Fragment Library

I just added a fragment library window. There are a few things left to
do, mainly because I haven’t handled some of these issues in Qt yet.
First the good news:

Here’s what works right now:

  1. You can add a set of directories with fragments. Clicking on a
    filename will allow you to insert that into the window.
  2. You can type a SMILES and insert that.
  3. We have a directory model which allows us to display whatever
    information we want to the user and can handle multiple directory
    paths (e.g., /home/.avogadro/molecules:/usr/share/avogadro/molecules
    etc.)
  4. Paths and SMILES are saved to the settings.

Now the bits that need work:

  1. I need to make sure the tree view properly updates when you add new
    directories. Right now, it appears to just crash.
    (Help would be appreciated.)

  2. I need to handle changes of focus in the window. What I want to
    happen is this:

  • if the user clicks on the tree view (i.e., it receives focus), the
    dialog should get a signal to turn off “insert mode.”
  • similarly, if the user clicks on the SMILES entry, the dialog
    should turn off "insert mode."
    I can clear focus from these widgets, but I don’t see how to get
    notified when they receive focus.
    (If anyone knows how to do this, pointers would be appreciated.)

We also need to install some fragments in a nice directory structure.
I think the Blue Obelisk chemical-structures project has a nice
selection, but I also think we need to prune to a nice subset. IMHO,
most people will want key, important fragments (e.g., not every carbon
for an alkane chain.)

Any ideas on where these fragments should be installed on Windows and
Linux? I’m guessing for UNIX-like systems, it should go into $(prefix)/
share/avogadro/molecules/*

Thoughts?
-Geoff

I think that $(prefix)/share/avogadro/templates/* would be a clearer name

I just added a fragment library window. There are a few things left to
do, mainly because I haven’t handled some of these issues in Qt yet.
First the good news:

Here’s what works right now:

  1. You can add a set of directories with fragments. Clicking on a
    filename will allow you to insert that into the window.
  2. You can type a SMILES and insert that.
  3. We have a directory model which allows us to display whatever
    information we want to the user and can handle multiple directory
    paths (e.g., /home/.avogadro/molecules:/usr/share/avogadro/molecules
    etc.)
  4. Paths and SMILES are saved to the settings.

Now the bits that need work:

  1. I need to make sure the tree view properly updates when you add new
    directories. Right now, it appears to just crash.
    (Help would be appreciated.)

  2. I need to handle changes of focus in the window. What I want to
    happen is this:

  • if the user clicks on the tree view (i.e., it receives focus), the
    dialog should get a signal to turn off “insert mode.”
  • similarly, if the user clicks on the SMILES entry, the dialog
    should turn off "insert mode."
    I can clear focus from these widgets, but I don’t see how to get
    notified when they receive focus.
    (If anyone knows how to do this, pointers would be appreciated.)

We also need to install some fragments in a nice directory structure.
I think the Blue Obelisk chemical-structures project has a nice
selection, but I also think we need to prune to a nice subset. IMHO,
most people will want key, important fragments (e.g., not every carbon
for an alkane chain.)

Any ideas on where these fragments should be installed on Windows and
Linux? I’m guessing for UNIX-like systems, it should go into $(prefix)/
share/avogadro/molecules/*

Thoughts?
-Geoff


This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
Don’t miss this year’s exciting event. There’s still time to save $100.
Use priority code J8TL2D2.
http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/java
one _______________________________________________
Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


Dr. Armando Navarro-Vázquez
Departamento de Química Orgánica
Phone:34981563100 ext 16231
Universidade de Santiago de Compostela
http://galileo.usc.es/~armando

On Fri, Apr 18, 2008 at 12:43 PM, Armando Navarro Vázquez qoajnv@usc.es wrote:

I think that $(prefix)/share/avogadro/templates/* would be a clearer name

I just added a fragment library window. There are a few things left to
do, mainly because I haven’t handled some of these issues in Qt yet.
First the good news:

Here’s what works right now:

  1. You can add a set of directories with fragments. Clicking on a
    filename will allow you to insert that into the window.
  2. You can type a SMILES and insert that.
  3. We have a directory model which allows us to display whatever
    information we want to the user and can handle multiple directory
    paths (e.g., /home/.avogadro/molecules:/usr/share/avogadro/molecules
    etc.)
  4. Paths and SMILES are saved to the settings.

Now the bits that need work:

  1. I need to make sure the tree view properly updates when you add new
    directories. Right now, it appears to just crash.
    (Help would be appreciated.)

  2. I need to handle changes of focus in the window. What I want to
    happen is this:

  • if the user clicks on the tree view (i.e., it receives focus), the
    dialog should get a signal to turn off “insert mode.”
  • similarly, if the user clicks on the SMILES entry, the dialog
    should turn off "insert mode."
    I can clear focus from these widgets, but I don’t see how to get
    notified when they receive focus.
    (If anyone knows how to do this, pointers would be appreciated.)

It’s in SVN now, I also disabled the directoryTreeView and the
smilesLineEdit while in inserting mode, this way you have to press
stop first before selecting another molecule or changing your smiles.

Tim

We also need to install some fragments in a nice directory structure.
I think the Blue Obelisk chemical-structures project has a nice
selection, but I also think we need to prune to a nice subset. IMHO,
most people will want key, important fragments (e.g., not every carbon
for an alkane chain.)

Any ideas on where these fragments should be installed on Windows and
Linux? I’m guessing for UNIX-like systems, it should go into $(prefix)/
share/avogadro/molecules/*

Thoughts?
-Geoff


This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
Don’t miss this year’s exciting event. There’s still time to save $100.
Use priority code J8TL2D2.
http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/java
one _______________________________________________
Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


Dr. Armando Navarro-Vázquez
Departamento de Química Orgánica
Phone:34981563100 ext 16231
Universidade de Santiago de Compostela
http://galileo.usc.es/~armando


This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
Don’t miss this year’s exciting event. There’s still time to save $100.
Use priority code J8TL2D2.
http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel