both. I think we are reasonably open to looking
at different proposals in this area.

Best,

Marcus

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Re: [Avogadro-devel] Hello GSoC-2016

[Marcus D. Hanwell]

On Mon, Mar 7, 2016 at 9:58 AM, Geoffrey Hutchison
 wrote:
>> I'm interested in the project "Python script bindings in Avogadro
>> 2". I see that there is already a boost-python branch for
>> avogadrolibs. Are you already settled on boost-python or are
>> other solutions still considered?
>
> Other solutions are definitely open. Indeed, that’s the key question for this 
> project. There are multiple technologies for scripting bindings in Qt apps, 
> but not all of them are ideal for Avogadro2 (PySide is not updated for Qt5, 
> SWIG, boost.python, and PyQt are also possible.)
>
To add a little more from my side, Qt-based solutions are great, and I
could see a good GSoC project developing them, but Avogadro 2's
libraries are more than just Qt now. I developed the Boost Python
based bindings to serve the needs of a web-based project, where we
needed to use Avogadro 2 API in a headless web server, so Qt, OpenGL,
X, etc were not available.

The requirements for server-based and desktop-based are quite
different, the core APIs can be used in more batch-oriented contexts,
whereas the desktop needs to align more closely with Qt's signal-slot
mechanism, etc.

Marcus

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Re: [Avogadro-devel] GitHub issue import test

[Marcus D. Hanwell]

On Sun, Apr 24, 2016 at 10:27 AM, Geoffrey Hutchison
 wrote:
> I started a test run of importing the Avogadro SourceForge bugs and feature 
> requests to GitHub issues:
> https://github.com/ghutchis/sfimporttest/issues
>
> * It's very difficult to script importing the milestone versions - but it 
> should be easy to make some batch changes (e.g., find the v_1_0 label and 
> assign a 1.0 milestone)
> * I think the "auto-migrated" and "source forge" labels are redundant. Which 
> one should I kill? (I'd keep the "auto-migrated" and kill the "source forge" 
> tag)

How many have contact details/any recent activity? So long as they
have a tag we can filter on I think either one works. Tougher job is
going through them and figuring out which are still relevant, and
whether is is possible to follow up with the reporters at all.

Thanks for working on this, what you have in the test looks good to
me. Not sure how much I would worry about historical milestones but if
it is easy it would be nice.

Best,

Marcus

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Re: [Avogadro-devel] Avo2 - no POVRay menu item?

[Marcus D. Hanwell]

On Thu, May 12, 2016 at 2:51 PM, Geoffrey Hutchison
 wrote:
> We're trying to port some of the VMRL export code to Avogadro 2 - so I 
> thought we should start with the POV-Ray export plugin: qtplugins/povray/
>
> But it doesn't appear in the interface, at least on Mac?! Any ideas?
>
I am at the airport, visiting somewhere all day tomorrow. I think I
got most of the basics working, but hadn't quite finished off the
POV-Ray exporter. I will see if I can take a look when I get to my
hotel room later and see where it was at, but I possibly didn't add
the menu item as it wasn't working properly for me (camera stuff
needed more work, possibly other stuff).

Marcus

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Re: [Avogadro-devel] Avogadro 2 release number simplification/jump

[Marcus D. Hanwell]

On Wed, May 11, 2016 at 3:49 PM, Michael Banck <mba...@debian.org> wrote:
> On Wed, May 11, 2016 at 03:43:19PM -0400, Marcus D. Hanwell wrote:
>> So I had one or two queries recently that made me realize I should
>> have done a better job on less ambiguous version numbering for
>> Avogadro 2 releases. I would like to make the next Avogadro 2 release
>> 1.90, and then after that 1.91, 1.92, 1.93, etc until we feel good
>> with sticking a 2.0 release out.
>
> What's the plan after 1.99?
>
> I assume it won't get to there, but it makes sense to plan for it.
> Calling it 1.100 wouldn't be a problem in my opinion, but if you don't
> like it now, maybe 1.90 isn't the best starting point.

I am fine with 1.100, but hope not to get there. I think it gives us a
good amount of space, I can start at 80 if people have feelings either
way. I am fine going up to 1.1000, but sincerely doubt we need that
many release numbers.

Marcus

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[Avogadro-devel] Avogadro 2 release number simplification/jump

[Marcus D. Hanwell]

Hi,

So I had one or two queries recently that made me realize I should
have done a better job on less ambiguous version numbering for
Avogadro 2 releases. I would like to make the next Avogadro 2 release
1.90, and then after that 1.91, 1.92, 1.93, etc until we feel good
with sticking a 2.0 release out.

This avoids repeating previous Avogadro release numbers, such as
0.8.0, 0.9.0, etc. It is also in line with several other projects that
use .90+ for releases before the next major version increment, and it
makes it clear that there are API changes in each release. Not much to
be done about previous releases.

I hope with our Google Summer of Code students, and general energy
around landing features we can get a few good releases out over the
summer. I would like to promote Avogadro 2 as a tool, and achieve
parity where features/polish are missing.

Thanks,

Marcus

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Re: [Avogadro-devel] "Active" Molecules Emit Interface Updates?

[Marcus D. Hanwell]

On Thu, May 5, 2016 at 2:13 PM, Barry Moore  wrote:
> All,
>
> I have been thinking about upgrades to the surfaces interface in Avogadro 2,
> but it brought me back to the "Molecules" widget (bottom left). Currently,
> it doesn't really do much but I think this would be a great interface to
> beef up. For example, it would be helpful if one could click a molecule to
> make it "active" then emit a signal for all other interfaces which are
> Molecule centric. Nearly all of the interfaces are linked to the current
> molecule and this would make it a lot easier to design interfaces. What do
> you guys think? Worth spending time on?
>
> In the future, one could open up multiple molecules and look at multiple
> properties, cubes, etc. all at the same time.
>
This is the design I was working towards there, and agree beefing it
up to make plugins more aware of active molecule changes would be
good. We should also let tools be aware of multiple molecules, and
look at what is needed to support that. I need to read through some of
what is there to remember how far I got with some of that.

Marcus

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Re: [Avogadro-devel] Extending Avo2 "Input Generators" to "Modify" scripts

[Marcus D. Hanwell]

On Tue, Aug 2, 2016 at 5:52 PM, Geoffrey Hutchison
 wrote:
> I’ve been talking with Paul Boone, an experienced Python programmer on staff
> here at Pitt (and soon to be PhD student) about the Python interface to
> Avo2.
>
> Short message - we think it's easy to add script support for a *lot* of use
> cases without much work.
> - Scripts could pop up an options dialog, receive a cjson molecule, and pass
> back a new cjson and optionally some messages.
>
> Consider the case of a script (Python or not) that modifies the molecule
> somehow. Maybe it scales the bonds. Maybe it generates a crystal structure…
> That script probably wants an options dialog in Avogadro and then a “run”
> script that passes back the modified molecule in cjson format. Avogadro adds
> an undo/redo between the two structures.
>
> The beauty is that it's really easy to write this kind of script, either for
> personal use, or to distribute and it's powerful. Imagine a "stack" script
> that replicates the molecule X times along the x/y/z axis after translating
> by Y Angstroms.
>
Sounds good.
>
> Much of the code we want is already there in the input generators - building
> the dialog GUI.
> - Except the input generators currently don’t allow floating point #s
> - They don’t (always) receive the current molecule when asked to create the
> input dialog JSON
> - They don’t have any sort of language / localization
> - They don't allow multiple tabs/panels
>
> My suggestion here is to refactor the InputDialog class to OptionsDialog
> - Allow floating point numbers (with constraints on precision and range)
> - Add a --language=en flag to the script to load different JSON depending on
> the user's default language
> - Always pass the molecule as CJSON (and drop the CML version) - allowing
> the dialog to change based on the molecule

I think for big molecules there is value in not passing the molecule
when the script won't do anything, but this seems like a simple flag
in the JSON to specify whether the molecule is desired or not.

>   .. for example maybe showing a different interface if a unit cell is
> present, or filtering basis sets based on atoms
> - Add a syntax for multiple panels, e.g.
> "Basic" : [ .. ],
> "Advanced": [ .. ]
>
> I'd also suggest that to better support an "installer" feature, that we
> change the scripts to live in separate directories:

What would the installer feature do? It isn't clear what install
means, but the package.json, and run.py etc seem to make sense.
>
> gaussian/
>  .. run
>  .. install
>  .. package.json
> qchem/
>  .. run
>  .. install
>  .. package.json
>
> This means that while we'd encourage Python, in principal, users could write
> their plugin scripts in *any* language as long as it meets the minimal API
> (i.e., pass back JSON for the dialog).
>
This feature was designed from the start to support any language, but
we never went beyond Python. The input/output is language agnostic,
but there is value in knowing that this package is Python, and that we
can use the Python interpreter path to run it. On Windows I don't
think the executable Python stuff works at all for example, but a
binary would of course work without issue.

I think it totally makes sense to pull the JSON stuff into a separate
file, most of what we wrote so far has no use for an install script as
far as I can tell, but maybe I am missing something. I think using
file endings/embedding in the JSON file the type of script would help
us use the appropriate interpreter when needed.

To make it easier to implement I wonder if we want to explore adding
this more dynamic scripting interface as a new feature, then port the
input generators if it looks general enough for them too, and allowing
us to merge an earlier version that perhaps doesn't have everything
working. There are also the file format scripts, that could be in any
language too but are currently hardwired for Python.

Slicer has some work that has gone in this direction, see the command
line modules, 
https://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/Modules
for some brief details. For the Tomviz project we have Python modules
that are currently hardwired in the application, and we are looking at
a very similar setup where these are all designed to operate on a cube
using Python, SciPy, NumPy, ITK, VTK etc. They are loaded into the
application's interpreter in the same memory space in the Tomviz case
though, whereas Slicer has executed command line interfaces.

I think this would be great, and I was hoping to find time to move our
Python stuff over to this style of layout to make installation/sharing
easier. We should also add support for running from home directory as
well as the system paths where the application gets installed.

Marcus

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