SF.net SVN: avogadro: branches/primitive/libavogadro/src/tools

On Nov 8, 2008, at 12:05 PM, timvdm@users.sourceforge.net wrote:

Add the AutoOpt tool again (works, but converting from/to OBMol
every update is not efficient)

Shouldn’t we just be copying coordinate updates unless the molecule
has really changed?

-Geoff

On Sat, Nov 8, 2008 at 6:09 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

On Nov 8, 2008, at 12:05 PM, timvdm@users.sourceforge.net wrote:

Add the AutoOpt tool again (works, but converting from/to OBMol
every update is not efficient)

Shouldn’t we just be copying coordinate updates unless the molecule
has really changed?

Yes, but this requires an additional function in OB. Didn’t want to
break anything at the moment.

-Geoff


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Yes, but this requires an additional function in OB. Didn’t want to
break anything at the moment.

There’s OBMol::GetCoordinates and OBMol::SetCoordinates(), plus
OBMol::GetConformers() and OBMol::SetConformers()

Shouldn’t those be enough?

Cheers,
-Geoff

On Saturday 08 November 2008 12:11:48 Tim Vandermeersch wrote:

On Sat, Nov 8, 2008 at 6:09 PM, Geoffrey Hutchison

geoff.hutchison@gmail.com wrote:

On Nov 8, 2008, at 12:05 PM, timvdm@users.sourceforge.net wrote:

Add the AutoOpt tool again (works, but converting from/to OBMol
every update is not efficient)

Shouldn’t we just be copying coordinate updates unless the molecule
has really changed?

Yes, but this requires an additional function in OB. Didn’t want to
break anything at the moment.

Tim and I talked on IRC last night. I am working on a scheme to reliably cache
the OBMol locally and this should cut overhead on many operations hopefully.
That is why I have the (currently unused) OBMol cached in the Molecule object.

I think we are getting close to having all of the original functionality back
in Avogadro, need to add some locking to add thread safety and then I hope to
merge these changes into trunk.

On Sat, Nov 8, 2008 at 6:17 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

Yes, but this requires an additional function in OB. Didn’t want to
break anything at the moment.

There’s OBMol::GetCoordinates and OBMol::SetCoordinates(), plus
OBMol::GetConformers() and OBMol::SetConformers()

Shouldn’t those be enough?

All these functions take an OBMol as parameter, they don’t directly
give you access to the coordinates.

bool GetCoordinates(OBMol &mol);

Cheers,
-Geoff