Adding fragments to your molecule in avogadro

On Nov 9, 2007, at 4:01 PM, Tim Vandermeersch wrote:

When using the tool, first you would have to select the ring fragment
you want to add. Then I was thinking of showing a new 3D window with
the fragment rendered, in that window you could then select which atom
(=atom index ib for the smarts pattern) to connect the fragment with.

I had a similar thought recently.

My current thought was for a modification to the draw tool. You’d pick
a fragment, then click somewhere and insert it. You’d then draw a bond
to connect with the rest of the structure.

As I mentioned to cryos this afternoon, I thought we could start with
a simple window – just a scrolling list of file names and molecule
titles. Then the window would have a button at the bottom for opening
up a new file (and adding it to the list). This might be best done as
a directory list – so you’d point this at a directory with subdirs of
rings, amino acids, etc.

You mentioned the last bit – adding a GLWidget to the top of the
window that lets you see a preview of the fragment. I think that can
be left off for a bit. It’s the right “polish,” and shouldn’t be too
hard to do.

Cheers,
-Geoff

On Nov 10, 2007 12:05 AM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

On Nov 9, 2007, at 4:01 PM, Tim Vandermeersch wrote:

When using the tool, first you would have to select the ring fragment
you want to add. Then I was thinking of showing a new 3D window with
the fragment rendered, in that window you could then select which atom
(=atom index ib for the smarts pattern) to connect the fragment with.

I had a similar thought recently.

My current thought was for a modification to the draw tool. You’d pick
a fragment, then click somewhere and insert it. You’d then draw a bond
to connect with the rest of the structure.

Yes, but that way the fragment would be placed “random”. After you do
a minimisation, the result would be the same. But I wanted to make it
so that the fragment would be placed at the correct position and
orientation if you clicked an atom to attatch it to.

As I mentioned to cryos this afternoon, I thought we could start with
a simple window – just a scrolling list of file names and molecule
titles. Then the window would have a button at the bottom for opening
up a new file (and adding it to the list). This might be best done as
a directory list – so you’d point this at a directory with subdirs of
rings, amino acids, etc.

You mentioned the last bit – adding a GLWidget to the top of the
window that lets you see a preview of the fragment. I think that can
be left off for a bit. It’s the right “polish,” and shouldn’t be too
hard to do.

Cheers,
-Geoff

On Nov 9, 2007, at 6:10 PM, Tim Vandermeersch wrote:

Yes, but that way the fragment would be placed “random”. After you do
a minimisation, the result would be the same. But I wanted to make it
so that the fragment would be placed at the correct position and
orientation if you clicked an atom to attatch it to.

Yes. What you describe is actually how Spartan does it. Click on atoms
or connection points.

I wouldn’t say my way is “random” placement – it’d go in the way it
looks in the preview. And you could perhaps directly switch to the
manipulate tool to rotate, etc.

But your way is definitely more precise for most people.

Cheers,
-Geoff