Builder

Hi,

I Added widgets to the drawtool to generate structures from smiles.
Howerver, I have no idea how to get access to the molecule from within
my function. Cuold someone give me some pointers?

MMFF94 shuold now be usable in avogadro. Validation is going good.
Some molecule total energies are still off by 1-4kcal/mol, but these
are exeptions. For “simple” molecules the error is something like
0.005kcal/mol or less. Could MMFF94 and UFF also be added to the
AutoOpt tool?

Is there any need for functions to export info about atom types,
forcefield parameters, etc. from the forcefield code? Or is the info
written to the “Messages” log enough?

Thanks,
Tim

0.005kcal/mol or less. Could MMFF94 and UFF also be added to the
AutoOpt tool?

What we really need to do is to rewrite the forcefieldextension and
the autoopttool code to use OBPlugin and grab the list of currently
installed force fields.

On the downside, this can’t be translated. (But I’m not sure force
fields should be translated, so this may not matter much.)

On the upside, it means that Avogadro will again benefit from any
improvements to Open Babel automatically. For example, if someone adds
a CHARMM or AMBER protein force field.

Is there any need for functions to export info about atom types,
forcefield parameters, etc. from the forcefield code? Or is the info
written to the “Messages” log enough?

I think for now the “messages” log is pretty good.

Cheers,
-Geoff

I’m not sure what you’re doing with the smiles thing but most likely you
need to implement this as an extension and not a tool. Tools are for
mouse inputs like, if you wanted to be able to click to insert a smiles
molecule that’d be the way to do it.

Thus, for the build tool, it gets passed the molecule when a mouse click
happens.

On the other hand, extensions appear as menu items and then are passed
the molecule as a function.

So, I do think this functionality is better suited for an extension as
opposed to a Tool.


Donald

(Thu, Nov 29, 2007 at 07:39:27PM +0100) Tim Vandermeersch tim.vandermeersch@gmail.com:

Hi,

I Added widgets to the drawtool to generate structures from smiles.
Howerver, I have no idea how to get access to the molecule from within
my function. Cuold someone give me some pointers?

MMFF94 shuold now be usable in avogadro. Validation is going good.
Some molecule total energies are still off by 1-4kcal/mol, but these
are exeptions. For “simple” molecules the error is something like
0.005kcal/mol or less. Could MMFF94 and UFF also be added to the
AutoOpt tool?

Is there any need for functions to export info about atom types,
forcefield parameters, etc. from the forcefield code? Or is the info
written to the “Messages” log enough?

Thanks,
Tim


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need to implement this as an extension and not a tool. Tools are for
mouse inputs like, if you wanted to be able to click to insert a
smiles
molecule that’d be the way to do it.

I’ve always thought of this as a tool – click at a point and you
insert a fragment. It’s simply a faster way than drawing everything. :slight_smile:

That said, there may be some need for extensions with similar
functionality. Look at AutoOpt tool vs. the force field extension.

Cheers,
-Geoff

On Nov 29, 2007 9:35 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

need to implement this as an extension and not a tool. Tools are for
mouse inputs like, if you wanted to be able to click to insert a
smiles
molecule that’d be the way to do it.

I’ve always thought of this as a tool – click at a point and you
insert a fragment. It’s simply a faster way than drawing everything. :slight_smile:

That said, there may be some need for extensions with similar
functionality. Look at AutoOpt tool vs. the force field extension.

We could do something similar for the builder tool. WE can also add it
as an extention where it will clear (ask to save first…) the current
molecule, and generate the new one. For the the peptide builder, an
extention is probably the best.

Cheers,
-Geoff