I’m interested in this feature because I have to draw a lot molecules like
and Avogadro is the only program I know that provides a calculation of the correct bond length and
coordination (vie the menu Extensions->Optimize geometry).
In the Wikipedia I often find there both versions, 3D and 2D:
So I gues that the 2D version is made out out of the 3D version - and that is exactly what I need.
Avogadro doesn’t do that short of “Chemical 2D” drawing.
the statmenent: “2D cleanup code improvements for 2D molecule files.”
This is for importing 2D chemical files into Avogadro (and creating a
rough 3D structure).
In the Wikipedia I often find there both versions, 3D and 2D: Tetraethyl orthosilicate - Wikipedia
So I gues that the 2D version is made out out of the 3D version -
and that is exactly what I need.
Actually, it’s probably the reverse – many people create the 2D
version, import into a program like Avogadro, optimize the geometry,
and then output the 3D graphic.
If you’d like suggestions on 2D drawing programs:
BKChem
SketchEl
MolSketch
On the proprietary side:
ChemSketch
ChemDraw
We can import 2D files from any of these programs.
-Geoff
Actually, it’s probably the reverse – many people create the 2D
version, import into a program like Avogadro, optimize the geometry, and
then output the 3D graphic.
The problem is that non of the 2D drawing programs is able to check that the bonds have the right
length and angle. So it is often a long fiddling to get the molecules drawn as wanted and even then
the drawing is often physical incorrect. Avogadro is the only program I know that is able to
calculate the force fields to have correct bonds.
So in my opinion it would be a nice feature when one could create a molecule in Avogadro with the
calculated correct bonds and Avogadro is able to draw/export an adequate 2D image from this.
The problem is that non of the 2D drawing programs is able to check
that the bonds have the right length and angle. So it is often a
long fiddling to get the molecules drawn as wanted and even then the
drawing is often physical incorrect. Avogadro is the only program I
know that is able to calculate the force fields to have correct bonds.
Well, 2D diagrams are stylized, but I’m sad to hear that none of the
open 2D programs have a “clean-up” feature. The proprietary ones do.
Do you already have SMILES for the compounds? If so, you could
probably use BKChem or another code to do 2D structure generation.
So in my opinion it would be a nice feature when one could create a
molecule in Avogadro with the calculated correct bonds and Avogadro
is able to draw/export an adequate 2D image from this.
It’s something we’ve considered, but so far no one has stepped forward
to do it.
just found the following: OASA
This seems to have some of the features requested …
Bye
Simon
Am Samstag, den 30.05.2009, 10:16 -0400 schrieb Geoffrey Hutchison:
On May 30, 2009, at 10:06 AM, Uwe Stöhr wrote:
The problem is that non of the 2D drawing programs is able to check
that the bonds have the right length and angle. So it is often a
long fiddling to get the molecules drawn as wanted and even then the
drawing is often physical incorrect. Avogadro is the only program I
know that is able to calculate the force fields to have correct bonds.
Well, 2D diagrams are stylized, but I’m sad to hear that none of the
open 2D programs have a “clean-up” feature. The proprietary ones do.
Do you already have SMILES for the compounds? If so, you could
probably use BKChem or another code to do 2D structure generation.
So in my opinion it would be a nice feature when one could create a
molecule in Avogadro with the calculated correct bonds and Avogadro
is able to draw/export an adequate 2D image from this.
It’s something we’ve considered, but so far no one has stepped forward
to do it.
Cheers,
-Geoff
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