Stereoisomers

Development
1

Hi all,

could you come up with a way to generate mirror image of the structure in
Avogadro? I am talking about stereoisomers common in chirality so I would need
to generate stereoisomer from a given struture. You could just invert everything
according to a plane right or left of the molecule. That is:

CH3OCH2CH2 | H2CH2COH3C

thanks

Jonas

2

28.10.2010, 05:33, “Jonas Baltrusaitis” jasius_1@yahoo.com:

Hi all,

could you come up with a way to generate mirror image of the structure in
Avogadro? I am talking about stereoisomers common in chirality so I would need
to generate stereoisomer from a given struture. You could just invert everything
according to a plane right or left of the molecule. That is:

CH3OCH2CH2 | H2CH2COH3C

Inversion is available in trunk (Build->Invert Chirality)

–
Regards,
Konstantin

3

BY the same token, could anybody build Windows executable in trunk since Linux
version is already there? I bet majority use windows version, me including

Jonas

----- Original Message ----
From: Konstantin Tokarev annulen@yandex.ru
To: Jonas Baltrusaitis jasius_1@yahoo.com
Cc: avogadro-devel@lists.sourceforge.net
Sent: Thu, October 28, 2010 2:07:00 AM
Subject: Re: [Avogadro-devel] stereoisomers

28.10.2010, 05:33, “Jonas Baltrusaitis” jasius_1@yahoo.com:

Hi all,

could you come up with a way to generate mirror image of the structure in
Avogadro? I am talking about stereoisomers common in chirality so I would need
to generate stereoisomer from a given struture. You could just invert
everything
according to a plane right or left of the molecule. That is:

CH3OCH2CH2 | H2CH2COH3C

Inversion is available in trunk (Build->Invert Chirality)

–
Regards,
Konstantin

4

28.10.2010, 16:25, “Jonas Baltrusaitis” jasius_1@yahoo.com:

BY the same token, could anybody build Windows executable in trunk since Linux
version is already there? I bet majority use windows version, me including

Hi David,
Could you upload your Windows build of trunk? IIRC you’ve made it not so long ago

P.S. You also could try
http://review.avogadro.openmolecules.net:8080/#change,194
it should fix gl2ps issue on Windows

–
Regards,
Konstantin

5

On Thu, Oct 28, 2010 at 9:10 AM, Konstantin Tokarev annulen@yandex.ru wrote:

28.10.2010, 16:25, “Jonas Baltrusaitis” jasius_1@yahoo.com:

BY the same token, could anybody build Windows executable in trunk since Linux
version is already there? I bet majority use windows version, me including

Hi David,
Could you upload your Windows build of trunk? IIRC you’ve made it not so long ago

P.S. You also could try
http://review.avogadro.openmolecules.net:8080/#change,194
it should fix gl2ps issue on Windows

I’ve been meaning to check that, but things are very busy around here.
My latest build for windows does not include the chirality fix, but
I’ll try to build a new one in the next week or so.

Dave

6

On Oct 28, 2010, at 12:29 PM, David Lonie wrote:

On Thu, Oct 28, 2010 at 9:10 AM, Konstantin Tokarev annulen@yandex.ru wrote:

28.10.2010, 16:25, “Jonas Baltrusaitis” jasius_1@yahoo.com:

BY the same token, could anybody build Windows executable in trunk since Linux
version is already there? I bet majority use windows version, me including

Hi David,
Could you upload your Windows build of trunk? IIRC you’ve made it not so long ago

P.S. You also could try
http://review.avogadro.openmolecules.net:8080/#change,194
it should fix gl2ps issue on Windows

I’ve been meaning to check that, but things are very busy around here.
My latest build for windows does not include the chirality fix, but
I’ll try to build a new one in the next week or so.

That would be great - I am hoping to get some Windows dashboards (among others) going again. I have a machine I have been meaning to get up and running for a while. We should get things fixed up and building now that Open Babel has made a release. It would be great to get a 1.1.0 out once we have fixed a few things up. Snapshots in the short term would work.

Marcus

7

On Thu, Oct 28, 2010 at 8:43 PM, Marcus Hanwell
mhanwell@gmail.com wrote:

On Oct 28, 2010, at 12:29 PM, David Lonie wrote:

On Thu, Oct 28, 2010 at 9:10 AM, Konstantin Tokarev annulen@yandex.ru wrote:

28.10.2010, 16:25, “Jonas Baltrusaitis” jasius_1@yahoo.com:

BY the same token, could anybody build Windows executable in trunk since Linux
version is already there? I bet majority use windows version, me including

Hi David,
Could you upload your Windows build of trunk? IIRC you’ve made it not so long ago

P.S. You also could try
http://review.avogadro.openmolecules.net:8080/#change,194
it should fix gl2ps issue on Windows

I’ve been meaning to check that, but things are very busy around here.
My latest build for windows does not include the chirality fix, but
I’ll try to build a new one in the next week or so.

That would be great - I am hoping to get some Windows dashboards (among others) going again. I have a machine I have been meaning to get up and running for a while. We should get things fixed up and building now that Open Babel has made a release. It would be great to get a 1.1.0 out once we have fixed a few things up. Snapshots in the short term would work.

If you have any scripts or know of a way to get automated builds going
on windows, I wouldn’t mind doing nightly builds for upload to
openmolecules.net along with CDash submissions. I have a workstation
that’s pretty much devoted to running a windows VM that would be
perfect for this.

Dave

8

On Oct 28, 2010, at 8:46 PM, David Lonie wrote:

On Thu, Oct 28, 2010 at 8:43 PM, Marcus Hanwell
mhanwell@gmail.com wrote:

On Oct 28, 2010, at 12:29 PM, David Lonie wrote:

On Thu, Oct 28, 2010 at 9:10 AM, Konstantin Tokarev annulen@yandex.ru wrote:

28.10.2010, 16:25, “Jonas Baltrusaitis” jasius_1@yahoo.com:

BY the same token, could anybody build Windows executable in trunk since Linux
version is already there? I bet majority use windows version, me including

Hi David,
Could you upload your Windows build of trunk? IIRC you’ve made it not so long ago

P.S. You also could try
http://review.avogadro.openmolecules.net:8080/#change,194
it should fix gl2ps issue on Windows

I’ve been meaning to check that, but things are very busy around here.
My latest build for windows does not include the chirality fix, but
I’ll try to build a new one in the next week or so.

That would be great - I am hoping to get some Windows dashboards (among others) going again. I have a machine I have been meaning to get up and running for a while. We should get things fixed up and building now that Open Babel has made a release. It would be great to get a 1.1.0 out once we have fixed a few things up. Snapshots in the short term would work.

If you have any scripts or know of a way to get automated builds going
on windows, I wouldn’t mind doing nightly builds for upload to
openmolecules.net along with CDash submissions. I have a workstation
that’s pretty much devoted to running a windows VM that would be
perfect for this.

The one in Geoff’s lab was doing that, but stopped submitting a while back. I will try to sit down and get this done soon, and share the scripts. We are also working on a very cool CDash@Home project, where people can donate systems to run tests. Another exciting project is integration of Gerrit submissions into a Gerrit continuous approach, using some of the work done for CDash@Home.

I blogged about Gerrit, and its increasing use at Kitware too. There are some wiki pages I have worked on for some of our own projects I intend to adapt for easier guides for Avogadro development, along with useful git aliases. I have been crazy busy recently, no rest since I got back from England but lots of exciting projects - even one involving some funded Avogadro development I will talk about more soon.

http://www.kitware.com/blog/home/post/70

I will get moving on this, and get some Windows dashboards up and running.

Marcus

9

On Thu, Oct 28, 2010 at 9:10 AM, Konstantin Tokarev annulen@yandex.ru wrote:

28.10.2010, 16:25, “Jonas Baltrusaitis” jasius_1@yahoo.com:

BY the same token, could anybody build Windows executable in trunk since Linux
version is already there? I bet majority use windows version, me including

Hi David,
Could you upload your Windows build of trunk? IIRC you’ve made it not so long ago

I uploaded an installer this morning, see the unstable windows section
on http://avogadro.openmolecules.net/wiki/Get_Avogadro

It does not have the gl2ps fixes in it yet. The reviewboard is down at
the moment, but I will test those ASAP.

Dave