SF.net SVN: avogadro: trunk/avogadro/src/extensions/propmodel.cpp

Development
1

On Dec 8, 2007, at 4:09 AM, benoitjacob@users.sourceforge.net wrote:

compilation fix. I hope someone knowing OB well can check I got it
right.

No. It is, perhaps the problem with using the bleeding edge of OB
development. Tim added that yesterday. I’ll go revert your change.

The benefit of using the absolute trunk of OB SVN is that we’re
finding bugs and little problems in the OB code and can fix them
immediately. Fortunately, I think OB development should settle down a
bit soon.

-Geoff

2

On Dec 8, 2007 2:14 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

On Dec 8, 2007, at 4:09 AM, benoitjacob@users.sourceforge.net wrote:

compilation fix. I hope someone knowing OB well can check I got it
right.

No. It is, perhaps the problem with using the bleeding edge of OB
development. Tim added that yesterday. I’ll go revert your change.

The benefit of using the absolute trunk of OB SVN is that we’re
finding bugs and little problems in the OB code and can fix them
immediately. Fortunately, I think OB development should settle down a
bit soon.

This is true, OB really benefits from the simultanious development
with avogadro. When you make the user interface at the same time you
make the API, the API will be easier to use, otherwise you always have
small problems you didn’t think of. Later today, I will probably do an
initial commit of the new OBDock class. After this I will try to
minimize additional featurs and get back to updating documentation,
writing user docs when have decided on the format, MMMFF94 validation,
fixing restraints, …

would it be possible to add an extra level to the menu, I would like
to have the following menu:
Extentions

Docking

Create ligand…
Create binding pocket…
Select

Select ligand
Select binding pocket
Select ligand + pocket
Dock…
View poses…

I also want to merge the OBBuilder::GetNewBondVector with the
OBAtom::GetNewBondVector in the near future. Don’t know if you have
noticed, but if you insert smiles “CCCCCCC” the torsion angles for the
hydrogen, are not correct. (this is from OBAtom::GetBondVector, from
OBMol::AddHydrogens()). Merging the two should fix this. But this
doesn’t change anything.

Is there a

3

Ugh, sorry about that, then. I should have guessed that my one-day-old
checkout of OB was too old :stuck_out_tongue:

Benoit

On Saturday 08 December 2007 14:14:40 Geoffrey Hutchison wrote:

On Dec 8, 2007, at 4:09 AM, benoitjacob@users.sourceforge.net wrote:

compilation fix. I hope someone knowing OB well can check I got it
right.

No. It is, perhaps the problem with using the bleeding edge of OB
development. Tim added that yesterday. I’ll go revert your change.

The benefit of using the absolute trunk of OB SVN is that we’re
finding bugs and little problems in the OB code and can fix them
immediately. Fortunately, I think OB development should settle down a
bit soon.

-Geoff

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4

OK, you are perfectly right. I just thought I was fixing a simple mistake
preventing compilation. It’s 100% true that it’s good to develop OB+Avo
simultaneously.

Benoit

On Saturday 08 December 2007 15:07:55 Tim Vandermeersch wrote:

On Dec 8, 2007 2:14 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

On Dec 8, 2007, at 4:09 AM, benoitjacob@users.sourceforge.net wrote:

compilation fix. I hope someone knowing OB well can check I got it
right.

No. It is, perhaps the problem with using the bleeding edge of OB
development. Tim added that yesterday. I’ll go revert your change.

The benefit of using the absolute trunk of OB SVN is that we’re
finding bugs and little problems in the OB code and can fix them
immediately. Fortunately, I think OB development should settle down a
bit soon.

This is true, OB really benefits from the simultanious development
with avogadro. When you make the user interface at the same time you
make the API, the API will be easier to use, otherwise you always have
small problems you didn’t think of. Later today, I will probably do an
initial commit of the new OBDock class. After this I will try to
minimize additional featurs and get back to updating documentation,
writing user docs when have decided on the format, MMMFF94 validation,
fixing restraints, …

would it be possible to add an extra level to the menu, I would like
to have the following menu:
Extentions

Docking

Create ligand…
Create binding pocket…
Select

Select ligand
Select binding pocket
Select ligand + pocket

Dock…
View poses…

I also want to merge the OBBuilder::GetNewBondVector with the
OBAtom::GetNewBondVector in the near future. Don’t know if you have
noticed, but if you insert smiles “CCCCCCC” the torsion angles for the
hydrogen, are not correct. (this is from OBAtom::GetBondVector, from
OBMol::AddHydrogens()). Merging the two should fix this. But this
doesn’t change anything.

Is there a

SF.Net email is sponsored by:
Check out the new SourceForge.net Marketplace.
It’s the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
avogadro-devel List Signup and Options