Strigisupport in Avo

Moin folks

I thought I might try a pet project: Strigisupport [1] in Avogadro. Strigi has
an exellent support for chemical filetypes [2]. The idea is to connect to to
the strigidaemon via DBus. I would create a GUI which would allow something
like this search:

“Return all molecules on my harddisc which have at least two Carbon atoms and
an atomic weight between 45 and 78units.”

The returned list would be shown in a QTableWidget, the user selects the
molecule clicks ok and Avo displays the molecule.

a) What do you think about this?

b) Is that an “Extension”? Or what would it be, technically?

Carsten

[1] http://www.vandenoever.info/software/strigi/
[2] http://neksa.blogspot.com/2007/08/strigi-chemical-gsoc-final-timeline.html

On Sep 20, 2007, at 1:10 PM, Carsten Niehaus wrote:

“Return all molecules on my harddisc which have at least two Carbon
atoms and
an atomic weight between 45 and 78units.”

The returned list would be shown in a QTableWidget, the user
selects the
molecule clicks ok and Avo displays the molecule.

(a) This is an awesome idea! If you do this, I’ll have to hack
together a Mac version which uses ChemSpotlight. :slight_smile:

(b) Yes, this should be an extension – it’s a GUI-only plugin, and
something that requires strigi, so not all platforms will have it (yet).

This also brings up the question of files with multiple molecules in
them. Should we have some mechanism like a QTableWidget to read
through the individual slices? (Saving, IMHO would be a real pain and
probably avoided for now.)

Cheers,
-Geoff

Am Donnerstag, 20. September 2007 19:14:49 schrieben Sie:

On Sep 20, 2007, at 1:10 PM, Carsten Niehaus wrote:

“Return all molecules on my harddisc which have at least two Carbon
atoms and
an atomic weight between 45 and 78units.”

The returned list would be shown in a QTableWidget, the user
selects the
molecule clicks ok and Avo displays the molecule.

(a) This is an awesome idea! If you do this, I’ll have to hack
together a Mac version which uses ChemSpotlight. :slight_smile:

To be precise, I would create the querries in XESAM [1] so that it doesn’t
matter if the user is using Strigi, Beagle, Tracker or whatever.

(b) Yes, this should be an extension – it’s a GUI-only plugin, and
something that requires strigi, so not all platforms will have it (yet).

Ok.

This also brings up the question of files with multiple molecules in
them. Should we have some mechanism like a QTableWidget to read
through the individual slices? (Saving, IMHO would be a real pain and
probably avoided for now.)

I attached my first draft of the GUI. I am not sure about the GroupBoxes… I
suck at UI-Design.

Carsten

[1] http://freedesktop.org/wiki/XesamAbout

There are a couple ways to do this. However, doesn’t strigi already
have a front-end query program? In that case it’s just about
associating the molecule MIME type with the Avgadro editor so when
someone searching with strigi finds a molecule, Avogadro opens it.

On the other hand I think what you’re asking is about having Avogadro
contain a strigi searcher which is fine and probably an Extension but
really all you’re doing is creating your own query daemon. I would
suggest figuring out the MIME stuff first. That would be the biggest
thing imo.


Donald

(Thu, Sep 20, 2007 at 07:10:59PM +0200) Carsten Niehaus cniehaus@gmx.de:

Moin folks

I thought I might try a pet project: Strigisupport [1] in Avogadro. Strigi has
an exellent support for chemical filetypes [2]. The idea is to connect to to
the strigidaemon via DBus. I would create a GUI which would allow something
like this search:

“Return all molecules on my harddisc which have at least two Carbon atoms and
an atomic weight between 45 and 78units.”

The returned list would be shown in a QTableWidget, the user selects the
molecule clicks ok and Avo displays the molecule.

a) What do you think about this?

b) Is that an “Extension”? Or what would it be, technically?

Carsten

[1] http://www.vandenoever.info/software/strigi/
[2] http://neksa.blogspot.com/2007/08/strigi-chemical-gsoc-final-timeline.html


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This sounds really good …

Moin folks

I thought I might try a pet project: Strigisupport [1] in Avogadro. Strigi
has an exellent support for chemical filetypes [2]. The idea is to connect
to to the strigidaemon via DBus. I would create a GUI which would allow
something like this search:

“Return all molecules on my harddisc which have at least two Carbon atoms
and an atomic weight between 45 and 78units.”

The returned list would be shown in a QTableWidget, the user selects the
molecule clicks ok and Avo displays the molecule.

a) What do you think about this?

b) Is that an “Extension”? Or what would it be, technically?

Carsten

[1] http://www.vandenoever.info/software/strigi/
[2]
http://neksa.blogspot.com/2007/08/strigi-chemical-gsoc-final-timeline.html


Dr. Armando Navarro Vazquez
Facultade de quimica
Organic Chemistry Department
e-mail: qoajnv@usc.es
http://galileo.usc.es/~armando

Am Donnerstag, 20. September 2007 19:37:38 schrieben Sie:

On the other hand I think what you’re asking is about having Avogadro
contain a strigi searcher which is fine and probably an Extension but
really all you’re doing is creating your own query daemon. I would
suggest figuring out the MIME stuff first. That would be the biggest
thing imo.

No, strigi-chemical does that for me. I just talked with Egon about it (he is
the mentor of neksa who wrote strigi-chemical as his SoC) and Egon confirmed
that those queries work.

Carsten

Hi

I need some help with CMake… Avo compiles with the DBusstuff and I found out
how all this is working. But it isn’t linking to QtDBus and I don’t know
why… For some reasons this patch isn’t working.

-LINK_DIRECTORIES({LINK_DIRECTORIES} {libavogadro_BINARY_DIR}/src)
+LINK_DIRECTORIES({LINK_DIRECTORIES} {libavogadro_BINARY_DIR}/src
${QT_QTDBUS_LIBRARY})

I already commited in the branch, would please one of you guys have a look at
this?

./avogadro/src/avogadro: symbol lookup
error: /home/kde4/build/avo/avogadro/src/extensions/libstrigiextension.so:
undefined symbol: _ZN15QDBusConnection10sessionBusEv

Carsten

On Fri, 21 Sep 2007, Carsten Niehaus wrote:

But it isn’t linking to QtDBus and I don’t know why…

-LINK_DIRECTORIES({LINK_DIRECTORIES} {libavogadro_BINARY_DIR}/src)
+LINK_DIRECTORIES({LINK_DIRECTORIES} {libavogadro_BINARY_DIR}/src
${QT_QTDBUS_LIBRARY})

The above lines only specify directories. You need to explicitly say you
want to link against QtDbus, and IIRC the correct CMake command is
TARGET_LINK_LIBRARY or something like that.

I’m at office now so I can’t check the code.

Benoit