Nabble - 3D Rendering

aqsis 1.4.1 failed on Fedora Rawhide for ppc64

2008-10-06T09:05:31Z

Hello all!

Just a reminder that aqsis 1.4.1 failed on Fedora Rawhide (F-10) on ppc64
http://koji.fedoraproject.org/koji/taskinfo?taskID=864029

I cannot update aqsis in Fedora stable until the problem is solved in
Rawhide.
Quote of
http://koji.fedoraproject.org/koji/getfile?taskID=864033&name=build.log
---------------------
/builddir/build/BUILD/aqsis-1.4.1/renderer/ddmanager/ddmanager.cpp:211:
error: invalid application of 'sizeof' to incomplete type
'boost::STATIC_ASSERTION_FAILURE<false>'
/builddir/build/BUILD/aqsis-1.4.1/renderer/ddmanager/ddmanager.cpp:212:
error: invalid application of 'sizeof' to incomplete type
'boost::STATIC_ASSERTION_FAILURE<false>'
make[2]: ***
[renderer/render/CMakeFiles/aqsislib.dir/__/ddmanager/ddmanager.o] Error 1
make[2]: *** Waiting for unfinished jobs....
---------------------

Thx for your care.

Nicolas (kwizart)

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From forum: aqsis-development

[ cdk-Feature Requests-1941417 ] JChemPaint background color

2008-10-06T09:04:59Z

Feature Requests item #1941417, was opened at 2008-04-13 18:46
Message generated for change (Settings changed) made by shk3
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=370024&aid=1941417&group_id=20024

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: Angel Herraez (aherraez)
Assigned to: Stefan Kuhn (shk3)
Summary: JChemPaint background color

Initial Comment:
It would be nice that
<param name="background" value="12632256">
would accept hexadecimal values for color, say:
<param name="background" value="#C0C0C0">

(Easier to code, particularly inside HTML, JS, CSS)

----------------------------------------------------------------------

Comment By: Stefan Kuhn (shk3)
Date: 2008-09-15 18:11

Message:
implemented in 1.0.x branch

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From forum: cdk-devel

[ cdk-Feature Requests-2117572 ] Detect Chiral Centers using 3D coordinates

2008-10-06T09:04:31Z

Feature Requests item #2117572, was opened at 2008-09-18 11:25
Message generated for change (Comment added) made by shk3
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=370024&aid=2117572&group_id=20024

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including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Sebastian Rohrer (srohrer)
>Assigned to: Nobody/Anonymous (nobody)
>Summary: Detect Chiral Centers using 3D coordinates

Initial Comment:
Here is a SD-File of compounds with Chiral Centers that are not detected by
org.openscience.cdk.geometry.BondTools.isStereo.

The compounds originate from PubChem, explicit Hs were added and 3D-structures generated with CORINA.

Thanks for having a look at it.

Sebastian

----------------------------------------------------------------------

>Comment By: Stefan Kuhn (shk3)
Date: 2008-10-06 18:04

Message:
The method only works on molecules containing wedge bonds. It does not take
3d coordinates into account. I put this into the javadoc comment. I make
this a bug request, but do not expect it to be done soon (3d handling is
weak in cdk overall, so the method would not be of much use _given the
current cdk - e. g. smiles generation also works on 2d/wedges as well, to
make this 3d more methods would need to be adopted etc.)

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From forum: cdk-devel

[Bug 17861] glGetObjectParameterivARB sets wrong error code

2008-10-06T08:57:10Z

http://bugs.freedesktop.org/show_bug.cgi?id=17861

--- Comment #2 from Brian Paul <brian.paul@...> 2008-10-06 08:57:09 PST ---
Created an attachment (id=19411)
--> (http://bugs.freedesktop.org/attachment.cgi?id=19411)
my take on this

What about this patch? AFAICT, we're just concerned about the case where the
ID doesn't name an existing shader object. The error code depends on the pname
being queried.

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From forum: mesa3d-dev

Improving Triangle Depth Sorting?

2008-10-06T08:27:34Z

I understand the depth sorting is relative to triangle centroid, instead of all three corners. Which give us a performance boost.

Any plans for more accurate depth sorting?

Carl Gloria - 2livelarge.com - cgvelocity.com

Maya, Flash and Papervision - no particular order, just love them all!

From forum: Papervision3D

Re: [Cdk-commits] SF.net SVN: cdk:[12559] cdk/branches/cdk-1.0.x

2008-10-06T08:10:42Z

On Mon, Oct 6, 2008 at 5:06 PM, <shk3@...> wrote:
> Revision: 12559
> http://cdk.svn.sourceforge.net/cdk/?rev=12559&view=rev
> Author: shk3
> Date: 2008-10-06 15:06:39 +0000 (Mon, 06 Oct 2008)
>
> Log Message:
> -----------
> mol files are now scaled to angstrom (roughly)

Not really, I hope... That does not really fit my laptop screen... :)

Egon

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From forum: cdk-devel

Re: help in MoleculeListViewer class

2008-10-06T08:09:45Z

Weirdly enough, this code works for me on windows. What operating
system are you using?

gilleain torrance

On Mon, Oct 6, 2008 at 4:04 PM, Rajarshi Guha <rguha@...> wrote:

> You could take a look at
>
> http://cheminfo.informatics.indiana.edu/~rguha/code/java/#depict
>
> On Oct 6, 2008, at 6:47 AM, Bipin Bihari wrote:
>
>> Dear sir,
>> I needed the coordinate of a molecule and wanted to display on
>> MoleculeListViewer, there were no error and I got the Panel for
>> MoleculeListviewer but there were no structure of molecule, it was
>> blank.
>> The program is give below and the same is attached.
>> I am using jdk1.6.
>> Please guide me what correctios are needed?
>>
>> package org.openscience.cdk.myPackage;
>>
>> import org.openscience.cdk.smiles.SmilesParser;
>> import org.openscience.cdk.interfaces.IMolecule;
>> import org.openscience.cdk.Molecule;
>> import org.openscience.cdk.layout.StructureDiagramGenerator;
>> import org.openscience.cdk.applications.swing.MoleculeListViewer;
>> import org.openscience.cdk.applications.swing.MoleculeViewer2D;
>> import org.openscience.cdk.exception.CDKException;
>>
>> public class MyMoleculeViewer
>> {
>> public MyMoleculeViewer()
>> {
>> SmilesParser smileParser = new SmilesParser();
>> MoleculeListViewer moleculeListViewer = new
>> MoleculeListViewer();
>> String smiles = new String("c1ccccc1");
>> try
>> {
>> IMolecule molecule = smileParser.parseSmiles
>> (smiles);
>> StructureDiagramGenerator
>> structureDiagramGenerator = new
>> StructureDiagramGenerator();
>> MoleculeViewer2D moleculeViewer2D = new
>> MoleculeViewer2D();
>> structureDiagramGenerator.setMolecule
>> ((Molecule)molecule.clone());
>>
>> structureDiagramGenerator.generateCoordinates();
>> moleculeViewer2D.setAtomContainer
>> (structureDiagramGenerator.getMolecule());
>> moleculeListViewer.addStructure
>> (moleculeViewer2D,
>> "Structure");
>> }
>> catch(Exception e)
>> {
>> e.printStackTrace();
>> }
>> }
>>
>> public static void main(String args[])
>> {
>> new MyMoleculeViewer();
>> }
>> }
>>
>> thanks
>> bipin
>> ---------------------------------------------------
>> Bipin Bihari,
>> Student(PGDB),
>> Institute of Bioinformatics and Applied Biotechmology(IBAB),
>> G-05, Tech Park Mall, ITPB, White field road,
>> Bangalore, Karnatka-560066,
>> India.
>> ---------------------------------------------------
>> <MyMoleculeViewer.java>-----------------------------------------------
>> --------------------------
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>> the world
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>
> -------------------------------------------------------------------
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> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
> -------------------------------------------------------------------
> All life evolves by the differential survival of replicating entities.
> -- Dawkins
>
>
>
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From forum: cdk-devel

Re: 3DS Pivot point

2008-10-06T08:05:40Z

in answer to my own question :)

I did this >

    /**
        * Resets the pivot point for the 3DS object to it's center.
        * @param    x
        * @param    y
        * @param    z
        */
        public function pivot3DS(x:Number, y:Number, z:Number):void
        {
            this.addChild(new PivotBox()); // adds a box in the 0,0,0 of the object
            var vertices:Array = this.geometry.vertices;

            for (var vertex:String in vertices)
            {
                var vertex3D:Vertex3D = vertices[vertex] as Vertex3D
                    vertex3D.x -= x
                    vertex3D.y -= y
                    vertex3D.z -= z
            }

            this.x = x
            this.y = z
            this.z = 0-y

        }

My problem was, import an object from 3DS Max, using the Max3DS class, all the vertices were in the correct location, but the DisplayObject3D itself was set at 0,0,0. This meant any rotations applied to this object, rotated around the center of the scene, rather than that object.

However this method put on the DisplayObject3D class, resolves this issue with manual coords, grabbed from the 3DS max app.

Matt

2008/10/6 Matthew Hare <matt.hare@...>

Hiya Guys,

Is there a way to pick up the 3DS pivot point in the Max3DS class? Or do I have to manual offset everything the code?

For example, I have a plane that has a material of a hedge, now i want to rotate that hedge along its bottom edge so that it appears to pop up, like a popup book. However, Max3DS seems to set every object at 0,0,0 and the set the vertices at the real location of the object, which means when i rotate the object it flies off :)

Is there a quick fix for this? or do I need to create DO3D and offset each object manually?

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Re: help in MoleculeListViewer class

2008-10-06T08:04:13Z

You could take a look at

http://cheminfo.informatics.indiana.edu/~rguha/code/java/#depict

On Oct 6, 2008, at 6:47 AM, Bipin Bihari wrote:

> Dear sir,
> I needed the coordinate of a molecule and wanted to display on
> MoleculeListViewer, there were no error and I got the Panel for
> MoleculeListviewer but there were no structure of molecule, it was
> blank.
> The program is give below and the same is attached.
> I am using jdk1.6.
> Please guide me what correctios are needed?
>
> package org.openscience.cdk.myPackage;
>
> import org.openscience.cdk.smiles.SmilesParser;
> import org.openscience.cdk.interfaces.IMolecule;
> import org.openscience.cdk.Molecule;
> import org.openscience.cdk.layout.StructureDiagramGenerator;
> import org.openscience.cdk.applications.swing.MoleculeListViewer;
> import org.openscience.cdk.applications.swing.MoleculeViewer2D;
> import org.openscience.cdk.exception.CDKException;
>
> public class MyMoleculeViewer
> {
> public MyMoleculeViewer()
> {
> SmilesParser smileParser = new SmilesParser();
> MoleculeListViewer moleculeListViewer = new
> MoleculeListViewer();
> String smiles = new String("c1ccccc1");
> try
> {
> IMolecule molecule = smileParser.parseSmiles
> (smiles);
> StructureDiagramGenerator
> structureDiagramGenerator = new
> StructureDiagramGenerator();
> MoleculeViewer2D moleculeViewer2D = new
> MoleculeViewer2D();
> structureDiagramGenerator.setMolecule
> ((Molecule)molecule.clone());
>
> structureDiagramGenerator.generateCoordinates();
> moleculeViewer2D.setAtomContainer
> (structureDiagramGenerator.getMolecule());
> moleculeListViewer.addStructure
> (moleculeViewer2D,
> "Structure");
> }
> catch(Exception e)
> {
> e.printStackTrace();
> }
> }
>
> public static void main(String args[])
> {
> new MyMoleculeViewer();
> }
> }
>
> thanks
> bipin
> ---------------------------------------------------
> Bipin Bihari,
> Student(PGDB),
> Institute of Bioinformatics and Applied Biotechmology(IBAB),
> G-05, Tech Park Mall, ITPB, White field road,
> Bangalore, Karnatka-560066,
> India.
> ---------------------------------------------------
> <MyMoleculeViewer.java>-----------------------------------------------
> --------------------------
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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T08:01:17Z

On Mon, Oct 6, 2008 at 4:02 PM, Rajarshi Guha <rguha@...> wrote:

>
> On Oct 6, 2008, at 9:44 AM, Egon Willighagen wrote:
>
>> On Mon, Oct 6, 2008 at 3:41 PM, Rajarshi Guha <rguha@...> wrote:
>>>
>>> On Oct 6, 2008, at 9:15 AM, Egon Willighagen wrote:
>>>
>>>> I identified at least the following constructs not supported:
>>>>
>>>> 1. [#G6] (or [#G7] etc)
>>>
>>> Shouldn't be difficult I expect
>
> Personally, I'd go for rewriting the above as an OR.
>
> Also if G6 indicates Group 6 of the periodic table then the elements are Cr,
> Mo, W so I'm not sure how it matches C, S etc

Maybe Group VI of the main group elements?

[1] describes [#G7!F] as "halogens (other than fluorine)"...

Egon

1.http://www.chemcomp.com/journal/sdtools.htm

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From forum: cdk-devel

Re: help in MoleculeListViewer class

2008-10-06T08:00:45Z

>From just looking at your code it is difficult to say what might be wrong.
There are a lot of things that might happen in Swing, including packing
issues, layout manager issues, etc.
You might try to set a preferred size for the moleculeViewer2D, for
example.
Try playing around with background color, etc., and setting window
titles, to see if what you are seeing is really what you think you see :-)

Cheers,

Chris

Bipin Bihari wrote:

> Dear sir,
> I needed the coordinate of a molecule and wanted to display on
> MoleculeListViewer, there were no error and I got the Panel for
> MoleculeListviewer but there were no structure of molecule, it was
> blank.
> The program is give below and the same is attached.
> I am using jdk1.6.
> Please guide me what correctios are needed?
>
> package org.openscience.cdk.myPackage;
>
> import org.openscience.cdk.smiles.SmilesParser;
> import org.openscience.cdk.interfaces.IMolecule;
> import org.openscience.cdk.Molecule;
> import org.openscience.cdk.layout.StructureDiagramGenerator;
> import org.openscience.cdk.applications.swing.MoleculeListViewer;
> import org.openscience.cdk.applications.swing.MoleculeViewer2D;
> import org.openscience.cdk.exception.CDKException;
>
> public class MyMoleculeViewer
> {
> public MyMoleculeViewer()
> {
> SmilesParser smileParser = new SmilesParser();
> MoleculeListViewer moleculeListViewer = new
> MoleculeListViewer();
> String smiles = new String("c1ccccc1");
> try
> {
> IMolecule molecule = smileParser.parseSmiles(smiles);
> StructureDiagramGenerator
> structureDiagramGenerator = new
> StructureDiagramGenerator();
> MoleculeViewer2D moleculeViewer2D = new
> MoleculeViewer2D();
> structureDiagramGenerator.setMolecule((Molecule)molecule.clone());
> structureDiagramGenerator.generateCoordinates();
> moleculeViewer2D.setAtomContainer(structureDiagramGenerator.getMolecule());
> moleculeListViewer.addStructure(moleculeViewer2D,
> "Structure");
> }
> catch(Exception e)
> {
> e.printStackTrace();
> }
> }
>
> public static void main(String args[])
> {
> new MyMoleculeViewer();
> }
> }
>
> thanks
> bipin
> ---------------------------------------------------
> Bipin Bihari,
> Student(PGDB),
> Institute of Bioinformatics and Applied Biotechmology(IBAB),
> G-05, Tech Park Mall, ITPB, White field road,
> Bangalore, Karnatka-560066,
> India.
> ---------------------------------------------------
>
>
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
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>
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--
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Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
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Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640

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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T07:58:54Z

On Mon, Oct 6, 2008 at 4:48 PM, Nina Jeliazkova <nina@...> wrote:
> I would also be interested in finding a solution to the MOE SMARTS
> extensions. Does MOE documentation come only with their products?
>
> With the supporting info the implementation is pretty quick and
> straightforward (here is mine from Friday evening :)
> https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/PKASmartsDescriptor.java

At least I got first post :)

Are your PkaNode use the SMARTSQueryTool too? How did you deal with
the difficult SMARTS?

Egon

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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T07:56:55Z

On Oct 6, 2008, at 10:48 AM, Nina Jeliazkova wrote:

> Hi all,
>
> I would also be interested in finding a solution to the MOE SMARTS
> extensions. Does MOE documentation come only with their products?

Apparently so. I've asked Adam if he can shed some light.

AFAICS, the G? identifier means group of periodic table, since they
have a entry in the table where they say G7 is a halogen. But the MOE
implementation is not using IUPAC group numbering system. So G6 does
mean C,S etc - but it's referring to VIB and VIA

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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T07:48:14Z

Hi all,

I would also be interested in finding a solution to the MOE SMARTS
extensions. Does MOE documentation come only with their products?

With the supporting info the implementation is pretty quick and
straightforward (here is mine from Friday evening :)
https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/PKASmartsDescriptor.java

Regards,
Nina

Egon Willighagen wrote:

> Hi all (and the Dazhi/Rajarshi in particular),
>
> I have playing with pKa prediction based on a JCIM paper release last
> Thursday [0] and ran into SMARTS parsing problems, because MOE extends
> the original specification in ways CDK does not support (yet):
>
> http://chem-bla-ics.blogspot.com/2008/10/pka-prediction-or-how-to-convert-jcim.html
>
> I identified at least the following constructs not supported:
>
> 1. [#G6] (or [#G7] etc)
> 2. [i]
> 3. [#X]
>
> Any possibility to see support for this in the CDK SMARTS engine?
>
> Egon
>
>
>

From forum: cdk-devel

Re: compilation errors, /usr/bin/ld: cannot find -lXi, and so on

2008-10-06T07:45:10Z

Hi, Cami:

I am new to Linux. I typed two commands "find" and "yum" on my system. The following is the output. It seems to me that I have the libraries installed, but the mesa compiling does not recognize the name of the library or which directory the library resides in. Thanks.

Sincerely,
Diao Jiasheng

[root@ lib]# find / -name "libXi*"
/usr/lib64/libXinerama.so.1.0.0
/usr/lib64/libXi.so.6
/usr/lib64/libXi.so.6.0.0
/usr/lib64/libXinerama.so.1
/usr/share/doc/libXinerama-1.0.1
/usr/share/doc/libXi-1.0.1
/usr/lib/libXinerama.so.1.0.0
/usr/lib/libXi.so.6
/usr/lib/libXi.so.6.0.0
/usr/lib/libXinerama.so.1
/var/cache/yum/rhel-x86_64-client-workstation-5/headers/libXinerama-devel-1.0.1-2.1.x86_64.hdr
/var/cache/yum/rhel-x86_64-client-workstation-5/headers/libXi-devel-1.0.1-3.1.x86_64.hdr

[root@ lib]# yum provides libXi
Loading "rhnplugin" plugin
rhel-x86_64-client-workst 100% |=========================| 1.4 kB 00:00
rhel-x86_64-client-5 100% |=========================| 1.4 kB 00:00
libXi.i386 : X.Org X11 libXi runtime library

libXi.x86_64 : X.Org X11 libXi runtime library

libXi.i386 : X.Org X11 libXi runtime library
libXi.x86_64 : X.Org X11 libXi runtime library

----------------------------------------

> Date: Sun, 5 Oct 2008 21:08:05 +0200
> From: francois.cami@...
> To: diaojs@...
> CC: mesa3d-users@...
> Subject: Re: [Mesa3d-users] compilation errors, /usr/bin/ld: cannot find -lXi, and so on
>
>
> Hi Diao,
>
> A "yum provides libXi" on my EL5 gives me the following result :
> libXi.i386 : X.Org X11 libXi runtime library
> libXi.x86_64 : X.Org X11 libXi runtime library
>
> By the way, 2.6.18-8.el5 is completely outdated...
>
> Best,
>
> Francois
>
>
> On Sun, 5 Oct 2008 14:45:54 -0400
> jiasheng diao wrote:
>
>> Hi, All:
>>
>> On a linux system I am compiling Mesa 7.2 including the three files: MesaDemos-7.2.tar MesaGLUT-7.2.tar MesaLib-7.2.tar.
>> uname -a gives me the following information on my system.
>> Linux 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
>> I used "make linux-x86-64" for compilation.
>>
>> The following is the end of compilation output. What should I do next?
>> Do my computer miss some library or the library exists somewhere else
>> which can not be found by gcc? Thanks.
>>
>> Sincerely,
>> Diao Jiasheng
>> ----------------------------------------------------------------------------------------------------------------------------------------------------
>> /bin/sh ../../../bin/mklib -o glut -linker 'gcc' -ldflags '' \
>> -major 3 -minor 7 -patch 1 \
>> -install ../../../lib64 \
>> -id /usr/local/lib64/libglut.3.dylib \
>>
>> -L../../../lib64 -lGLU -lGL -L/usr/X11R6/lib64 -lX11 -lXmu -lXi -lm
>> glut_8x13.o glut_9x15.o glut_bitmap.o glut_bwidth.o glut_cindex.o
>> glut_cmap.o glut_cursor.o glut_dials.o glut_dstr.o glut_event.o
>> glut_ext.o glut_fcb.o glut_fullscrn.o glut_gamemode.o glut_get.o
>> glut_glxext.o glut_hel10.o glut_hel12.o glut_hel18.o glut_init.o
>> glut_input.o glut_joy.o glut_key.o glut_keyctrl.o glut_keyup.o
>> glut_menu.o glut_menu2.o glut_mesa.o glut_modifier.o glut_mroman.o
>> glut_overlay.o glut_roman.o glut_shapes.o glut_space.o glut_stroke.o
>> glut_swap.o glut_swidth.o glut_tablet.o glut_teapot.o glut_tr10.o
>> glut_tr24.o glut_util.o glut_vidresize.o glut_warp.o glut_win.o
>> glut_winmisc.o layerutil.o
>> mklib: Making Linux shared library: libglut.so.3.7.1
>> /usr/bin/ld: cannot find -lXi
>> collect2: ld returned 1 exit status
>> mklib: Installing libglut.so.3.7.1 libglut.so.3 libglut.so in ../../../lib64
>> mv: cannot stat `libglut.so.3.7.1': No such file or directory
>> make[3]: *** [../../../lib64/libglut.so] Error 1
>> make[3]: Leaving directory `/home/diao/Mesa/Mesa-7.2/src/glut/glx'
>> make[2]: *** [subdirs] Error 1
>> make[2]: Leaving directory `/home/diao/Mesa/Mesa-7.2/src'
>> make[1]: *** [default] Error 1
>> make[1]: Leaving directory `/home/diao/Mesa/Mesa-7.2'
>> make: *** [linux-x86-64] Error 2
>>
>>
>> _________________________________________________________________
>> Stay up to date on your PC, the Web, and your mobile phone with Windows Live.
>> http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct/01/

_________________________________________________________________
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From forum: mesa3d-users

Re: build broken

2008-10-06T07:24:07Z

On Mon, Oct 6, 2008 at 4:17 PM, Rajarshi Guha <rguha@...> wrote:
> fixed

Thanx. Sorry about that...

Egon

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From forum: cdk-devel

How a JavaDoc fix breaks compilation... (was: [Cdk-commits] SF.net SVN: cdk:[12558] cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk /isomorphism/matchers)

2008-10-06T07:23:37Z

Ah, unforseen implications... thanx for catching that. Who would have
thought that fixing JavaDoc could break compiling code ... hahaha...
stupid me.

On Mon, Oct 6, 2008 at 4:17 PM, <rajarshi@...> wrote:

> Log Message:
> -----------
> Rmoved unescessary import reducing a dependnecy
> @@ -21,11 +21,10 @@
> package org.openscience.cdk.isomorphism.matchers;
>
> import org.openscience.cdk.interfaces.IAtom;
> -import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
>
> /**
> * Defines the ability to be matched against {@link IAtom}'s. Most prominent application
> - * is in isomorphism and substructure matching in the {@link UniversalIsomorphismTester}.
> + * is in isomorphism and substructure matching in the {@link org.openscience.cdk.isomorphism.UniversalIsomorphismTester}.
> *
> * @cdk.module interfaces
> * @cdk.svnrev $Revision$

Egon

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From forum: cdk-devel

Re: Gallium + llvm integration

2008-10-06T07:22:16Z

On Mon, Oct 6, 2008 at 4:08 PM, Brian Paul
<brian.paul@...> wrote:

> Stephane Marchesin wrote:
>> On Tue, Sep 30, 2008 at 8:34 PM, Keith Whitwell
>> <keith@...> wrote:
>>> On Tue, Sep 30, 2008 at 7:21 PM, Stephane Marchesin
>>> <marchesin@...> wrote:
>>>> Hi again,
>>>>
>>>> I've adapted (but didn't push it) gallivm to llvm 2.4 (svn) API
>>>> changes. But then there's an obvious question about what we're doing
>>>> with those API changes ? Do we settle on a given version, or do we
>>>> want to adapt it as the llvm API changes ?
>>> It's always been my hope that we'd be able to target stable versions
>>> of llvm... at least when we're creating stable versions of our own
>>> software. IE. at some future Mesa 7.6 or 8.0 stable version, we would
>>> have settled on a stable llvm to go with it.
>>
>> Hmm ok. There are a number of side issues though, for example
>> compiling clang on top of the chosen llvm version. Because clang is
>> under development, there are no releases that "match" llvm releases.
>> To put it clearly, you can't compile clang svn on llvm 2.2 or 2.3.
>>
>> Also, from discussing with the llvm developers, it seems that clang is
>> still pretty buggy so they advise to use a version that's as new as
>> possible (this is why I updated llvm in the first place).
>>
>>> However, while we're in development & on a development branch, it
>>> probably makes sense to track llvm's development version. Certainly
>>> I'd like to see the Cell driver make use of the llvm Cell backend,
>>> which itself I understand is not fully done, so to achieve that we'd
>>> want to track/contribute to the llvm svn repo.
>>
>> Yeah I was wondering why you were all busy working on doing a gallium
>> cell backend while llvm could've done the trick. Btw there is someone
>> who recently revived the cell backend in llvm so chances are it'll get
>> better now.
>
> That's good news. I've played with the LLVM Cell code generator and
> clang and found that very little of it actually worked properly.
>

FWIW, you can probably blame a part of this on clang itself. Even on
x86 it has issues (there's a reason it didn't get a release yet).

Stephane

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From forum: mesa3d-dev

Re: SW rasterized antialiased triangles

2008-10-06T07:21:36Z

Shachar Kaufman wrote:
> Hi all,
>
> s_aatritemp.h notes: "NOTE: this code hasn't been optimized yet.
> That'll come after it works correctly."
> Are there really correctness issues with this code still?

It works correctly, and has for years now. No plans to optimize it.

-Brian

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From forum: mesa3d-dev

Re: build broken

2008-10-06T07:21:00Z

1.2.x

On Oct 6, 2008, at 10:15 AM, Egon Willighagen wrote:

> On Mon, Oct 6, 2008 at 4:11 PM, Rajarshi Guha <rguha@...>
> wrote:
>> interfaces module depends on the UIT code
>
> Where? Branch or trunk? 1.0.x or 1.2.x?
>
> Egon
>
> --
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> http://chem-bla-ics.blogspot.com/
>
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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T07:18:05Z

On Oct 6, 2008, at 10:16 AM, Egon Willighagen wrote:

> On Mon, Oct 6, 2008 at 4:14 PM, Rajarshi Guha <rguha@...>
> wrote:
>> On Oct 6, 2008, at 10:11 AM, Egon Willighagen wrote:
>>> BTW, can we parse a MQL query into a IQueryAtomContainer in the CDK
>>> already?
>>
>> Dazhi mentioned something on these lines sometime back, but I
>> don't know for
>> sure. My understanding is that it'd be difficult, since MQL goes
>> beyond what
>> SMARTS provides
>
> Ah, that would be translating MQL into SMARTS... I was wondering about
> MQL directly into IQueryAtomContainer...

Oh, OK. Don't know about that

-------------------------------------------------------------------
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From forum: cdk-devel

Re: build broken

2008-10-06T07:17:29Z

fixed

On Oct 6, 2008, at 10:11 AM, Rajarshi Guha wrote:

> interfaces module depends on the UIT code
>
> -------------------------------------------------------------------
> Rajarshi Guha <rguha@...>
> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
> -------------------------------------------------------------------
> All great discoveries are made by mistake.
> -- Young
>
>
>
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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T07:16:13Z

On Mon, Oct 6, 2008 at 4:14 PM, Rajarshi Guha <rguha@...> wrote:
> On Oct 6, 2008, at 10:11 AM, Egon Willighagen wrote:
>> BTW, can we parse a MQL query into a IQueryAtomContainer in the CDK
>> already?
>
> Dazhi mentioned something on these lines sometime back, but I don't know for
> sure. My understanding is that it'd be difficult, since MQL goes beyond what
> SMARTS provides

Ah, that would be translating MQL into SMARTS... I was wondering about
MQL directly into IQueryAtomContainer...

Egon

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From forum: cdk-devel

Re: build broken

2008-10-06T07:15:15Z

On Mon, Oct 6, 2008 at 4:11 PM, Rajarshi Guha <rguha@...> wrote:
> interfaces module depends on the UIT code

Where? Branch or trunk? 1.0.x or 1.2.x?

Egon

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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T07:14:51Z

On Oct 6, 2008, at 10:11 AM, Egon Willighagen wrote:

> BTW, can we parse a MQL query into a IQueryAtomContainer in the CDK
> already?

Dazhi mentioned something on these lines sometime back, but I don't
know for sure. My understanding is that it'd be difficult, since MQL
goes beyond what SMARTS provides

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From forum: cdk-devel

Re: Support for SMARTS extensions by MOE?

2008-10-06T07:11:59Z

On Mon, Oct 6, 2008 at 4:02 PM, Rajarshi Guha <rguha@...> wrote:
>>>> 1. [#G6] (or [#G7] etc)
>>>
>>> Shouldn't be difficult I expect
>
> Personally, I'd go for rewriting the above as an OR.

Yes, that's what I did... though it becomes rather long then...
Moreover, there are a lot of variants (from my Perl script):

$cdkSmarts =~ s/#G6H/#6H,#16H/g;
$cdkSmarts =~ s/#G6;H/#6;H,#16;H/g;
$cdkSmarts =~ s/#G4!H0/#4!H0,#14H0/g;

I still have to check if I have rewritten the second and third
variants correctly...

> Also if G6 indicates Group 6 of the periodic table then the elements are Cr,
> Mo, W so I'm not sure how it matches C, S etc

Right... so my analysis that it meant 'Group' was so wrong...

> Without MOE documentation, implementing these extensions is tricky. I'd
> rather not guess

Agreed.

>>> I'd most preferably see one fixed open standard, but I'd rather see
>>
>> support for these extensions *than* to have *approximating* SMARTS
>> queries... that was my thought behind it...
>
> I see your point.
>
> We should also then publicize the CDK extension :)

Indeed :) I so only good in that... more papers, more citations :)

BTW, can we parse a MQL query into a IQueryAtomContainer in the CDK already?

Egon

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From forum: cdk-devel

build broken

2008-10-06T07:11:24Z

interfaces module depends on the UIT code

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From forum: cdk-devel

Re: Gallium + llvm integration

2008-10-06T07:08:38Z

Stephane Marchesin wrote:

> On Tue, Sep 30, 2008 at 8:34 PM, Keith Whitwell
> <keith@...> wrote:
>> On Tue, Sep 30, 2008 at 7:21 PM, Stephane Marchesin
>> <marchesin@...> wrote:
>>> Hi again,
>>>
>>> I've adapted (but didn't push it) gallivm to llvm 2.4 (svn) API
>>> changes. But then there's an obvious question about what we're doing
>>> with those API changes ? Do we settle on a given version, or do we
>>> want to adapt it as the llvm API changes ?
>> It's always been my hope that we'd be able to target stable versions
>> of llvm... at least when we're creating stable versions of our own
>> software. IE. at some future Mesa 7.6 or 8.0 stable version, we would
>> have settled on a stable llvm to go with it.
>
> Hmm ok. There are a number of side issues though, for example
> compiling clang on top of the chosen llvm version. Because clang is
> under development, there are no releases that "match" llvm releases.
> To put it clearly, you can't compile clang svn on llvm 2.2 or 2.3.
>
> Also, from discussing with the llvm developers, it seems that clang is
> still pretty buggy so they advise to use a version that's as new as
> possible (this is why I updated llvm in the first place).
>
>> However, while we're in development & on a development branch, it
>> probably makes sense to track llvm's development version. Certainly
>> I'd like to see the Cell driver make use of the llvm Cell backend,
>> which itself I understand is not fully done, so to achieve that we'd
>> want to track/contribute to the llvm svn repo.
>
> Yeah I was wondering why you were all busy working on doing a gallium
> cell backend while llvm could've done the trick. Btw there is someone
> who recently revived the cell backend in llvm so chances are it'll get
> better now.

That's good news. I've played with the LLVM Cell code generator and
clang and found that very little of it actually worked properly.

-Brian

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From forum: mesa3d-dev

Static build broken

2008-10-06T07:08:31Z

Greetings,

probably due to a bug in libtool the static Mesa3D build (for atleast Linux)
is currently broken (Mesa3D 7.2). After
make linux-x86-static
one gets static libraries that do not contain vital symbols (glVertex** and
the like). This is because libtool somehow creates an ar archive with
other ar archives as members (and ld can not handle archives in archives).

One can manually extract/remove the offending archives, extract all objects
from them and add those objects to libGL.a with ar to make it work.

kind regards,
Randolf

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From forum: mesa3d-users

Re: How do you use animated MovieAssetMaterial in AS2?

2008-10-06T07:04:26Z

Thank You! Thank You! Thank You!

Man, I've worked on this for days. Thanks for finally clearing that up for me!

Cheers,
Shahin

dimjas wrote:

Hi,
You must insert
scene.push(material5);
if you want to see animation

From forum: Papervision3D