First Avogadro 2 beta release

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

Hi Marcus,

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.

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.

Best wishes,

Jens

Bugs:

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: “”

On 11 April 2013 19:54, Marcus D. Hanwell mhanwell@gmail.comwrote:

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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Hi Jens,

On Fri, Apr 12, 2013 at 5:00 AM, Jens linucks42@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.

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 :wink: ). I’ve filed a
bug for this here:

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

Thanks for the feedback!

Dave

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

Hi Jens,

On Fri, Apr 12, 2013 at 5:00 AM, Jens linucks42@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 :wink: ). 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

Hi Dave and Marcus,

No problem - like I said it’s great to see Avogadro2 getting underway and
I’m glad to be able to help.

The molecule I looked at earlier was just under 9000 atoms. Avogadro 1
crashes on reading it unless I import the molecule and turn off the bond
order perceiving functionality, and there is a noticeable lag when I rotate
the molecule. With Avogadro2, it whizzes round instantly.

Keep up the great work!

Jens

PS - having said that I just tried loading a pdb of a protein I’m working
on (3HAP) and I just get a big yellow blob, so there may still be the odd
niggle to iron out… :wink: I’ll file a bug report as soon as my account on
the tracker is activated.

On 12 April 2013 15:35, Marcus D. Hanwell mhanwell@gmail.comwrote:

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

Hi Jens,

On Fri, Apr 12, 2013 at 5:00 AM, Jens linucks42@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 :wink: ). 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