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From: swinnen <sw...@us...> - 2006-02-22 17:31:55
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Update of /cvsroot/nanodesigner/HelpDocs/help In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4377/HelpDocs/help Modified Files: 3dcanvas.html introduction.html default.css preferences.html commandline.html index.html Log Message: Index: 3dcanvas.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/3dcanvas.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** 3dcanvas.html 21 Jul 2005 17:09:51 -0000 1.1 --- 3dcanvas.html 22 Feb 2006 17:31:43 -0000 1.2 *************** *** 4,11 **** <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> - <meta name="description" content="nanodesigner 3d canvas pane"> - <meta name="keywords" content="nanodesigner 3d universe mouse movement"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.1 - 3D canvas</title> </head> --- 4,9 ---- <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - 3D canvas</title> </head> *************** *** 14,22 **** <h2>3D canvas</h2><hr> ! <p class="pref">Moving the 3D universe.</p> <ul class="text"> <li>Moving the content of the 3D universe is primarily done by the mouse, i.e. the mouse buttons and the mouse wheel if available. <ul> ! <li><b>Left button:</b> rotate the universe.</li> <li><b>Mousewheel:</b> zoom in or out.</li> <li><b>Right button:</b> translate the universe.</li> --- 12,20 ---- <h2>3D canvas</h2><hr> ! <p class="pref">Moving around in the 3D universe.</p> <ul class="text"> <li>Moving the content of the 3D universe is primarily done by the mouse, i.e. the mouse buttons and the mouse wheel if available. <ul> ! <li><b>Left button:</b> rotate the universe around the X and Y coordinate axis.</li> <li><b>Mousewheel:</b> zoom in or out.</li> <li><b>Right button:</b> translate the universe.</li> *************** *** 26,32 **** <h3>Remarks:</h3> ! <ol class="numbered"> ! <li>When a pdb file is loaded its content is displayed as a wireframe by default. Biomolecules often contain few or no bond information so it might be possible that nothing appears on the screen when loaded. Wireframe display mode does not show atoms only bonds. The default display mode will probably change in future releases.</li> ! <li>Due to the lack of optimization the mouse responsiveness decreases as the molecule size increases. This problem will also be dealt with in future releases.</li> </ol> --- 24,34 ---- <h3>Remarks:</h3> ! <ol> ! <li>When a chemical data file is loaded its content is displayed in: ! <ul> ! <li>wireframe mode if any bond information is available</li> ! <li>space-filled display mode if no bond information is included in the file <br></li> ! </ul></li> ! <li>Due to the lack of optimization the mouse responsiveness decreases as the molecule size increases. This problem will be dealt with in future releases.</li> </ol> Index: preferences.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/preferences.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** preferences.html 21 Jul 2005 17:09:51 -0000 1.1 --- preferences.html 22 Feb 2006 17:31:43 -0000 1.2 *************** *** 4,11 **** <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> - <meta name="description" content="nanodesigner preferences"> - <meta name="keywords" content="nanodesigner preferences gui opengl"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.1 - Program preferences</title> </head> --- 4,9 ---- <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - Program preferences</title> </head> *************** *** 14,18 **** <h2>Preferences</h2><hr> ! <h3 class="under">GUI</h3> <p class="pref">One window</p> --- 12,16 ---- <h2>Preferences</h2><hr> ! <h3 class="u">GUI</h3> <p class="pref">One window</p> *************** *** 24,54 **** <li>The part on the right-hand side containing the 3D canvas. </ul> ! With this check box the user can concatenate (or separate) these three parts into one (or three) window(s). In the three windows mode the 3D canvas can be maximized to fill the entire screen so as to get the best possible view on its content.</li> </ul> ! <h3 class="under">OpenGL</h3> <p class="pref">Anti-aliasing</p> <ul class="text"> ! <li>Reduction of jagged borders between colours in an image. Using smoothing algorithms always comes with a performance penalty so if not needed keep these boxes unchecked. It is included here to be able to create a smooth static picture that can, for example, be exported as an image. The boxes are unchecked by default.</li> ! <li><ul> <li>Point and line smoothing check box: used to smooth out points and lines.</li> ! <li>Polygon smoothing check box: used to smooth out polygon edges.<br /><b>Polygon smoothing is not supported on all OpenGL implementations, only on high-end graphic cards!</b></li> </ul></li></ul> <p class="pref">Background colour</p> <ul class="text"> ! <li>Background colour of the 3D canvas. It can be changed by inserting a value between 0 and 255 for the red, green and blue colour, thus selecting one specific colour in the RGB colourspace. The default background colour is black (r=0, g=0, b=0).</li> </ul> <p class="pref">Colourmap</p> <ul class="text"> ! <li>Three colourmaps of existing, often used, free visualization programs are included, namely:</li> ! <li><ul> ! <li><a href="http://www.jmol.org">Jmol</a> ! <li><a href="http://www.umass.edu/microbio/rasmol/">Rasmol/Chime</a> ! <li><a href="http://pymol.sourceforge.net/">PyMOL</a> ! </ul><br></li> ! <li>The Jmol colourmap is the default.</li> </ul> --- 22,53 ---- <li>The part on the right-hand side containing the 3D canvas. </ul> ! With this check box the user can separate (or concatenate) these three parts into three (or one) window(s). In the three windows mode the 3D canvas can be maximized so as to get the best possible view on its content.</li> </ul> ! <h3 class="u">OpenGL</h3> <p class="pref">Anti-aliasing</p> <ul class="text"> ! <li>Reduction of jagged borders between colours in an image. Using smoothing algorithms always comes with a performance penalty so if not needed keep these boxes unchecked. It is included here to be able to create a smooth static picture that can, for example, be exported as an image. The boxes are unchecked by default. ! <ul> <li>Point and line smoothing check box: used to smooth out points and lines.</li> ! <li>Polygon smoothing check box: used to smooth out polygon edges.<br> ! <b>Polygon smoothing is not supported on all OpenGL implementations, only on high-end graphic cards.</b></li> </ul></li></ul> <p class="pref">Background colour</p> <ul class="text"> ! <li>Background colour of the 3D canvas. It can be changed by inserting a value between 0 and 255 for the red, green and blue colour, thus selecting one of the colours in the RGB colourspace. The default background colour is black (r = 0, g = 0, b = 0).</li> </ul> <p class="pref">Colourmap</p> <ul class="text"> ! <li>Three colourmaps of existing, often used, free visualization programs are included, namely: ! <ul> ! <li>Jmol (http://www.jmol.org)</li> ! <li>Rasmol/Chime (http://www.umass.edu/microbio/rasmol/)</li> ! <li>PyMOL (http://pymol.sourceforge.net/)</li> ! </ul> ! <p>The Jmol colourmap is the default. </ul> Index: commandline.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/commandline.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** commandline.html 21 Jul 2005 17:09:51 -0000 1.1 --- commandline.html 22 Feb 2006 17:31:43 -0000 1.2 *************** *** 4,11 **** <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> - <meta name="description" content="Nanodesigner command line options"> - <meta name="keywords" content="command line debug"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1 - Commandline options</title> </head> --- 4,9 ---- <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - Commandline options</title> </head> *************** *** 15,22 **** <h3>-debug</h3> <ul class="text"> ! <li>Adding this option will display extensive additional information in the launch window (DOS) while running.<br> ! Alter the line that launches the program in the file nanodesigner.bat (windows) or the file nanodesigner.sh (linux) to: <br> ! <p class="center"><b>java -jar .\jars\core.jar -debug</b></p></li> </ul> --- 13,21 ---- <h3>-debug</h3> <ul class="text"> ! <li>Adding this option will display extensive additional information in the launch window (DOS window)<br> while running. ! Particularly useful is that it now shows detailed information about the OpenGL version supported by the videocard of the system the program is running on.<br> ! Alter the line that launches the program in the file nanodesigner.bat (Windows OS) or the file nanodesigner.sh (Linux OS) to: <br> ! <p class="center"><b>java -Dsun.java2d.noddraw=true -jar .\jars\core.jar -debug</b></p></li> </ul> Index: index.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/index.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** index.html 21 Jul 2005 17:09:51 -0000 1.1 --- index.html 22 Feb 2006 17:31:43 -0000 1.2 *************** *** 1,31 **** ! <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.</title> </head> <body> ! <center><h1>Nanodesigner v0.1</h1></center> <h2>Table of contents.</h2><hr> <ul> ! 1. <a href="introduction.html">Introduction</a><br> ! 2. <a href="commandline.html">Command line options</a><br> ! 3. Menus ! <ul> ! - <a href="menus.html">File</a><br> ! - <a href="menus.html#help">Help</a> ! </ul> ! 4. Toolboxes <ul> ! - <a href="toolboxes.html">Top</a><br> ! - <a href="toolboxes.html#middle">Middle</a><br> ! - <a href="toolboxes.html#bottom">Bottom</a><br> ! </ul> ! 5. <a href="canvas.html">3D canvas</a> ! </ul> <hr> ! <h5>The Nanodesigner development team.</h5> </body> ! </html> \ No newline at end of file --- 1,32 ---- ! <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" ! "http://www.w3.org/TR/html4/loose.dtd"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.2.</title> </head> <body> ! <h1 class="center">Nanodesigner v0.1.2</h1> <h2>Table of contents.</h2><hr> + <ol> + <li><a href="introduction.html">Introduction</a></li> + <li><a href="commandline.html">Command line options</a></li> + <li>Menus <ul> ! <li><a href="menu/file.html">File</a></li> ! <li><a href="menu/help.html">Help</a></li> ! </ul></li> ! <li>Toolboxes <ul> ! <li><a href="toolbox/top.html">Top</a></li> ! <li><a href="toolbox/middle.html">Middle</a></li> ! <li><a href="toolbox/bottom.html">Bottom</a></li> ! </ul></li> ! <li><a href="3Dcanvas.html">3D canvas</a> ! </ol> <hr> ! <p class="sign">The Nanodesigner development team.</p> </body> ! </html> Index: introduction.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/introduction.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** introduction.html 21 Jul 2005 17:09:51 -0000 1.1 --- introduction.html 22 Feb 2006 17:31:43 -0000 1.2 *************** *** 4,11 **** <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> - <meta name="description" content="nanodesigner introduction"> - <meta name="keywords" content="nanodesigner introduction molecular visualisation free open source"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.1 - Introduction</title> </head> --- 4,9 ---- <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - Introduction</title> </head> *************** *** 14,18 **** <hr> <p>Nanodesigner is a free, open source, software tools platform intended for the design of atomic structures from the ground up, atom-by-atom, molecule by molecule.</p> ! <p>Version 0.1.1 has a very limited functionality and can best be seen as a simple molecular visualisation program. At the moment only molecules stored in a <a href="http://www.rcsb.org/pdb/">PDB file format</a> can be viewed.</p> <br> <hr> --- 12,16 ---- <hr> <p>Nanodesigner is a free, open source, software tools platform intended for the design of atomic structures from the ground up, atom-by-atom, molecule by molecule.</p> ! <p>Version 0.1.2 has a very limited functionality and can best be seen as a simple molecular visualisation program. At the moment only molecules stored in a PDB (http://www.rcsb.org/pdb/) and XYZ (http://openbabel.sourceforge.net/formats/xyz.shtml) file format can be viewed.</p> <br> <hr> Index: default.css =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/default.css,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** default.css 21 Jul 2005 17:09:51 -0000 1.1 --- default.css 22 Feb 2006 17:31:43 -0000 1.2 *************** *** 2,10 **** text-decoration: none } - a:visited { text-decoration: none } - a:active { text-decoration: none --- 2,8 ---- *************** *** 18,48 **** background: #ffffff } ! ! p.sign { ! font-size: 8px } ! ! p.center { ! text-align:center } ! ! p.centered-caption { ! font-size: 8px; ! text-align:center } ! h3.under { ! text-decoration: underline } ! ul.text { ! list-style-type: none } ! ol.numbered { ! list-style-type: decimal } ! td.width { ! width: 50px } --- 16,43 ---- background: #ffffff } ! p.sign ! { font-size: 8px } ! p.center ! { text-align: center } ! p.centered-caption ! { font-size: 8px; ! text-align: center } ! ul.text ! { list-style-type: none } ! td.width ! { width: 80px } ! h3.u ! { text-decoration: underline } ! h1.center ! { text-align: center } |
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From: swinnen <sw...@us...> - 2006-02-22 17:31:47
|
Update of /cvsroot/nanodesigner/HelpDocs/help/menu In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4377/HelpDocs/help/menu Modified Files: file.html help.html Log Message: Index: file.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/menu/file.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** file.html 21 Jul 2005 17:09:51 -0000 1.1 --- file.html 22 Feb 2006 17:31:43 -0000 1.2 *************** *** 4,11 **** <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> - <meta name="description" content="nanodesigner file menu items"> - <meta name="keywords" content="nanodesigner file menu items import export preferences"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.1 - All menus</title> </head> --- 4,9 ---- <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - All menus</title> </head> *************** *** 13,29 **** <h2>File menu</h2><hr> ! <p class="pref">Import PDB file...</p> <ul class="text"> ! <li>Import a molecule in the <a href="http://www.rcsb.org/pdb/">PDB format</a> and show it in the 3D canvas. At this point the PDB format is only partially supported (records ATOM, HETATM, CONECT, SEQRES, MODEL/ENDMDL and END). In case more than one model is included in the PDB file, only the first one is loaded.<br> <b>Only the bonds included in the PDB file (CONECT records) are shown at this point.</b> <p>The following bond types are supported:</p> <ul> ! <li>Single bonds ! <li>Double bonds ! <li>Triple bonds ! <li>Hydrogen bonds </ul> <p>A hydrogen bonds is shown as a dashed line. They are <b>not</b> shown in the 'space filled' display mode.<br> ! Double and triple bonds are only shown in 'balls & sticks' and 'wireframe' display mode.</p></li> </ul> --- 11,34 ---- <h2>File menu</h2><hr> ! <p class="pref">Import chemical data file...</p> ! <ul> ! <li>PDB format <ul class="text"> ! <li>Import a molecule in the PDB format (http://www.rcsb.org/pdb/) and show it in the 3D canvas. At this point the PDB format is only partially supported (records ATOM, HETATM, CONECT, SEQRES, MODEL/ENDMDL and END). In case more than one model is included in the PDB file, only the first one is loaded.<br> <b>Only the bonds included in the PDB file (CONECT) are shown at this point.</b> <p>The following bond types are supported:</p> <ul> ! <li>Single bonds</li> ! <li>Double bonds</li> ! <li>Triple bonds</li> ! <li>Hydrogen bonds</li> </ul> <p>A hydrogen bonds is shown as a dashed line. They are <b>not</b> shown in the 'space filled' display mode.<br> ! Double and triple bonds are only shown in 'balls & sticks' and 'wireframe' display mode.</p> ! </ul> ! <li>XYZ format ! <ul class="text"> ! <li>Import a molecule in the XYZ format (http://openbabel.sourceforge.net/formats/xyz.shtml) and show it in the 3D canvas. This format does not include any bond information. ! </ul> </ul> *************** *** 42,47 **** <li>The preference panel as a whole contains two buttons: <ul> ! <li>OK: apply the values of the preferences that have been changed and disposes of the panel.</li> ! <li>Cancel: disposes of the preference panel without doing anything. </ul></li> </ul> --- 47,52 ---- <li>The preference panel as a whole contains two buttons: <ul> ! <li>OK: apply the values of the preferences that have been changed and dispose of this panel.</li> ! <li>Cancel: dispose of the preference panel without doing anything. </ul></li> </ul> Index: help.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/menu/help.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** help.html 21 Jul 2005 17:09:51 -0000 1.1 --- help.html 22 Feb 2006 17:31:43 -0000 1.2 *************** *** 4,11 **** <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> - <meta name="description" content="nanodesigner help menu items"> - <meta name="keywords" content="nanodesigner help menu items contents about"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.1 - Help menu</title> </head> --- 4,9 ---- <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - Help menu</title> </head> *************** *** 14,35 **** <p class="pref">Help contents...</p> <ul class="text"> ! <li>Online documentation system enabling the user to navigate, search and display information concerning the Nanodesigner application.<br> ! <li>Included in the system are: ! <ul> ! <li>Table of contents</li> ! <li>Search facility</li> ! <li>Favorites</li> ! <li>Glossary/Index</li> ! <li>Print facility</li> ! </ul> ! </li> </ul> <p class="pref">About...</p> <ul class="text"> ! <li>Version and credits concerning Nanodesigner v0.1.1.</li> </ul> <hr> <p class="sign">The Nanodesigner development team.</p> </body> </html> --- 12,26 ---- <p class="pref">Help contents...</p> <ul class="text"> ! <li>Online help pages concerning all aspects of Nanodesigner. ! <br>Included are a full-featured search facility, favorites and an index.</li> </ul> <p class="pref">About...</p> <ul class="text"> ! <li>Version and credits about Nanodesigner v0.1.2.</li> </ul> <hr> <p class="sign">The Nanodesigner development team.</p> + </body> </html> |
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From: swinnen <sw...@us...> - 2006-02-22 17:31:47
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Update of /cvsroot/nanodesigner/HelpDocs/help/toolbox In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4377/HelpDocs/help/toolbox Modified Files: bottom.html middle.html top.html Log Message: Index: bottom.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/toolbox/bottom.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** bottom.html 21 Jul 2005 17:09:50 -0000 1.1 --- bottom.html 22 Feb 2006 17:31:42 -0000 1.2 *************** *** 4,11 **** <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> - <meta name="description" content="nanodesigner bottom panel toolboxes"> - <meta name="keywords" content="nanodesigner bottom panel toolboxes"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.1 - Bottom panel toolboxes</title> </head> --- 4,9 ---- <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - Bottom panel toolboxes</title> </head> *************** *** 18,33 **** <ul class="text"><li> <table width="100%" border="0"> ! <tr><td class="width" valign=top><img src="../images/axis.gif" width="35" height="35" alt="Show/remove axis button"></td> ! <td valign="top">Show the coordinate axis at the center of the 3D universe.<br> </td></tr> ! <tr><td valign="top"><img src="../images/center.gif" width="35" height="35" alt="Center content button"></td> ! <td valign="top">Move the center of the 3D universe to the center of the 3D canvas. This does not necessarily imply that the center of the 3D universe is shown in the canvas. It can be behind the camera.<br> </td></tr> ! <tr><td valign="top"><img src="../images/all.gif" width="35" height="35" alt="Show all button"></td> ! <td valign="top">Show the entire content of the 3D universe in the 3D canvas.<br> </td></tr> ! <tr><td valign="top"><img src="../images/xy.gif" width="35" height="35" alt="Show front button"></td> ! <td valign="top">Move the camera so that the view is perpendicular to the XY-plane (also called 'front view').<br> </td></tr> ! <tr><td valign="top"><img src="../images/xz.gif" width="35" height="35" alt="Show top button"></td> ! <td valign="top">Move the camera so that the view is perpendicular to the XZ-plane (also called 'top view').<br> </td></tr> ! <tr><td valign="top"><img src="../images/yz.gif" width="35" height="35" alt="Show right side button"></td> ! <td valign="top">Move the camera so that the view is perpendicular to the YZ-plane (also called 'side view').<br> </td></tr> </table></li></ul> --- 16,33 ---- <ul class="text"><li> <table width="100%" border="0"> ! <tr><td class="width" valign=top><img src="../images/ortho.gif" width="35" height="35" alt="Show orthographic projection"> <img src="../images/pers.gif" width="35" height="35" alt="Show perspective projection"></td> ! <td>Toggle between perspective and orthogonal projection.<br> </td></tr> ! <tr><td valign="top"><img src="../images/axis.gif" width="35" height="35" alt="Show axis"> <img src="../images/noaxis.gif" width="35" height="35" alt="Don't show axis"></td> ! <td>Show the coordinate axis at the center of the 3D universe.<br>red line ~ x-axis, green line ~ y-axis, blue line ~ z-axis<br> </td></tr> ! <tr><td valign="top" align="center"><img src="../images/center.gif" width="35" height="35" alt="Center content button"></td> ! <td>Move the center of the 3D universe to the center of the 3D canvas. This does not necessarily imply that the center itself is shown on the canvas. It can be behind the camera.<br> </td></tr> ! <tr><td valign="top" align="center"><img src="../images/all.gif" width="35" height="35" alt="Show all button"></td> ! <td>Show the entire content of the 3D universe on the 3D canvas.<br> </td></tr> ! <tr><td valign="top" align="center"><img src="../images/xy.gif" width="35" height="35" alt="Show front button"></td> ! <td>Move the camera so that the view is perpendicular to the XY-plane.<br> </td></tr> ! <tr><td valign="top" align="center"><img src="../images/xz.gif" width="35" height="35" alt="Show top button"></td> ! <td>Move the camera so that the view is perpendicular to the XZ-plane.<br> </td></tr> ! <tr><td valign="top" align="center"><img src="../images/yz.gif" width="35" height="35" alt="Show right side button"></td> ! <td>Move the camera so that the view is perpendicular to the YZ-plane.<br> </td></tr> </table></li></ul> Index: top.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/toolbox/top.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** top.html 21 Jul 2005 17:09:50 -0000 1.1 --- top.html 22 Feb 2006 17:31:42 -0000 1.2 *************** *** 3,11 **** <html> <head> ! <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> ! <meta name="description" content="nanodesigner top panel toolboxes"> ! <meta name="keywords" content="nanodesigner top panel toolboxes"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.1 - Top panel toolboxes</title> </head> --- 3,9 ---- <html> <head> ! <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - Top panel toolboxes</title> </head> *************** *** 20,24 **** <table width="100%" border="0"> <tr><td class="width" valign="top"><img src="../images/import.gif" width="35" height="35" alt="Import button"></td> ! <td>Read PDB file and show its contents on the 3D canvas.<br> </td></tr> <tr><td valign="top"><img src="../images/export.gif" width="35" height="35" alt="Export button"></td> <td>Save the content of the 3D canvas to a file in the PNG image format. The extension '.png' is added to the filename if not supplied by the user.</td></tr> --- 18,22 ---- <table width="100%" border="0"> <tr><td class="width" valign="top"><img src="../images/import.gif" width="35" height="35" alt="Import button"></td> ! <td>Read chemical data file and show its contents on the 3D canvas.<br> </td></tr> <tr><td valign="top"><img src="../images/export.gif" width="35" height="35" alt="Export button"></td> <td>Save the content of the 3D canvas to a file in the PNG image format. The extension '.png' is added to the filename if not supplied by the user.</td></tr> Index: middle.html =================================================================== RCS file: /cvsroot/nanodesigner/HelpDocs/help/toolbox/middle.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** middle.html 21 Jul 2005 17:09:50 -0000 1.1 --- middle.html 22 Feb 2006 17:31:42 -0000 1.2 *************** *** 4,11 **** <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> - <meta name="description" content="nanodesigner middle panel toolbox"> - <meta name="keywords" content="nanodesigner middle panel toolbox"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.1 - Middle panel toolboxes</title> </head> --- 4,9 ---- <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link rel="stylesheet" href="../default.css" type="text/css"> ! <title>Nanodesigner v0.1.2 - Middle panel toolboxes</title> </head> |
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From: swinnen <sw...@us...> - 2006-02-22 17:30:34
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Update of /cvsroot/nanodesigner/HelpDocs/help/images In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3811/HelpDocs/help/images Added Files: noaxis.gif ortho.gif pers.gif Log Message: --- NEW FILE: pers.gif --- (This appears to be a binary file; contents omitted.) --- NEW FILE: noaxis.gif --- (This appears to be a binary file; contents omitted.) --- NEW FILE: ortho.gif --- (This appears to be a binary file; contents omitted.) |
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From: swinnen <sw...@us...> - 2006-02-22 17:19:10
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Update of /cvsroot/nanodesigner In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29231 Modified Files: Release notes.html nanodesigner.bat Installation notes.html manifest.mf Added Files: nanodesigner.bash Log Message: Index: manifest.mf =================================================================== RCS file: /cvsroot/nanodesigner/manifest.mf,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** manifest.mf 26 Jul 2005 17:05:23 -0000 1.4 --- manifest.mf 22 Feb 2006 17:18:39 -0000 1.5 *************** *** 1,3 **** Manifest-Version: 1.0 Main-Class: org.nanodesigner.core.Init ! Class-Path: g3d.jar gui.jar jh.jar nd_help.jar \ No newline at end of file --- 1,3 ---- Manifest-Version: 1.0 Main-Class: org.nanodesigner.core.Init ! Class-Path: g3d.jar gui.jar jh.jar nd_help.jar jogl.jar vecmath.jar \ No newline at end of file Index: nanodesigner.bat =================================================================== RCS file: /cvsroot/nanodesigner/nanodesigner.bat,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** nanodesigner.bat 26 Jul 2005 17:05:54 -0000 1.3 --- nanodesigner.bat 22 Feb 2006 17:18:39 -0000 1.4 *************** *** 1,2 **** @echo off ! java -Dsun.java2d.noddraw=true -jar .\jars\core.jar \ No newline at end of file --- 1,3 ---- @echo off ! set path=%path%;%NANODESIGNER%\jars ! java -Dsun.java2d.noddraw=true -jar .\jars\core.jar Index: Release notes.html =================================================================== RCS file: /cvsroot/nanodesigner/Release notes.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Release notes.html 26 Jul 2005 17:06:50 -0000 1.1 --- Release notes.html 22 Feb 2006 17:18:39 -0000 1.2 *************** *** 1,3 **** ! <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <html> <head> --- 1,3 ---- ! <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <html> <head> *************** *** 10,48 **** h2 { font-size: 14px; ! font-weight: bold; ! border-bottom: 1px solid #808080; ! margin-top: 5px; ! margin-bottom: 5px; ! color: #D20005; ! background: #ffffff ! } ! p.center { ! text-align: center ! } ! p.centerbold { ! text-align: center; ! font-weight: bold ! } ! p.small-bold { ! font-family: serif; ! font-size: 11px; ! font-weight: bold ! } ! ul.text { ! list-style-type: none ! } --> </style> ! <title>Nanodesigner release notes 0.1.1.</title> </head> <body> ! <p class="centerbold">Nanodesigner</p> ! <p class="centerbold">Release notes version 0.1.1.</p> ! <p class="center">Last revised: July 21, 2005.</p> <h2>Contents.</h2> <blockquote> - <dl> <dt><a href="#intro">Introduction</a></dt> <dt><a href="#requirements">System requirements</a></dt> --- 10,32 ---- h2 { font-size: 14px; ! font-weight:bold; ! margin:0px; ! border-bottom:1px solid #808080; ! margin-top:5px; ! margin-bottom:5px; ! color:#D20005; ! } --> </style> ! <title>Nanodesigner 0.1.2 release notes.</title> </head> <body> ! <center><h1>Nanodesigner v0.1.2</h1> ! <h3>Release Notes.</h3><br> ! Last revised: February 20, 2006.</p></center> <h2>Contents.</h2> <blockquote> <dt><a href="#intro">Introduction</a></dt> <dt><a href="#requirements">System requirements</a></dt> *************** *** 55,134 **** <dt><a href="#documentation">Documentation</a></dt> <dt><a href="#information">More information</a></dt> - </dl> </blockquote> ! <h2><a name="intro"><b>Introduction.</b></a></h2> <p>Nanodesigner is a free, open source, software tools platform intended for the design of atomic structures from the ground up, atom-by-atom, molecule by molecule. Nanodesigner is written in the Java programming language.</p> ! <h2><a name="requirements"><b>System requirements.</b></a></h2> <ul> ! <li><a name="hardware"><b>Recommended hardware</b></a><br /> ! <ul class="text"> ! <li><b>Processor</b>: 1 GHz or higher<br> <b>Memory</b>: 256 megabytes or more<br> <b>Video card</b>: supporting OpenGL v1.2 or higher<br> <b>Virtual memory</b>: 500 megabytes or more<br> ! <b>Disk space</b>: 10 megabytes of free space</li> </ul> ! <p><a name="software"><b>Software</b></a></p> <ul> ! <li>Nanodesigner needs Java v1.5 or higher to run: ! <ul class="text"> ! <li>1. Use the <a href="http://java.sun.com/j2se/1.5.0/download.jsp">Java runtime environment (JRE) v1.5 or higher</a>, or<br> ! 2. Use the <a href="http://java.sun.com/j2se/1.5.0/download.jsp">Java development environment (J2SE) v1.5 or higher</a></li> </ul><br> ! <li>Nanodesigner uses the vecmath.jar library which is part of Java3D.<br> ! The latest releases can be found at <a href="https://java3d.dev.java.net/binary-builds.html">this location.</a><br /> </li> ! <li>Nanodesigner also needs Java bindings for OpenGL (JOGL) to run.<br> ! This release will only run using <a href="https://jogl.dev.java.net/servlets/ProjectDocumentList?folderID=2869&expandFolder=2869&folderID=0">JOGL v1.1 beta 10</a> or higher.</li> </ul> </ul> ! <h2><a name="installation"><b>Installation.</b></a></h2> ! <ul class="text"> ! <li><p><a name="windows"><b>Windows</b></a></p> ! <p>Nanodesigner has been tested on Windows2000 and WindowsXP.<br />The installation is fairly straightforward:</p> <ul> ! <li>Install a Java environment v1.5 or higher, if not already available on your system, by downloading JRE or JDK v1.5 or higher (see <a href="#software">System requirements/Software</a> above). Remember the directory where the Java environment is located. Set JAVA_HOME in case of the installation of a JDK. The JRE version is normally installed in the directory C:\Program Files\Java.<br /> </li> ! <li>Install JOGL by downloading jogl.jar and jogl-natives-win32.jar from the location mentioned in <a href="#software">System requirements/Software</a> above. <ul> ! <li>Copy jogl.jar to the directory jre1.5.x\lib\ext (or jdk1.5.x\jre\lib\ext in case only the JDK is installed).</li> ! <li>Copy the content of jogl-natives-win32.jar, i.e. the files jogl.dll and jogl_cg.dll, to the directory jre1.5.x\bin (or jdk1.5.x\jre\bin in case only the JDK is installed).</li> ! </ul><br /></li> ! <li>Extract vecmath.jar from the file java3d-1_3_x-windows-i586.zip. Inside this zip file you will find a file j3d-13x-win.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory jre1.5.x\lib\ext (or jdk1.5.x\jre\lib\ext in case only the JDK is installed).<br /> </li> ! <li>Choose a directory on the hard disk and unzip the content of Nanodesigner-0.1.1-bin.zip into this directory.</li> ! </ul><br /></li> ! <li><a name="linux"><b>Linux</b></a> ! <p>Nanodesigner has been tested on RedHat Fedora 2.</p> ! <ul> ! <li>Install a Java environment v1.5 or higher, if not already available on your system, by downloading JRE or JDK v1.5 or higher (see <a href="#software">System requirements/Software</a> above). Remember the directory where the Java environment is located.<br /> </li> ! <li>Install JOGL by downloading jogl.jar and jogl-natives-linux.jar from the location mentioned in <a href="#software">System requirements/Software</a> above. <ul> ! <li>Copy jogl.jar to the directory jre1.5.x/lib/ext (or jdk1.5.x/jre/lib/ext in case JDK is installed instead).</li> ! <li>Copy the content of jogl-natives-linux.jar, i.e. the files libjogl.so and libjogl_cg.so, to the directory /usr/lib.</li> ! </ul><br /></li> ! <li>Extract vecmath.jar from the file java3d-1_3_x-linux-i586.zip. Inside this zip file you will find a file j3d-13x-linux.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory jre1.5.x/lib/ext (or jdk1.5.x/jre/lib/ext in case a JDK is installed).<br /> </li> ! <li>Choose a directory on the hard disk and unzip the content of Nanodesigner-0.1.1-bin.zip into this directory.</li> </ul> </ul> ! <h2><a name="issues"><b>Known Issues.</b></a></h2> ! <ul class="text"> ! <li><b>Performance</b> ! <ul class="text"> ! <li>Performance largely depends on the hardware the program is running. No attempt is made yet to optimize the creation of the display lists so the size of the molecules that can be displayed is limited. Small molecules up to 1000 atoms can be displayed without a problem. Performance is best in wireframe display mode which is the default display mode. In general performance seems a bit slower on Linux than on Windows systems.</li> </ul> </ul> ! <h2><a name="documentation"><b>Documentation.</b></a></h2> ! <p>A full-featured build-in help system is included in the program starting this release. ! <h2><a name="information"><b>More information.</b></a></h2> <p>For more information, visit our website at <a href="http://www.nanodesigner.org/">www.nanodesigner.org</a>.</p> <hr> ! <p class="small-bold">The Nanodesigner development team.</p> </body> ! </html> --- 39,107 ---- <dt><a href="#documentation">Documentation</a></dt> <dt><a href="#information">More information</a></dt> </blockquote> ! <h2><a name="intro" /><b>Introduction.</b></h2> <p>Nanodesigner is a free, open source, software tools platform intended for the design of atomic structures from the ground up, atom-by-atom, molecule by molecule. Nanodesigner is written in the Java programming language.</p> ! <h2><a name="requirements" /><b>System requirements.</b></h2> <ul> ! <p><a name="hardware" /><b>Recommended hardware</b></p> ! <ul> ! <b>Processor</b>: 1 GHz or higher<br> <b>Memory</b>: 256 megabytes or more<br> <b>Video card</b>: supporting OpenGL v1.2 or higher<br> <b>Virtual memory</b>: 500 megabytes or more<br> ! <b>Disk space</b>: 10 megabytes of free space </ul> ! <p><a name="software" /><b>Software</b></p> <ul> ! <li>Nanodesigner needs Java v1.5 or higher to run:</p> ! <ul> ! 1. Use the <a href="http://java.sun.com/j2se/1.5.0/download.jsp">Java runtime environment (JRE) v1.5 or higher</a>, or<br> ! 2. Use the <a href="http://java.sun.com/j2se/1.5.0/download.jsp">Java development environment (J2SE) v1.5 or higher</a> </ul><br> ! <li>Nanodesigner uses the vecmath.jar library which is part of Java3D.<br />The latest version of vecmath (1.3.2) is included in the release.<br /> </li> ! <li>Nanodesigner also needs Java bindings for OpenGL (JOGL) libraries to run.<br />The latest version of the JOGL libraries (JSR 231 beta 2) are included in the release.</li> </ul> </ul> ! <h2><a name="installation" /><b>Installation.</b></h2> <ul> ! <p><a name="windows" /><b>Windows OS</b></p> <ul> ! <p>Nanodesigner has been tested on Windows2000, XP and XP 64bit (in WOW).<br>The installation is fairly straightforward:</p> ! <li>Install a Java environment v1.5 or higher, if not already available on your system, by downloading JRE or JDK v1.5 or higher (see <a href="#software">System requirements/Software</a> above). In case of a JDK installation put the installation directory in the environment variable $JAVA_HOME.<br> </li> ! <li>Choose a directory on your hard disk and unzip the content of Nanodesigner-0.1.2-win.zip into this directory. A subdirectory Nanodesigner-0.1.2 will be created.<br> </li> ! <li>Create the environment variable NANODESIGNER and set it to: path_to\Nanodesigner-0.1.2<br> </li> ! <li>Run the program by typing <b>nanodesigner</b> in a DOS window in the directory path_to\Nanodesigner-0.1.2, or, create a shortcut on your desktop to nanodesigner.bat in this directory.</li> ! </ul> ! <p><a name="linux" /><b>Linux distributions</b></p> <ul> ! <p>Nanodesigner has been tested on the RedHat Fedora distribution.</p> ! <li>Install a Java environment v1.5 or higher, if not already available on your system, by downloading JRE or JDK v1.5 or higher (see <a href="#software">System requirements/Software</a> above). In case of a JDK installation put the installation directory in the environment variable $JAVA_HOME.<br> </li> ! <li>Choose a directory on your hard disk and unzip the content of Nanodesigner-0.1.2-linux.zip into this directory. A subdirectory Nanodesigner-0.1.2 will be created.<br> </li> ! <li>Create the environment variable NANODESIGNER and set it to: path_to/Nanodesigner-0.1.2<br> </li> ! <li>Run the program by typing <b>nanodesigner.bash</b> in a terminal window in the directory path_to/Nanodesigner-0.1.2. </ul> </ul> ! <h2><a name="issues" /><b>Known Issues.</b></h2> ! <ul> ! <p><b>Performance</b> ! <ul> ! Performance largely depends on the hardware the program is running on. Nothing much is done towards optimization yet so the size of the molecules that can be displayed is limited. Small molecules up to a couple of 1000's of atoms can be displayed without a problem. Performance is best in wireframe display mode. In general performance seems a bit slower on Linux than on Windows systems. </ul> </ul> ! <h2><a name="documentation" /><b>Documentation.</b></h2> ! <p>A full-featured build-in help system is included in the program. ! <h2><a name="information" /><b>More information.</b></h2> <p>For more information, visit our website at <a href="http://www.nanodesigner.org/">www.nanodesigner.org</a>.</p> <hr> ! <h5>The Nanodesigner development team.</h5> </body> ! </html> \ No newline at end of file Index: Installation notes.html =================================================================== RCS file: /cvsroot/nanodesigner/Installation notes.html,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Installation notes.html 26 Jul 2005 17:07:03 -0000 1.1 --- Installation notes.html 22 Feb 2006 17:18:39 -0000 1.2 *************** *** 1,3 **** ! <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <html> <head> --- 1,3 ---- ! <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <html> <head> *************** *** 10,105 **** h2 { font-size: 14px; ! font-weight: bold; ! border-bottom: 1px solid #808080; ! margin-top: 5px; ! margin-bottom: 5px; ! color: #D20005; ! background: #ffffff ! } ! p.center { ! text-align: center ! } ! p.centerbold { ! text-align: center; ! font-weight: bold ! } ! p.small-bold { ! font-family: serif; ! font-size: 11px; ! font-weight: bold ! } ! ul.text { ! list-style-type: none ! } --> </style> ! <title>Nanodesigner version 0.1.1 installation notes.</title> </head> <body> ! <p class="centerbold">Nanodesigner</p> ! <p class="centerbold">Installation notes version 0.1.1.</p> ! <p class="center">Last revised: July 21, 2005.</p> <h2>Contents.</h2> <blockquote> - <dl> <dt><a href="#install">Installation</a></dt> <dt><a href="#compile">Compilation</a></dt> <dt><a href="#documentation">Documentation</a></dt> <dt><a href="#information">More information</a></dt> - </dl> </blockquote> ! <h2><a name="install"><b>Installation.</b></a></h2> ! <ul class="text"> ! <li>You will need to have the following software packages installed:<br /> <ul> <li><a href="http://java.sun.com/j2se/1.5.0/download.jsp">J2SE v1.5 or higher</a></li> <li><a href="http://ant.apache.org/bindownload.cgi">A recent version of Ant</a> (if you are not using an IDE that is)</li> <li><a href="http://java.sun.com/products/javahelp/download_binary.html">JavaHelp 2.x</a></li> ! <li><a href="https://jogl.dev.java.net/servlets/ProjectDocumentList?folderID=2869&expandFolder=2869&folderID=0">JOGL 1.1 beta 10</a> or higher. <p><b>Windows:</b><br /> ! Install JOGL by downloading jogl.jar and jogl-natives-win32.jar. Copy jogl.jar to the directory jdk1.5.x\jre\lib\ext. Copy the content of jogl-natives-win32.jar, i.e. the files libjogl.so and libjogl_cg.so, to the directory jdk1.5.x\jre\lib\i386.</p> <p><b>Linux:</b><br /> ! Install JOGL by downloading jogl.jar and jogl-natives-linux.jar. Copy jogl.jar to the directory jdk1.5.x/jre/lib/ext. Copy the content of jogl-natives-linux.jar, i.e. the files libjogl.so and libjogl_cg.so, to the /usr/lib directory.</p></li> ! <li><a href="https://java3d.dev.java.net/binary-builds.html">Vecmath 1.3 library</a> <p><b>Windows:</b><br /> ! Extract vecmath.jar from the file java3d-1_3_x-windows-i586.zip. Inside this zip file you will find a file j3d-13x-win.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory jdk1.5.x\jre\lib\ext.</p> <p><b>Linux:</b><br /> ! Extract vecmath.jar from the file java3d-1_3_x-linux-i586.zip. Inside this zip file you will find a file j3d-13x-linux.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory jdk1.5.x/jre/lib/ext.</p></li> </ul> ! <p>Make sure that you update your path environment variable so that the programs can run (javac, javadoc, ant and jhindexer).</p> </ul> ! <h2><a name="compile"><b>Compilation.</b></a></h2> ! <ul class="text"> ! <li><a name="windows"><b>Windows</b></a> <ul> ! <li>Open a dos window and run 'ant' in the Nanodesigner-0.1.1 directory. This command will create three jar files called core.jar, g3d.jar and gui.jar and will put thes files in Nanodesigner-0.1.1\jars. ! <li>Go to the Nanodesigner-0.1.1\HelpDocs directory and run 'jhindexer help'. This command will create the JavaHelpSearch directory. ! <li>While still in the Helpdocs directory create a jar file with the help documents by running the command 'jar -cvf nd_help.jar *'. ! <li>Copy nd_help.jar to the Nanodesigner-0.1.1\jars directory ! <li>Copy jh.jar from the JavaHelp directory (jh2.0\javahelp\lib) to the Nanodesigner-0.1.1\jars directory </ul> ! <p><a name="linux"><b>Linux</b></a></p> <ul> ! <li>Open a terminal window and run 'ant' in the Nanodesigner-0.1.1 directory. This command will create three jar files called core.jar, g3d.jar and gui.jar and put these files in the Nanodesigner-0.1.1/jars directory. ! <li>Go to the Nanodesigner-0.1.1/HelpDocs directory and run 'jhindexer help'. This command will create the JavaHelpSearch directory. ! <li>While still in the Helpdocs directory create a jar file with the help documents by running the command 'jar -cvf nd_help.jar *'. ! <li>Copy nd_help.jar to the Nanodesigner-0.1.1/jars directory ! <li>Copy jh.jar from the JavaHelp directory (jh2.0/javahelp/lib) to the Nanodesigner-0.1.1/jars directory </ul> </ul> ! <h2><a name="documentation"><b>Documentation.</b></a></h2> <p>The Nanodesigner API documents can be generated by running the ! command 'ant doc' in a dos (windows) or terminal (linux) window in the Nanodesigner-0.1.1 directory. A directory called 'api-doc' will be created with all API documentation in html format.</p> ! <h2><a name="information"><b>More information.</b></a></h2> <p>For more information, visit our website at <a href="http://www.nanodesigner.org/">www.nanodesigner.org</a>.</p> <hr> ! <p class="small-bold">The Nanodesigner development team.</p> </body> ! </html> --- 10,102 ---- h2 { font-size: 14px; ! font-weight:bold; ! margin:0px; ! border-bottom:1px solid #808080; ! margin-top:5px; ! margin-bottom:5px; ! color:#D20005; ! } --> </style> ! <title>Nanodesigner 0.1.2 installation notes</title> </head> <body> ! <center><h1>Nanodesigner v0.1.2</h1> ! <h3>Installation Notes.</h3><br> ! Last revised: February 20, 2006</center> <h2>Contents.</h2> <blockquote> <dt><a href="#install">Installation</a></dt> <dt><a href="#compile">Compilation</a></dt> + <dt><a href="#run">Run</a></dt> <dt><a href="#documentation">Documentation</a></dt> <dt><a href="#information">More information</a></dt> </blockquote> ! <h2><a name="install" /><b>Installation.</b></h2> ! <p>Download Nanodesigner-0.1.2-src.zip and unzip it in a directory of your choice. A subdirectory Nanodesigner-0.1.2 will be created.</p> ! <p>You will need to have the following software packages installed: <ul> <li><a href="http://java.sun.com/j2se/1.5.0/download.jsp">J2SE v1.5 or higher</a></li> <li><a href="http://ant.apache.org/bindownload.cgi">A recent version of Ant</a> (if you are not using an IDE that is)</li> <li><a href="http://java.sun.com/products/javahelp/download_binary.html">JavaHelp 2.x</a></li> ! <li><a href="https://jogl.dev.java.net/servlets/ProjectDocumentList?folderID=4650&expandFolder=4650&folderID=4649">JOGL JSR beta 2</a> or higher. <p><b>Windows:</b><br /> ! Install JOGL by downloading jogl.jar and jogl-natives-win32.jar. Copy jogl.jar to the directory Nanodesigner-0.1.2\jars. Copy the content of jogl-natives-win32.jar, i.e. the libraries jogl.dll, jogl_awt.dll and jogl_cg.dll, to the directory Nanodesigner-0.1.2\jars.</p> <p><b>Linux:</b><br /> ! Install JOGL by downloading jogl.jar and jogl-natives-linux.jar. Copy jogl.jar to the directory Nanodesigner-0.1.2/jars. Extract the files libjogl.so, libjogl_awt.so and libjogl_cg.so from jogl-natives-linux.jar to the Nanodesigner-0.1.2/jars directory.</p></li> ! <li><a href="https://java3d.dev.java.net/binary-builds.html">Vecmath 1.3.2 library</a> <p><b>Windows:</b><br /> ! Extract vecmath.jar from the file java3d-1_3_2-windows-i586.zip. Inside this zip file you will find a file j3d-13x-win.zip. Inside this zip file you will find vecmath.jar. Extract this file to the directory Nanodesigner-0.1.2\jars.</p> <p><b>Linux:</b><br /> ! Extract vecmath.jar from the file java3d-1_3_2-linux-i586.zip. Inside this zip file you will find a file j3d-13x-linux.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory Nanodesigner-0.1.2/jars.</p></li> </ul> ! <p>Make sure that you update your path environment variable so that the following programs can run:<br>javac, javadoc, ant and jhindexer.</p> ! ! <h2><a name="compile" /><b>Compilation.</b></h2> ! <ul> ! <p><a name="windows" /><b>Windows</b></p> ! <ul> ! <li>Open a dos window and run 'ant' in the Nanodesigner-0.1.2 directory. This command will create three jar files called core.jar, g3d.jar and gui.jar and will put these files in a jars subdirectory.</li> ! <li>Go into the HelpDocs subdirectory and run 'jhindexer help'. This command will create a JavaHelpSearch subdirectory.</li> ! <li>While still in the Helpdocs subdirectory create a jar file of the help documents and search database by running the command 'jar -cvf ..\jars\nd_help.jar *'.</li> ! <li>Copy jh.jar from the JavaHelp directory (jh2.0\javahelp\lib) to the Nanodesigner-0.1.2\jars directory</li> </ul> ! <p><a name="linux" /><b>Linux</b></p> <ul> ! <li>Open a terminal window and run 'ant' in the Nanodesigner-0.1.2 directory. This command will create three jar files called core.jar, g3d.jar and gui.jar and will put thes files in Nanodesigner-0.1.2/jars.</li> ! <li>Go to the HelpDocs directory and run 'jhindexer help'. This command will create a JavaHelpSearch subdirectory.</li> ! <li>While still in the Helpdocs subdirectory create a jar file of the help documents and search database by running the command 'jar -cvf ../jars/nd_help.jar *'.</li> ! <li>Copy jh.jar from the JavaHelp directory (jh2.0/javahelp/lib) to the Nanodesigner-0.1.2/jars directory.</li> </ul> ! </ul> ! ! <h2><a name="run" /><b>Run.</b></h2> <ul> ! <p><a name="windows" /><b>Windows</b></p> ! <ul> ! <li>Create the environment variable NANODESIGNER and set it to: path_to\Nanodesigner-0.1.2</li> ! <li>Run the program by typing <b>nanodesigner</b> in a DOS window in the directory path_to\Nanodesigner-0.1.2, or, create a shortcut on your desktop to nanodesigner.bat in this directory.</li> ! </ul> ! <p><a name="linux" /><b>Linux</b></p> ! <ul> ! <li>Create the environment variable NANODESIGNER and set it to: path_to/Nanodesigner-0.1.2</li> ! <li>Make sure <b>nanodesigner.bash</b> is executable (execute the command 'chmod +x nanodesigner.bash' if not) ! <li>Run the program by typing <b>nanodesigner.bash</b> in a terminal window in the directory path_to/Nanodesigner-0.1.2. </ul> </ul> ! <h2><a name="documentation" /><b>Documentation.</b></h2> <p>The Nanodesigner API documents can be generated by running the ! command 'ant doc' in a dos (windows) or terminal (linux) window in the Nanodesigner-0.1.2 directory. A directory called 'api-doc' will be created with all API documentation in html format.</p> ! <h2><a name="information" /><b>More information.</b></h2> <p>For more information, visit our website at <a href="http://www.nanodesigner.org/">www.nanodesigner.org</a>.</p> <hr> ! <h5>The Nanodesigner development team.</h5> </body> ! </html> \ No newline at end of file --- NEW FILE: nanodesigner.bash --- #!/bin/bash LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NANODESIGNER/jars export LD_LIBRARY_PATH java -Dsun.java2d.noddraw=true -jar ./jars/core.jar |
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From: swinnen <sw...@us...> - 2006-02-22 16:01:39
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/images In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19326/src/org/nanodesigner/gui/toolbox/images Modified Files: bpt1b5.gif bpt1b3.gif bpt1b1a.gif bpt1b6.gif bpt1b4.gif bpt1b1b.gif Added Files: bpt1b7.gif bpt1b2a.gif bpt1b2b.gif Log Message: Index: bpt1b4.gif =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/images/bpt1b4.gif,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 Binary files /tmp/cvsoZyrDn and /tmp/cvs5ee9gh differ --- NEW FILE: bpt1b2b.gif --- (This appears to be a binary file; contents omitted.) Index: bpt1b6.gif =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/images/bpt1b6.gif,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 Binary files /tmp/cvslcoQ2A and /tmp/cvsEFSH8u differ Index: bpt1b3.gif =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/images/bpt1b3.gif,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 Binary files /tmp/cvsCPVE8R and /tmp/cvsaQk2VM differ Index: bpt1b1b.gif =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/images/bpt1b1b.gif,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 Binary files /tmp/cvsIxUrj5 and /tmp/cvs6o2aK0 differ Index: bpt1b5.gif =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/images/bpt1b5.gif,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 Binary files /tmp/cvsFbIl6h and /tmp/cvs4anPle differ Index: bpt1b1a.gif =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/images/bpt1b1a.gif,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 Binary files /tmp/cvsQLcP0w and /tmp/cvswILaYt differ --- NEW FILE: bpt1b7.gif --- (This appears to be a binary file; contents omitted.) --- NEW FILE: bpt1b2a.gif --- (This appears to be a binary file; contents omitted.) |
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From: swinnen <sw...@us...> - 2006-02-22 16:00:08
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18265/src/org/nanodesigner/gui/toolbox Modified Files: ParallelCmd.java CentreCmd.java ShortcutBttns.java AxisCmd.java GlobalBttns.java Log Message: Index: CentreCmd.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/CentreCmd.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** CentreCmd.java 13 Apr 2005 16:07:26 -0000 1.1 --- CentreCmd.java 22 Feb 2006 15:59:55 -0000 1.2 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Mar 15, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Dec 8, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 24,28 **** import org.nanodesigner.g3d.*; - import org.nanodesigner.gui.*; import org.nanodesigner.gui.menu.*; --- 24,27 ---- *************** *** 38,40 **** renderer.getButtonHandler().setCentre(); } ! } --- 37,39 ---- renderer.getButtonHandler().setCentre(); } ! } \ No newline at end of file Index: ParallelCmd.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/ParallelCmd.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** ParallelCmd.java 13 Apr 2005 16:07:26 -0000 1.1 --- ParallelCmd.java 22 Feb 2006 15:59:55 -0000 1.2 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Mar 11, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Dec 8, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 23,27 **** package org.nanodesigner.gui.toolbox; - import org.nanodesigner.gui.*; import org.nanodesigner.gui.menu.*; import org.nanodesigner.g3d.*; --- 23,26 ---- Index: AxisCmd.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/AxisCmd.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** AxisCmd.java 21 Jul 2005 16:57:08 -0000 1.2 --- AxisCmd.java 22 Feb 2006 15:59:55 -0000 1.3 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 20, 2005 * * Copyright © 2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Dec 20, 2005 * * Copyright © 2005, The Nanodesigner Development Team *************** *** 27,31 **** /** ! * Toggles coordinate axis. */ public class AxisCmd implements Command { --- 27,31 ---- /** ! * Toggles axis on/off. */ public class AxisCmd implements Command { *************** *** 38,42 **** public void execute() { ! renderer.getOGLStructure().toggleCoordinateAxis(); renderer.getDrawable().display(); } --- 38,42 ---- public void execute() { ! renderer.getOGLStructure().toggleCoordinateAxis(); renderer.getDrawable().display(); } Index: GlobalBttns.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/GlobalBttns.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** GlobalBttns.java 13 Apr 2005 16:07:26 -0000 1.1 --- GlobalBttns.java 22 Feb 2006 15:59:55 -0000 1.2 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Mar 11, 2005 * * Copyright © 2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Dec 8, 2005 * * Copyright © 2005, The Nanodesigner Development Team *************** *** 27,31 **** import java.awt.*; import java.awt.event.*; - import javax.swing.*; import java.net.*; --- 27,30 ---- *************** *** 99,101 **** public void mouseReleased(MouseEvent e) { } ! } --- 98,100 ---- public void mouseReleased(MouseEvent e) { } ! } \ No newline at end of file Index: ShortcutBttns.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/ShortcutBttns.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** ShortcutBttns.java 21 Jul 2005 16:57:08 -0000 1.3 --- ShortcutBttns.java 22 Feb 2006 15:59:55 -0000 1.4 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 20, 2005 * * Copyright © 2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Dec 20, 2005 * * Copyright © 2005, The Nanodesigner Development Team *************** *** 34,38 **** public class ShortcutBttns extends JPanel implements ActionListener, MouseListener { private ButtonCommand button[]; ! private String tooltext[] = {"Import PDB file", "Export PNG image"}; /** Creates a new instance of MenuShorts */ --- 34,38 ---- public class ShortcutBttns extends JPanel implements ActionListener, MouseListener { private ButtonCommand button[]; ! private String tooltext[] = {"Import chemical data file", "Export PNG image"}; /** Creates a new instance of MenuShorts */ |
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From: swinnen <sw...@us...> - 2006-02-22 15:59:41
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18142/src/org/nanodesigner/gui/toolbox Added Files: ProjectionCmd.java Log Message: Toggle between orthograpic and perspective projection --- NEW FILE: ProjectionCmd.java --- (This appears to be a binary file; contents omitted.) |
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From: swinnen <sw...@us...> - 2006-02-22 15:58:21
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17425/src/org/nanodesigner/gui/toolbox Modified Files: ChangeViewBttns.java Log Message: Added projection button Index: ChangeViewBttns.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/toolbox/ChangeViewBttns.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** ChangeViewBttns.java 14 May 2005 07:31:32 -0000 1.2 --- ChangeViewBttns.java 22 Feb 2006 15:58:16 -0000 1.3 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.2 ! * @date May 10, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jan 26, 2006 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 27,42 **** import javax.swing.*; import java.net.*; import org.nanodesigner.g3d.*; import org.nanodesigner.gui.*; - import org.nanodesigner.gui.io.*; import org.nanodesigner.gui.menu.*; public class ChangeViewBttns extends JPanel implements ActionListener, MouseListener { private ButtonCommand button[]; ! private Icon axisOn, axisOff; private boolean cBox[] = {false, false}; private String tooltext[] = { ! "", "", "Show coordinate axis", "Hide coordinate axis", "Move origin of the 3D universe to the center of the 3D canvas", "Zoom towards a global view", --- 27,44 ---- import javax.swing.*; import java.net.*; + import java.util.prefs.Preferences; + import org.nanodesigner.core.*; import org.nanodesigner.g3d.*; import org.nanodesigner.gui.*; import org.nanodesigner.gui.menu.*; public class ChangeViewBttns extends JPanel implements ActionListener, MouseListener { private ButtonCommand button[]; ! private Icon axisOn, axisOff, perspectiveOn, perspectiveOff; ! private Preferences prefs; private boolean cBox[] = {false, false}; private String tooltext[] = { ! "Perspective projection", "Orthographic projection", "Show coordinate axis", "Hide coordinate axis", "Move origin of the 3D universe to the center of the 3D canvas", "Zoom towards a global view", *************** *** 45,53 **** /** Creates a new instance of ChangeView */ public ChangeViewBttns(OGLRenderer renderer) { ! button = new ButtonCommand[7]; setLayout(new FlowLayout(FlowLayout.CENTER, 2, 2)); // Filler filler(); ! // Checkbox button[1] = new ButtonCommand(); button[1].setPreferredSize(new Dimension(35, 35)); --- 47,59 ---- /** Creates a new instance of ChangeView */ public ChangeViewBttns(OGLRenderer renderer) { ! button = new ButtonCommand[8]; setLayout(new FlowLayout(FlowLayout.CENTER, 2, 2)); + prefs = Preference.getG3DPrefs(); + // Type of projection preference handling + cBox[0] = prefs.getBoolean(Defines.PERSPECTIVE_PROJECTION, Defines.PERSPECTIVE_PROJECTION_DEF); + // Filler filler(); ! // Toggle orthograpic/perspective projection button[1] = new ButtonCommand(); button[1].setPreferredSize(new Dimension(35, 35)); *************** *** 55,84 **** button[1].addMouseListener(this); add(button[1]); ! axisOn = createImageIcon("images/bpt1b1a.gif"); ! axisOff = createImageIcon("images/bpt1b1b.gif"); ! button[1].setIcon(axisOn); ! button[1].setCommand(new AxisCmd(renderer)); // Normal buttons ! for(int i = 2; i < 7; i++) { button[i] = new ButtonCommand(); button[i].setPreferredSize(new Dimension(35, 35)); button[i].addActionListener(this); button[i].addMouseListener(this); ! if(i==4) // Filler filler(); add(button[i]); } ! button[2].setCommand(new CentreCmd(renderer)); ! button[2].setIcon(createImageIcon("images/bpt1b2.gif")); ! button[3].setCommand(new FullViewCmd(renderer)); button[3].setIcon(createImageIcon("images/bpt1b3.gif")); ! button[4].setCommand(new ParallelCmd(renderer, 1)); button[4].setIcon(createImageIcon("images/bpt1b4.gif")); ! button[5].setCommand(new ParallelCmd(renderer, 2)); button[5].setIcon(createImageIcon("images/bpt1b5.gif")); ! button[6].setCommand(new ParallelCmd(renderer, 3)); button[6].setIcon(createImageIcon("images/bpt1b6.gif")); } --- 61,103 ---- button[1].addMouseListener(this); add(button[1]); + perspectiveOn = createImageIcon("images/bpt1b1a.gif"); + perspectiveOff = createImageIcon("images/bpt1b1b.gif"); + if(cBox[0]) + button[1].setIcon(perspectiveOff); + else + button[1].setIcon(perspectiveOn); + button[1].setCommand(new ProjectionCmd(renderer)); + // Toggle axis on/off + button[2] = new ButtonCommand(); + button[2].setPreferredSize(new Dimension(35, 35)); + button[2].addActionListener(this); + button[2].addMouseListener(this); + add(button[2]); ! axisOn = createImageIcon("images/bpt1b2a.gif"); ! axisOff = createImageIcon("images/bpt1b2b.gif"); ! button[2].setIcon(axisOff); ! button[2].setCommand(new AxisCmd(renderer)); // Normal buttons ! for(int i = 3; i < 8; i++) { button[i] = new ButtonCommand(); button[i].setPreferredSize(new Dimension(35, 35)); button[i].addActionListener(this); button[i].addMouseListener(this); ! if(i==5) // Filler filler(); add(button[i]); } ! button[3].setCommand(new CentreCmd(renderer)); button[3].setIcon(createImageIcon("images/bpt1b3.gif")); ! button[4].setCommand(new FullViewCmd(renderer)); button[4].setIcon(createImageIcon("images/bpt1b4.gif")); ! button[5].setCommand(new ParallelCmd(renderer, 1)); button[5].setIcon(createImageIcon("images/bpt1b5.gif")); ! button[6].setCommand(new ParallelCmd(renderer, 2)); button[6].setIcon(createImageIcon("images/bpt1b6.gif")); + button[7].setCommand(new ParallelCmd(renderer, 3)); + button[7].setIcon(createImageIcon("images/bpt1b7.gif")); } *************** *** 88,92 **** public void filler() { JLabel label = new JLabel(); ! label.setPreferredSize(new Dimension(35, 35)); add(label); } --- 107,111 ---- public void filler() { JLabel label = new JLabel(); ! label.setPreferredSize(new Dimension(15, 15)); add(label); } *************** *** 106,110 **** } } - /** --- 125,128 ---- *************** *** 123,127 **** for(int i = 0; i < 2; i++) { ! if(obj == button[i]) { if(cBox[i]) MessageBar.setText(tooltext[i * 2 + 1]); --- 141,145 ---- for(int i = 0; i < 2; i++) { ! if(obj == button[i + 1]) { if(cBox[i]) MessageBar.setText(tooltext[i * 2 + 1]); *************** *** 132,136 **** for(int i = 4; i < 9; i++) { ! if(obj == button[i - 2]) MessageBar.setText(tooltext[i]); } --- 150,154 ---- for(int i = 4; i < 9; i++) { ! if(obj == button[i - 1]) MessageBar.setText(tooltext[i]); } *************** *** 143,151 **** public void mousePressed(MouseEvent e) { Object obj = e.getSource(); if(obj == button[1]) { ! if(cBox[1]) ! button[1].setIcon(axisOn); ! else ! button[1].setIcon(axisOff); cBox[1] = !cBox[1]; } --- 161,185 ---- public void mousePressed(MouseEvent e) { Object obj = e.getSource(); + if(obj == button[1]) { ! if(cBox[0]) { ! button[1].setIcon(perspectiveOn); ! MessageBar.setText(tooltext[0]); ! } ! else { ! button[1].setIcon(perspectiveOff); ! MessageBar.setText(tooltext[1]); ! } ! cBox[0] = !cBox[0]; ! } ! if(obj == button[2]) { ! if(cBox[1]) { ! button[2].setIcon(axisOff); ! MessageBar.setText(tooltext[2]); ! } ! else { ! button[2].setIcon(axisOn); ! MessageBar.setText(tooltext[3]); ! } cBox[1] = !cBox[1]; } |
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From: swinnen <sw...@us...> - 2006-02-22 15:56:28
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/model In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16621/src/org/nanodesigner/gui/model Modified Files: DisplayMode.java ChemObject.java Bond.java Structure.java Atom.java Log Message: Index: ChemObject.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/model/ChemObject.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** ChemObject.java 18 Dec 2004 15:31:44 -0000 1.1 --- ChemObject.java 22 Feb 2006 15:56:23 -0000 1.2 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Nov 2, 2004 * ! * Copyright © 2004, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Sep 8, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 23,28 **** package org.nanodesigner.gui.model; - import java.io.*; - public class ChemObject extends AbstractProperty { private String objectIdentifier; --- 23,26 ---- Index: DisplayMode.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/model/DisplayMode.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** DisplayMode.java 20 Jan 2005 16:28:24 -0000 1.1 --- DisplayMode.java 22 Feb 2006 15:56:23 -0000 1.2 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Jan 19, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Dec 19, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 27,30 **** --- 27,31 ---- * NONE - No display mode at this level<br> * SPACEFILL - CPK mode<br> + * TRANSPARANT - Transparant CPK mode<br> * B_AND_S - Atoms are represented as spheres, bonds as cylinders<br> * STICKS - Bonds are represented as cylinders, atoms are represented as caps of cylinders<br> *************** *** 32,34 **** * BLOB - collection of a number of atoms represented as a solid volume */ ! public enum DisplayMode {NONE, SPACEFILL, B_AND_S, STICKS, WIREFRAME, BLOB}; \ No newline at end of file --- 33,35 ---- * BLOB - collection of a number of atoms represented as a solid volume */ ! public enum DisplayMode {NONE, SPACEFILL, TRANSPARANT, B_AND_S, STICKS, WIREFRAME, BLOB}; \ No newline at end of file Index: Atom.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/model/Atom.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** Atom.java 13 Apr 2005 15:58:13 -0000 1.3 --- Atom.java 22 Feb 2006 15:56:23 -0000 1.4 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.3 ! * @date Apr 10, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Sep 8, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 23,27 **** package org.nanodesigner.gui.model; - import java.io.*; import java.util.*; import javax.vecmath.*; --- 23,26 ---- *************** *** 29,33 **** public class Atom extends ChemObject { private int elementNumber; - private boolean solvent = false; private Vector3d location = null; private Vector<Integer> bondedToAtom; --- 28,31 ---- Index: Structure.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/model/Structure.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** Structure.java 21 Jul 2005 16:58:10 -0000 1.6 --- Structure.java 22 Feb 2006 15:56:23 -0000 1.7 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 8, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Jan 26, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 41,45 **** // Hashtable with orientation of each group public int groupCounter = 1; ! protected DisplayMode dMode = DisplayMode.WIREFRAME; protected Group activeGroup = null; private Logger logger; --- 41,45 ---- // Hashtable with orientation of each group public int groupCounter = 1; ! protected DisplayMode dMode = DisplayMode.NONE; protected Group activeGroup = null; private Logger logger; *************** *** 48,51 **** --- 48,54 ---- // Coordinates should be in nm. protected double boundingBox[]; + // Radius of bounding sphere of structure + // Default radius in case no molecule is shown but the three axis' + private double radiusOfBoundingSphere = 1.0; // Maximum size of the coordinate axis found from the bounding box protected float axisSize = 0.1f; *************** *** 86,90 **** ChemFileLoader readFile = new ChemFileLoader(filename); MessageBar.setText("Importing datafile: " + filename); ! readFile.read(); // Remove group from hashtable (only temporary for version 0.1) groups.remove(groupCounter); --- 89,103 ---- ChemFileLoader readFile = new ChemFileLoader(filename); MessageBar.setText("Importing datafile: " + filename); ! ! readFile.read (); ! ! // Depending on the existence of bonds set DisplayMode to: ! if(activeGroup.getAllBonds().isEmpty()) ! // No bonds in group ! activeGroup.setDisplayMode(DisplayMode.SPACEFILL); ! else ! // Some/all bonds are listed in this group ! activeGroup.setDisplayMode(DisplayMode.WIREFRAME); ! // Remove group from hashtable (only temporary for version 0.1) groups.remove(groupCounter); *************** *** 136,140 **** } ! /* * Updates the bounding box of the entire structure after loading a group. */ --- 149,153 ---- } ! /** * Updates the bounding box of the entire structure after loading a group. */ *************** *** 144,147 **** --- 157,161 ---- Arrays.fill(boundingBox, 0.0f); + radiusOfBoundingSphere = 0.0; axisSize = 0.0f; *************** *** 161,166 **** for(int i = 0; i < 6; i++) axisSize = (float)Math.max(axisSize, Math.abs(boundingBox[i])); ! if(Globals.debug) ! System.out.println("Size of axis = " + axisSize); } --- 175,198 ---- for(int i = 0; i < 6; i++) axisSize = (float)Math.max(axisSize, Math.abs(boundingBox[i])); ! ! if(Globals.debug) ! System.out.println("Size of axis = " + axisSize); ! ! // Calculate radius of bounding sphere (needed to calculate far clipping plane(zFar)) ! for(int i = 0; i < 3; i++){ ! radiusOfBoundingSphere += (boundingBox[i+3] - boundingBox[i]) * (boundingBox[i+3] - boundingBox[i]); ! } ! radiusOfBoundingSphere /= 4.0; ! ! if(Globals.debug) ! System.out.println("Radius of bounding sphere = " + radiusOfBoundingSphere); ! } ! ! /** ! * Get radius of bounding sphere ! * @return the radius of the sphere ! */ ! public double getRadiusOfBoundingSphere() { ! return radiusOfBoundingSphere; } *************** *** 195,199 **** * depending on the extension of the file to be read. */ ! private class ChemFileLoader { private String fname; private ChemDataReader reader; --- 227,231 ---- * depending on the extension of the file to be read. */ ! private class ChemFileLoader extends Thread { private String fname; private ChemDataReader reader; *************** *** 231,238 **** * @return the Group instance */ ! private void read() { ! reader.open(fname); ! activeGroup = reader.read(); ! reader.close(); MessageBar.setDefaultText(); if(Globals.debug) --- 263,271 ---- * @return the Group instance */ ! public void read() { ! reader.open(fname); ! activeGroup = reader.read(); ! reader.close(); ! MessageBar.setDefaultText(); if(Globals.debug) *************** *** 240,242 **** } } ! } --- 273,275 ---- } } ! } \ No newline at end of file Index: Bond.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/model/Bond.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** Bond.java 13 Apr 2005 15:58:40 -0000 1.3 --- Bond.java 22 Feb 2006 15:56:23 -0000 1.4 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.3 ! * @date Apr 8, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Dec 8, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 23,27 **** package org.nanodesigner.gui.model; - import java.io.*; import javax.vecmath.*; --- 23,26 ---- |
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From: swinnen <sw...@us...> - 2006-02-22 15:54:38
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/menu In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15624/src/org/nanodesigner/gui/menu Modified Files: NDMenu.java ImportCmd.java Log Message: Index: NDMenu.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/menu/NDMenu.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** NDMenu.java 21 Jul 2005 16:52:30 -0000 1.6 --- NDMenu.java 22 Feb 2006 15:54:35 -0000 1.7 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 12, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Dec 6, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 50,54 **** this.designer = designer; ! // Initialize logger logger = Logger.getLogger(NDMenu.class.getName()); logger.addHandler(Environment.getLogFileHandler()); --- 50,54 ---- this.designer = designer; ! // Initialize logger logger = Logger.getLogger(NDMenu.class.getName()); logger.addHandler(Environment.getLogFileHandler()); *************** *** 85,89 **** // Import menu item ! importItem = new MenuCommand("Import PDB file..."); importItem.setCommand(new ImportCmd(designer.getRenderer())); importItem.addActionListener(this); --- 85,89 ---- // Import menu item ! importItem = new MenuCommand("Import data file..."); importItem.setCommand(new ImportCmd(designer.getRenderer())); importItem.addActionListener(this); Index: ImportCmd.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/menu/ImportCmd.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** ImportCmd.java 14 May 2005 07:23:20 -0000 1.3 --- ImportCmd.java 22 Feb 2006 15:54:35 -0000 1.4 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Nov 23, 2004 * ! * Copyright © 2004, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Dec 6, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 27,31 **** import org.nanodesigner.core.*; - import org.nanodesigner.gui.*; import org.nanodesigner.gui.io.*; import org.nanodesigner.g3d.*; --- 27,30 ---- *************** *** 59,61 **** } } ! } --- 58,60 ---- } } ! } \ No newline at end of file |
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From: swinnen <sw...@us...> - 2006-02-22 15:52:40
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/io In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14662/src/org/nanodesigner/gui/io Modified Files: PictureIO.java PDBReader.java ChemDataReader.java ImageFilter.java Log Message: Index: ImageFilter.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/io/ImageFilter.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** ImageFilter.java 14 May 2005 07:22:31 -0000 1.1 --- ImageFilter.java 22 Feb 2006 15:52:32 -0000 1.2 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Apr 15, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Dec 8, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 23,27 **** package org.nanodesigner.gui.io; - import javax.swing.*; import javax.swing.filechooser.*; import java.io.File; --- 23,26 ---- Index: PictureIO.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/io/PictureIO.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** PictureIO.java 14 May 2005 07:22:31 -0000 1.1 --- PictureIO.java 22 Feb 2006 15:52:32 -0000 1.2 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date April 14, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Nov 29, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 25,33 **** import java.awt.image.*; import javax.swing.*; ! import javax.imageio.ImageIO; ! import java.net.*; import java.io.*; ! import net.java.games.jogl.*; import org.nanodesigner.core.*; --- 25,34 ---- import java.awt.image.*; import javax.swing.*; ! import javax.imageio.*; ! import java.nio.*; import java.io.*; ! import javax.media.opengl.*; ! import com.sun.opengl.utils.*; import org.nanodesigner.core.*; *************** *** 39,52 **** /** ! * Capture 3D canvas picture. ! * @param drawable the reference to the GLDrawable */ ! public void capture(GLDrawable drawable) { ! GL gl = drawable.getGL(); ! // read pixels from canvas ! int width = drawable.getSize().width; ! int height = drawable.getSize().height; ! int[] raw = new int[width * height]; BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB); --- 40,57 ---- /** ! * Capture 3D canvas image. ! * @param drawable the reference to the GLAutoDrawable */ ! public void capture(GLAutoDrawable drawable) { ! int width, height, imageSize; ! int[] arr; ! ! GL gl = drawable.getGL(); // read pixels from canvas ! width = drawable.getWidth(); ! height = drawable.getHeight(); ! imageSize = width * height; ! arr = new int[imageSize]; ! IntBuffer raw = BufferUtils.newIntBuffer(imageSize); BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB); *************** *** 58,64 **** convertImageData(width, height, raw); ! image.setRGB(0, 0, width, height, raw, 0, width); saveImage(image); ! } /** --- 63,70 ---- convertImageData(width, height, raw); ! raw.get(arr, 0, imageSize); ! image.setRGB(0, 0, width, height, arr, 0, width); saveImage(image); ! } /** *************** *** 69,73 **** * @param rawData the canvas data in RGBA format */ ! private static void convertImageData(int width, int height, int[] rawData) { int tempStore, top, bottom; --- 75,79 ---- * @param rawData the canvas data in RGBA format */ ! private static void convertImageData(int width, int height, IntBuffer rawData) { int tempStore, top, bottom; *************** *** 76,82 **** top = y1 * width + x; bottom = y2 * width + x; ! tempStore = rawData[top]; ! rawData[top] = rawData[bottom] >>> 8; ! rawData[bottom] = tempStore >>> 8; } } --- 82,88 ---- top = y1 * width + x; bottom = y2 * width + x; ! tempStore = rawData.get(top); ! rawData.put(top, rawData.get(bottom) >>> 8); ! rawData.put(bottom, tempStore >>> 8); } } *************** *** 88,92 **** */ public void saveImage(BufferedImage image) { - File outputFile; String filename, pngExtension = ".png"; JFileChooser chooser = new JFileChooser(); --- 94,97 ---- Index: ChemDataReader.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/io/ChemDataReader.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** ChemDataReader.java 18 Dec 2004 15:22:46 -0000 1.1 --- ChemDataReader.java 22 Feb 2006 15:52:32 -0000 1.2 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Dec 10, 2004 * ! * Copyright © 2004, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jan 30, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 23,34 **** package org.nanodesigner.gui.io; import org.nanodesigner.gui.model.*; /** ! * Interface for all chemical data file readers */ ! public interface ChemDataReader { ! public void open(String fn); ! public Group read(); ! public void close(); } \ No newline at end of file --- 23,76 ---- package org.nanodesigner.gui.io; + import java.io.*; + import java.util.logging.*; + + import org.nanodesigner.core.*; import org.nanodesigner.gui.model.*; /** ! * Open/close for all chemical data file readers */ ! public abstract class ChemDataReader { ! protected Logger logger; ! private String fname; ! protected Group newGroup; ! protected BufferedReader input; ! ! public ChemDataReader(){ ! newGroup = new Group(); ! logger = Logger.getLogger(PDBReader.class.getName()); ! logger.addHandler(Environment.getLogFileHandler()); ! } ! ! /** ! * Open chemical data file. Create a data stream. ! */ ! public void open(String filename){ ! fname = filename; ! try { ! input = new BufferedReader(new FileReader(fname)); ! } catch(FileNotFoundException fnfe) { ! logger.warning("File " + filename + " not found.\n"); ! } ! } ! ! /** ! * Read data from chemical data file ! * @return Group data structure, contains all data in chemical data file ! */ ! public Group read(){ ! return newGroup; ! } ! ! /** ! * Close input stream ! */ ! public void close(){ ! try { ! input.close(); ! } catch(IOException ioe) { ! logger.warning("IO exception while closing file " + fname); ! } ! } } \ No newline at end of file Index: PDBReader.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/io/PDBReader.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** PDBReader.java 14 May 2005 07:22:31 -0000 1.3 --- PDBReader.java 22 Feb 2006 15:52:32 -0000 1.4 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.0.3 ! * @date May 12, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jan 30, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 24,32 **** import javax.swing.*; - import java.io.*; import java.util.*; - import java.util.logging.*; - import org.nanodesigner.core.*; import org.nanodesigner.gui.model.*; --- 24,29 ---- *************** *** 34,42 **** * Read a PDB file and create a Group object with its data content. */ ! public class PDBReader implements ChemDataReader { // Maximum number of entries (atoms) in a pdb file is 99999. private final int OHT = 100000; private final String BLANC = new String(" "); - private BufferedReader input; /* * List of bonds. --- 31,38 ---- * Read a PDB file and create a Group object with its data content. */ ! public class PDBReader extends ChemDataReader { // Maximum number of entries (atoms) in a pdb file is 99999. private final int OHT = 100000; private final String BLANC = new String(" "); /* * List of bonds. *************** *** 46,52 **** */ private Hashtable<Integer, Integer> numberOfBonds; ! private Logger logger; ! private Group newGroup; ! private String fname, line; private boolean hasBonds, seqIsPresent = false, oldFormat = false, firstAtomEntry = true; private boolean noChainName = false; --- 42,46 ---- */ private Hashtable<Integer, Integer> numberOfBonds; ! private String /*fname,*/ line; private boolean hasBonds, seqIsPresent = false, oldFormat = false, firstAtomEntry = true; private boolean noChainName = false; *************** *** 55,74 **** /** Creates a new instance of PDBReader */ public PDBReader() { - newGroup = new Group(); numberOfBonds = new Hashtable<Integer, Integer> (); - logger = Logger.getLogger(PDBReader.class.getName()); - logger.addHandler(Environment.getLogFileHandler()); - } - - /** - * Open PDB file. Creation of a data stream. - */ - public void open(String filename) { - fname = filename; - try { - input = new BufferedReader(new InputStreamReader(new FileInputStream(fname))); - } catch(FileNotFoundException fnfe) { - logger.warning("File " + filename + " not found.\n"); - } } --- 49,53 ---- *************** *** 78,88 **** */ public Group read() { - Atom atom; String recordName, remarks = ""; hasBonds = false; try { ! while((line = new String(input.readLine().trim())) != null) { ! lineLength = line.length(); if(lineLength > 6) recordName = line.substring(0, 6).toUpperCase(); --- 57,66 ---- */ public Group read() { String recordName, remarks = ""; hasBonds = false; try { ! while((line = input.readLine().trim()) != null) { ! lineLength = line.length(); if(lineLength > 6) recordName = line.substring(0, 6).toUpperCase(); *************** *** 105,111 **** if(recordName.equals("HEADER") || recordName.equals("COMPND") || recordName.equals("SOURCE") || recordName.contains("TITLE") || ! recordName.equals("FTNOTE") || recordName.equals("REVDAT") || recordName.equals("KEYWDS") || recordName.equals("EXPDTA") || ! recordName.equals("AUTHOR") || recordName.equals("REMARK")) { remarks = remarks + line.substring(6, line.length()).trim() + "\n"; continue; --- 83,91 ---- if(recordName.equals("HEADER") || recordName.equals("COMPND") || recordName.equals("SOURCE") || recordName.contains("TITLE") || ! recordName.equals("REMARK") || recordName.equals("REVDAT") || recordName.equals("KEYWDS") || recordName.equals("EXPDTA") || ! recordName.equals("CAVEAT") || recordName.equals("SPRSDE") || ! recordName.equals("AUTHOR") || recordName.equals("JRNL ") || ! recordName.equals("FTNOTE")) { remarks = remarks + line.substring(6, line.length()).trim() + "\n"; continue; *************** *** 146,150 **** */ private void readAtomData() { ! String atomSymbol, chainID, resName; Atom atom = new Atom(); --- 126,130 ---- */ private void readAtomData() { ! String chainID, resName; Atom atom = new Atom(); *************** *** 154,160 **** atomSerialNumberInFile = Integer.parseInt(line.substring(6, 11).trim()); // Atom co-ordinates in nanometer (nm) ! atom.setLocation(Double.parseDouble(line.substring(30, 38).trim()) / 10, ! Double.parseDouble(line.substring(38, 46).trim()) / 10, ! Double.parseDouble(line.substring(46, 54).trim()) / 10); // Extract residue name, number and insertion code --- 134,140 ---- atomSerialNumberInFile = Integer.parseInt(line.substring(6, 11).trim()); // Atom co-ordinates in nanometer (nm) ! atom.setLocation(Double.parseDouble(line.substring(30, 38).trim()) / 10.0, ! Double.parseDouble(line.substring(38, 46).trim()) / 10.0, ! Double.parseDouble(line.substring(46, 54).trim()) / 10.0); // Extract residue name, number and insertion code *************** *** 201,211 **** if(firstAtomEntry) { if(lineLength >= 78) { ! elementSymbol = line.substring(76, 78).trim(); ! try { ! Integer tmp = Integer.valueOf(elementSymbol); ! } ! catch(NumberFormatException nfe) { ! oldFormat = true; ! } } else --- 181,186 ---- if(firstAtomEntry) { if(lineLength >= 78) { ! if(line.substring(76, 78).trim().length() == 0) ! oldFormat = true; } else *************** *** 213,216 **** --- 188,192 ---- } + if(oldFormat) { elementSymbol = line.substring(12, 14).trim(); *************** *** 319,332 **** newGroup.getAtom(second).addBond(Structure.bondID); } ! ! /** ! * Close input stream ! */ ! public void close() { ! try { ! input.close(); ! } catch(IOException ioe) { ! logger.warning("IO exception while closing file " + fname); ! } ! } ! } --- 295,297 ---- newGroup.getAtom(second).addBond(Structure.bondID); } ! } \ No newline at end of file |
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From: swinnen <sw...@us...> - 2006-02-22 15:52:13
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/io In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14569/src/org/nanodesigner/gui/io Added Files: XYZReader.java Log Message: Support for XYZ chemical data file format --- NEW FILE: XYZReader.java --- (This appears to be a binary file; contents omitted.) |
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From: swinnen <sw...@us...> - 2006-02-22 15:51:33
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/io In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14072/src/org/nanodesigner/gui/io Modified Files: LoadGroupFilter.java Log Message: Added filter for xyz extentions Index: LoadGroupFilter.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/io/LoadGroupFilter.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** LoadGroupFilter.java 14 May 2005 07:22:31 -0000 1.1 --- LoadGroupFilter.java 22 Feb 2006 15:51:22 -0000 1.2 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Apr 15, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Dec 8, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 23,27 **** package org.nanodesigner.gui.io; - import javax.swing.*; import javax.swing.filechooser.*; import java.io.File; --- 23,26 ---- *************** *** 39,43 **** String extension = getExtension(file); if (extension != null) { ! if(extension.equals("pdb")) { return true; } --- 38,42 ---- String extension = getExtension(file); if (extension != null) { ! if(extension.equals("pdb") || extension.equals("xyz")) { return true; } *************** *** 69,73 **** */ public String getDescription() { ! return "PDB files"; } } \ No newline at end of file --- 68,72 ---- */ public String getDescription() { ! return "Chemical data files"; } } \ No newline at end of file |
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From: swinnen <sw...@us...> - 2006-02-22 15:49:41
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Update of /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12892/src/org/nanodesigner/gui Modified Files: CorePrefsPanel.java About.java Designer.java Log Message: Index: About.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/About.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** About.java 21 Jul 2005 16:55:31 -0000 1.2 --- About.java 22 Feb 2006 15:49:37 -0000 1.3 *************** *** 1,8 **** /* * @author Kiandi Wangsa ! * @version 0.1 ! * @date Jul 20, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,9 ---- /* * @author Kiandi Wangsa ! * @co-author Valère Swinnen ! * @version 0.1.1 ! * @date Jan 30, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 47,54 **** jTextField4 = new javax.swing.JTextField(); jTextField5 = new javax.swing.JTextField(); - jPanel2 = new javax.swing.JPanel(); - jScrollPane1 = new javax.swing.JScrollPane(); - jTextPane1 = new javax.swing.JTextPane(); - jButton2 = new javax.swing.JButton(); jPanel3 = new javax.swing.JPanel(); jTextField1 = new javax.swing.JTextField(); --- 48,51 ---- *************** *** 81,85 **** jTextField2.setFont(new java.awt.Font("Tahoma", 0, 18)); jTextField2.setHorizontalAlignment(javax.swing.JTextField.CENTER); ! jTextField2.setText("Copyright © 2004-2005"); jTextField2.setBorder(null); gridBagConstraints = new java.awt.GridBagConstraints(); --- 78,82 ---- jTextField2.setFont(new java.awt.Font("Tahoma", 0, 18)); jTextField2.setHorizontalAlignment(javax.swing.JTextField.CENTER); ! jTextField2.setText("Copyright © 2004-2006"); jTextField2.setBorder(null); gridBagConstraints = new java.awt.GridBagConstraints(); *************** *** 118,122 **** jTextField5.setFont(new java.awt.Font("Tahoma", 1, 24)); jTextField5.setHorizontalAlignment(javax.swing.JTextField.CENTER); ! jTextField5.setText("Nanodesigner v0.1.1"); jTextField5.setBorder(null); gridBagConstraints = new java.awt.GridBagConstraints(); --- 115,119 ---- jTextField5.setFont(new java.awt.Font("Tahoma", 1, 24)); jTextField5.setHorizontalAlignment(javax.swing.JTextField.CENTER); ! jTextField5.setText("Nanodesigner v0.1.2"); jTextField5.setBorder(null); gridBagConstraints = new java.awt.GridBagConstraints(); *************** *** 206,210 **** jTextField6.setFont(new java.awt.Font("Tahoma", 1, 18)); jTextField6.setHorizontalAlignment(javax.swing.JTextField.CENTER); ! jTextField6.setText("Third-party software"); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; --- 203,207 ---- jTextField6.setFont(new java.awt.Font("Tahoma", 1, 18)); jTextField6.setHorizontalAlignment(javax.swing.JTextField.CENTER); ! jTextField6.setText("Third-party libraries"); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; *************** *** 223,233 **** new javax.swing.JLabel("<html><body> <b>Java bindings for OpenGL API</b>" + "<ul>Provides hardware-accelerated 3D graphics for the application.<br>" + ! "Distributed by a BSD License.<br>" + ! "See http://jogl.dev.java.net</p></ul>" + " <b>JavaHelp API</b>" + "<ul>JavaHelp software is a full-featured, platform-independent, extensible<br>" + "help system that enables to incorporate online help in applets and applications.<br>" + ! "Distributed by the JavaHelp Binary Code License.<br>" + ! "See https://javahelp.dev.java.net/</p></ul></body></html>"); jScrollPane4.setViewportView(label); --- 220,235 ---- new javax.swing.JLabel("<html><body> <b>Java bindings for OpenGL API</b>" + "<ul>Provides hardware-accelerated 3D graphics for the application.<br>" + ! "Distributed by the BSD License.<br>" + ! "See http://jogl.dev.java.net</ul>" + " <b>JavaHelp API</b>" + "<ul>JavaHelp software is a full-featured, platform-independent, extensible<br>" + "help system that enables to incorporate online help in applets and applications.<br>" + ! "Distributed by the Binary Code License.<br>" + ! "See https://javahelp.dev.java.net/</ul>" + ! " <b>Vecmath package</b>" + ! "<ul>3D vector math package.<br>" + ! "Distributed by the Binary Code License.<br>" + ! "See https://vecmath.dev.java.net/</ul>" + ! "</body></html>"); jScrollPane4.setViewportView(label); *************** *** 261,265 **** jPanel4.add(jButton4, gridBagConstraints); ! jTabbedPane1.addTab("Third-party software", jPanel4); getContentPane().add(jTabbedPane1, java.awt.BorderLayout.CENTER); --- 263,267 ---- jPanel4.add(jButton4, gridBagConstraints); ! jTabbedPane1.addTab("Third-party libraries", jPanel4); getContentPane().add(jTabbedPane1, java.awt.BorderLayout.CENTER); *************** *** 287,296 **** } - private void jButton2ActionPerformed(java.awt.event.ActionEvent evt) { - - setVisible(false); - dispose(); - } - private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) { setVisible(false); --- 289,292 ---- *************** *** 301,317 **** // Variables declaration - do not modify private javax.swing.JButton jButton1; - private javax.swing.JButton jButton2; private javax.swing.JButton jButton3; private javax.swing.JButton jButton4; private javax.swing.JPanel jPanel1; - private javax.swing.JPanel jPanel2; private javax.swing.JPanel jPanel3; private javax.swing.JPanel jPanel4; - private javax.swing.JScrollPane jScrollPane1; private javax.swing.JScrollPane jScrollPane3; private javax.swing.JScrollPane jScrollPane4; private javax.swing.JTabbedPane jTabbedPane1; private javax.swing.JTable jTable1; - private javax.swing.JTable jTable2; private javax.swing.JTextField jTextField1; private javax.swing.JTextField jTextField2; --- 297,309 ---- *************** *** 320,324 **** private javax.swing.JTextField jTextField5; private javax.swing.JTextField jTextField6; - private javax.swing.JTextPane jTextPane1; // End of variables declaration } \ No newline at end of file --- 312,315 ---- Index: Designer.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/Designer.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** Designer.java 14 May 2005 07:32:05 -0000 1.6 --- Designer.java 22 Feb 2006 15:49:37 -0000 1.7 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.0.6 ! * @date May 11, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jan 9, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 30,34 **** import java.util.prefs.PreferenceChangeEvent; ! import net.java.games.jogl.*; import org.nanodesigner.core.*; --- 30,34 ---- import java.util.prefs.PreferenceChangeEvent; ! import javax.media.opengl.*; import org.nanodesigner.core.*; *************** *** 55,59 **** private boolean firstTime = true; private int minimumFrameHeight; ! private int winWidth, winHeight = 0, titlebarHeight; /** Creates a new instance of Designer */ --- 55,59 ---- private boolean firstTime = true; private int minimumFrameHeight; ! private int winWidth, winHeight = 0;//, titlebarHeight; /** Creates a new instance of Designer */ *************** *** 85,90 **** toolFrame = new ToolFrame("Toolboxes", TOOLFRAMEWIDTH); oglFrame = new ThreeDFrame("3D canvas"); ! // Create opengl canvas ! canvas = GLDrawableFactory.getFactory().createGLCanvas(new GLCapabilities()); renderer = new OGLRenderer(this); canvas.addGLEventListener(renderer); --- 85,90 ---- toolFrame = new ToolFrame("Toolboxes", TOOLFRAMEWIDTH); oglFrame = new ThreeDFrame("3D canvas"); ! // Create opengl canvas and add to the UI ! canvas = new GLCanvas(); renderer = new OGLRenderer(this); canvas.addGLEventListener(renderer); *************** *** 113,118 **** pack(); minimumFrameHeight = getPreferredSize().height; ! titlebarHeight = minimumFrameHeight - (int)menu.getPreferredSize().getHeight() + ! (int)message.getPreferredSize().getHeight(); // Hide splash window splash.hideNow(); --- 113,118 ---- pack(); minimumFrameHeight = getPreferredSize().height; ! // titlebarHeight = minimumFrameHeight - (int)menu.getPreferredSize().getHeight() + ! // (int)message.getPreferredSize().getHeight(); // Hide splash window splash.hideNow(); Index: CorePrefsPanel.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.gui/src/org/nanodesigner/gui/CorePrefsPanel.java,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** CorePrefsPanel.java 2 Mar 2005 13:52:45 -0000 1.1 --- CorePrefsPanel.java 22 Feb 2006 15:49:37 -0000 1.2 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Feb 20, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Feb 17, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 26,30 **** import java.awt.*; import java.awt.event.*; - import java.text.*; public class CorePrefsPanel extends PrefsPanels { --- 26,29 ---- |
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From: swinnen <sw...@us...> - 2006-02-22 15:46:34
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Update of /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10947/src/org/nanodesigner/g3d Modified Files: OGLButtonHandler.java OGLShow.java OGLStructure.java OGLEventHandler.java Log Message: Index: OGLStructure.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/OGLStructure.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** OGLStructure.java 21 Jul 2005 16:51:41 -0000 1.3 --- OGLStructure.java 22 Feb 2006 15:46:27 -0000 1.4 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 20, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1.2 ! * @date Dec 6, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 29,34 **** import java.util.prefs.PreferenceChangeEvent; ! import net.java.games.jogl.*; ! import net.java.games.jogl.util.*; import org.nanodesigner.core.*; --- 29,35 ---- import java.util.prefs.PreferenceChangeEvent; ! import javax.media.opengl.*; ! import javax.media.opengl.glu.*; ! import com.sun.opengl.utils.*; import org.nanodesigner.core.*; *************** *** 39,45 **** private GL gl; private GLU glu; ! private GLUT glut; private GLUquadric quadric; ! private int numberOfBonds, groupNumber, startGroupList, startGroupContentList; // Is display list of this group created and ready to be displayed? // Index equals possible groupListIndex numbers --- 40,46 ---- private GL gl; private GLU glu; ! // private GLUT glut; private GLUquadric quadric; ! private int groupNumber; //, startGroupList, startGroupContentList; // Is display list of this group created and ready to be displayed? // Index equals possible groupListIndex numbers *************** *** 62,66 **** this.gl = gl; this.glu = glu; ! this.glut = glut; this.quadric = quadric; // Initialize here because of the fact that GL init() is called if there is --- 63,67 ---- this.gl = gl; this.glu = glu; ! // this.glut = glut; this.quadric = quadric; // Initialize here because of the fact that GL init() is called if there is *************** *** 104,124 **** gl.glNewList(listNumber, GL.GL_COMPILE); gl.glDisable(GL.GL_LIGHTING); - gl.glColor3f(1.0f, 1.0f, 1.0f); // Draw axis lines gl.glBegin(GL.GL_LINES); gl.glVertex3f(0.0f, 0.0f, 0.0f); gl.glVertex3f(axisSize, 0.0f, 0.0f); gl.glVertex3f(0.0f, 0.0f, 0.0f); gl.glVertex3f(0.0f, axisSize, 0.0f); gl.glVertex3f(0.0f, 0.0f, 0.0f); gl.glVertex3f(0.0f, 0.0f, axisSize); gl.glEnd(); - // Add appropriate label on each axis - gl.glRasterPos3f(axisSize, 0, 0); - glut.glutBitmapString(gl, GLUT.BITMAP_HELVETICA_12, "X"); - gl.glRasterPos3f(0, axisSize, 0); - glut.glutBitmapString(gl, GLUT.BITMAP_HELVETICA_12, "Y"); - gl.glRasterPos3f(0, 0, axisSize); - glut.glutBitmapString(gl, GLUT.BITMAP_HELVETICA_12, "Z"); gl.glEnable(GL.GL_LIGHTING); gl.glEndList(); --- 105,120 ---- gl.glNewList(listNumber, GL.GL_COMPILE); gl.glDisable(GL.GL_LIGHTING); // Draw axis lines gl.glBegin(GL.GL_LINES); + gl.glColor3f(1.0f, 0.5f, 0.5f); gl.glVertex3f(0.0f, 0.0f, 0.0f); gl.glVertex3f(axisSize, 0.0f, 0.0f); + gl.glColor3f(0.5f, 1.0f, 0.5f); gl.glVertex3f(0.0f, 0.0f, 0.0f); gl.glVertex3f(0.0f, axisSize, 0.0f); + gl.glColor3f(0.5f, 0.5f, 1.0f); gl.glVertex3f(0.0f, 0.0f, 0.0f); gl.glVertex3f(0.0f, 0.0f, axisSize); gl.glEnd(); gl.glEnable(GL.GL_LIGHTING); gl.glEndList(); *************** *** 130,135 **** public boolean groupsIsEmpty(int startGroupList, int startGroupContentList) { ! this.startGroupList = startGroupList; ! this.startGroupContentList = startGroupContentList; return groups.isEmpty(); } --- 126,131 ---- public boolean groupsIsEmpty(int startGroupList, int startGroupContentList) { ! // this.startGroupList = startGroupList; ! // this.startGroupContentList = startGroupContentList; return groups.isEmpty(); } *************** *** 182,186 **** Atom atom, atom2; Bond bond; ! DisplayMode mode; Set<Integer> atomKeySet, bondKeySet; --- 178,182 ---- Atom atom, atom2; Bond bond; ! //DisplayMode mode; Set<Integer> atomKeySet, bondKeySet; *************** *** 192,201 **** gl.glLoadName(groupNumber); ! if((mode = activeGroup.getDisplayMode()) == DisplayMode.NONE) ! mode = dMode; ! ! switch(mode) { ! case SPACEFILL: ! // Space filled display mode atomKeySet = atoms.keySet(); --- 188,194 ---- gl.glLoadName(groupNumber); ! switch(activeGroup.getDisplayMode()) { ! case SPACEFILL: ! // Space filled display mode atomKeySet = atoms.keySet(); Index: OGLShow.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/OGLShow.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** OGLShow.java 21 Jul 2005 16:51:41 -0000 1.2 --- OGLShow.java 22 Feb 2006 15:46:27 -0000 1.3 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 20, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Dec 6, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 23,27 **** package org.nanodesigner.g3d; ! import net.java.games.jogl.*; /** --- 23,27 ---- package org.nanodesigner.g3d; ! import javax.media.opengl.*; /** *************** *** 30,34 **** public class OGLShow { static final int GROUPSALLOWED = 1; ! private GL gl; private OGLStructure structure; private int startGroupContentList, groupContentListIndex; --- 30,34 ---- public class OGLShow { static final int GROUPSALLOWED = 1; ! private GL gls; private OGLStructure structure; private int startGroupContentList, groupContentListIndex; *************** *** 46,56 **** */ public void initialize(GL gl) { ! this.gl = gl; ! startGroupContentList = gl.glGenLists(GROUPSALLOWED); groupContentListIndex = startGroupContentList; ! startGroupList = gl.glGenLists(GROUPSALLOWED); groupListIndex = startGroupList; ! startAxisList = gl.glGenLists(1); } --- 46,56 ---- */ public void initialize(GL gl) { ! this.gls = gl; ! startGroupContentList = gls.glGenLists(GROUPSALLOWED); groupContentListIndex = startGroupContentList; ! startGroupList = gls.glGenLists(GROUPSALLOWED); groupListIndex = startGroupList; ! startAxisList = gls.glGenLists(1); } *************** *** 62,66 **** structure.showCoordinateAxis(startAxisList); ! if(!structure.groupsIsEmpty(startGroupList, startGroupContentList)) structure.showGroups(GROUPSALLOWED); } --- 62,66 ---- structure.showCoordinateAxis(startAxisList); ! if(!structure.groupsIsEmpty(groupListIndex, groupContentListIndex)) structure.showGroups(GROUPSALLOWED); } Index: OGLButtonHandler.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/OGLButtonHandler.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** OGLButtonHandler.java 21 Jul 2005 16:51:41 -0000 1.3 --- OGLButtonHandler.java 22 Feb 2006 15:46:27 -0000 1.4 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 18, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Nov 25, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 23,27 **** package org.nanodesigner.g3d; ! import net.java.games.jogl.*; /** --- 23,27 ---- package org.nanodesigner.g3d; ! import javax.media.opengl.*; /** *************** *** 31,35 **** public class OGLButtonHandler { private Camera camera; ! private GLDrawable drawable; private OGLStructure structure; --- 31,35 ---- public class OGLButtonHandler { private Camera camera; ! private GLAutoDrawable drawable; private OGLStructure structure; *************** *** 44,48 **** * @params drawable the reference */ ! public void setDrawable(GLDrawable drawable) { this.drawable = drawable; } --- 44,48 ---- * @params drawable the reference */ ! public void setDrawable(GLAutoDrawable drawable) { this.drawable = drawable; } Index: OGLEventHandler.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/OGLEventHandler.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** OGLEventHandler.java 21 Jul 2005 16:51:41 -0000 1.4 --- OGLEventHandler.java 22 Feb 2006 15:46:27 -0000 1.5 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 18, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Jan 9, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 36,40 **** private int button, mouseX, mouseY; private float thetaX, thetaY; ! private boolean actionOnGroup = false; /** Creates a new instance of OGLEventHandler */ --- 36,40 ---- private int button, mouseX, mouseY; private float thetaX, thetaY; ! private boolean zChange = false, actionOnGroup = false; /** Creates a new instance of OGLEventHandler */ *************** *** 55,66 **** * @params camera contains all information about camera position and orientation */ ! public void process(Camera camera) { int x, y; if(event.getEventType() != null) { ie = event.getEvent(); - size = ((MouseEvent)ie).getComponent().getSize(); switch(event.getEventType()) { case MOUSE_DRAGGED: x = ((MouseEvent)ie).getX(); y = ((MouseEvent)ie).getY(); --- 55,66 ---- * @params camera contains all information about camera position and orientation */ ! public boolean process(Camera camera) { int x, y; if(event.getEventType() != null) { ie = event.getEvent(); switch(event.getEventType()) { case MOUSE_DRAGGED: + size = ((MouseEvent)ie).getComponent().getSize(); x = ((MouseEvent)ie).getX(); y = ((MouseEvent)ie).getY(); *************** *** 82,85 **** --- 82,86 ---- case MOUSE_PRESSED: + size = ((MouseEvent)ie).getComponent().getSize(); button = ((MouseEvent)ie).getButton(); mouseX = ((MouseEvent)ie).getX(); *************** *** 101,108 **** --- 102,111 ---- case MOUSE_WHEEL_MOVED: camera.addTranslation(new Vector3f(0.0f, 0.0f, ((MouseWheelEvent)ie).getWheelRotation() * 0.1f)); + zChange = true; break; } event.set(null, null); } + return zChange; } } \ No newline at end of file |
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From: swinnen <sw...@us...> - 2006-02-22 15:46:10
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Update of /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10567/src/org/nanodesigner/g3d Modified Files: InputListener.java Log Message: Index: InputListener.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/InputListener.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** InputListener.java 21 Jul 2005 16:51:41 -0000 1.3 --- InputListener.java 22 Feb 2006 15:46:00 -0000 1.4 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 18, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Nov 25, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 25,29 **** import java.awt.event.*; ! import net.java.games.jogl.*; /** --- 25,29 ---- import java.awt.event.*; ! import javax.media.opengl.*; /** *************** *** 32,36 **** public class InputListener implements KeyListener, MouseListener, MouseMotionListener, MouseWheelListener { private NDEvent event; ! private GLDrawable drawable; /** Creates a new instance of InputListener */ --- 32,36 ---- public class InputListener implements KeyListener, MouseListener, MouseMotionListener, MouseWheelListener { private NDEvent event; ! private GLAutoDrawable drawable; /** Creates a new instance of InputListener */ *************** *** 39,43 **** } ! public void setDrawable(GLDrawable drawable) { this.drawable = drawable; } --- 39,43 ---- } ! public void setDrawable(GLAutoDrawable drawable) { this.drawable = drawable; } |
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From: swinnen <sw...@us...> - 2006-02-22 15:45:45
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Update of /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10480/src/org/nanodesigner/g3d Modified Files: Camera.java Log Message: Index: Camera.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/Camera.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** Camera.java 21 Jul 2005 16:51:12 -0000 1.4 --- Camera.java 22 Feb 2006 15:45:41 -0000 1.5 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 19, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Jan 9, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 38,42 **** // Initializing far and near plane zNear = 0.1f; ! zFar = 1000.0f; } --- 38,42 ---- // Initializing far and near plane zNear = 0.1f; ! zFar = 100.0f; } *************** *** 82,85 **** --- 82,93 ---- /* + * Set the far clipping plane. + * @params z the value of the farthest clipping plane + */ + public void setFarPlane(float z){ + zFar = z; + } + + /* * Get the near clipping plane. * @return the value of the nearest clipping plane |
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From: swinnen <sw...@us...> - 2006-02-22 15:45:08
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Update of /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10054/src/org/nanodesigner/g3d Modified Files: OGLRenderer.java Log Message: Added orthogonal/perspective switch Index: OGLRenderer.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/OGLRenderer.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** OGLRenderer.java 21 Jul 2005 16:45:27 -0000 1.5 --- OGLRenderer.java 22 Feb 2006 15:44:58 -0000 1.6 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 16, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Jan 30, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 23,28 **** package org.nanodesigner.g3d; ! import net.java.games.jogl.*; ! import net.java.games.jogl.util.*; import org.nanodesigner.core.*; --- 23,32 ---- package org.nanodesigner.g3d; ! import java.nio.*; ! import java.util.prefs.Preferences; ! ! import javax.media.opengl.*; ! import javax.media.opengl.glu.*; ! import com.sun.opengl.utils.*; import org.nanodesigner.core.*; *************** *** 31,39 **** public class OGLRenderer implements GLEventListener { private GL gl; private GLU glu; private GLUT glut; private GLUquadric quadratic; ! private GLDrawable drawable; private OGLInit init; private Camera camera; --- 35,45 ---- public class OGLRenderer implements GLEventListener { + // Field-of-view angle (45 degrees) + private final float FOVY = 45.0f; private GL gl; private GLU glu; private GLUT glut; private GLUquadric quadratic; ! private GLAutoDrawable drawable; private OGLInit init; private Camera camera; *************** *** 42,49 **** private OGLStructure structure; private OGLShow dLists; private InputListener input; private NDEvent event; private PictureIO screenImage; ! private boolean screenshot = false; /** Creates a new instance of Renderer */ --- 48,58 ---- private OGLStructure structure; private OGLShow dLists; + private Preferences prefs; private InputListener input; private NDEvent event; private PictureIO screenImage; ! private float atanHalfTheta; ! private float[] proMat; ! private boolean zoom, perspective, projectionChanged = false, screenshot = false; /** Creates a new instance of Renderer */ *************** *** 59,62 **** --- 68,78 ---- screenImage = new PictureIO(); designer.addKeyListener(input); + + proMat = new float[16]; + atanHalfTheta = (float)Math.atan(FOVY / 2.0f); + prefs = Preference.getG3DPrefs(); + // Type of projection preference handling + perspective = prefs.getBoolean(Defines.PERSPECTIVE_PROJECTION, Defines.PERSPECTIVE_PROJECTION_DEF); + // prefs.putBoolean(Defines.POINT_LINE_SMOOTH, perspective); } *************** *** 67,73 **** * @param drawable The GLDrawable object. */ ! public void init(GLDrawable drawable) { gl = drawable.getGL(); ! glu = drawable.getGLU(); this.drawable = drawable; // OpenGL debugger --- 83,90 ---- * @param drawable The GLDrawable object. */ ! public void init(GLAutoDrawable drawable) { gl = drawable.getGL(); ! glu = new GLU(); ! this.drawable = drawable; // OpenGL debugger *************** *** 75,81 **** drawable.setGL(new DebugGL(drawable.getGL())); // drawable must be known before initialization ! init = new OGLInit(); quadratic = glu.gluNewQuadric(); ! drawable.setRenderingThread(Thread.currentThread()); // Add listeners drawable.addMouseListener(input); --- 92,98 ---- drawable.setGL(new DebugGL(drawable.getGL())); // drawable must be known before initialization ! init = new OGLInit(glu); quadratic = glu.gluNewQuadric(); ! //drawable.setRenderingThread(Thread.currentThread()); // Add listeners drawable.addMouseListener(input); *************** *** 96,100 **** * @param drawable The GLDrawable object. */ ! public void display(GLDrawable drawable) { // Clear Color Buffer, Depth Buffer gl.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT ); --- 113,122 ---- * @param drawable The GLDrawable object. */ ! public void display(GLAutoDrawable drawable) { ! // Handle user interactions in queue ! zoom = oglEvents.process(camera); ! // Create perspective or orthogonal projection matrix ! if(projectionChanged || zoom) ! createProjectionMatrix(); // Clear Color Buffer, Depth Buffer gl.glClear(GL.GL_COLOR_BUFFER_BIT | GL.GL_DEPTH_BUFFER_BIT ); *************** *** 104,111 **** init.reinitialize(); - // Handle user interactions in queue - oglEvents.process(camera); // Position the universe relative to the camera ! gl.glMultMatrixf(camera.getTransform()); // (Re)Create the display lists dLists.showAll(); --- 126,131 ---- init.reinitialize(); // Position the universe relative to the camera ! gl.glMultMatrixf(camera.getTransform(), 0); // (Re)Create the display lists dLists.showAll(); *************** *** 125,129 **** * @param deviceChanged Indicates if the video device has changed. */ ! public void displayChanged(GLDrawable gLDrawable, boolean modeChanged, boolean deviceChanged) { } --- 145,149 ---- * @param deviceChanged Indicates if the video device has changed. */ ! public void displayChanged(GLAutoDrawable gLDrawable, boolean modeChanged, boolean deviceChanged) { } *************** *** 142,146 **** * @param height The new height of the window. */ ! public void reshape(GLDrawable gLDrawable, int x, int y, int width, int height) { height = (height == 0) ? 1 : height; // Set on every reshape/resize (in three window gui!) --- 162,166 ---- * @param height The new height of the window. */ ! public void reshape(GLAutoDrawable gLDrawable, int x, int y, int width, int height) { height = (height == 0) ? 1 : height; // Set on every reshape/resize (in three window gui!) *************** *** 148,158 **** camera.setAspectRatioVP(ratio); ! gl.glMatrixMode(GL.GL_PROJECTION); gl.glLoadIdentity(); ! glu.gluPerspective(45, camera.getAspectRatioVP(), camera.getNearPlane(), camera.getFarPlane()); gl.glMatrixMode(GL.GL_MODELVIEW); gl.glLoadIdentity(); } --- 168,216 ---- camera.setAspectRatioVP(ratio); ! createProjectionMatrix(); ! } ! ! private void createProjectionMatrix(){ ! float zFar, zNear = camera.getNearPlane(); ! //float zMin; ! ! gl.glMatrixMode(GL.GL_PROJECTION); gl.glLoadIdentity(); ! zFar = Math.abs(camera.getZ()) + Math.abs((float)structure.getRadiusOfBoundingSphere()); + if(!perspective){ + // Instead of using zNear use Math.abs(z) to make + // sure there is no zooming effect + proMat[5] = atanHalfTheta / Math.abs(camera.getZ()); + proMat[0] = proMat[5] / camera.getAspectRatioVP(); + proMat[10] = 2.0f / (zNear - zFar); + proMat[11] = 0.0f; + proMat[14] = (zFar + zNear) / (zNear - zFar); + proMat[15] = 1.0f; + } + else { + proMat[0] = atanHalfTheta / camera.getAspectRatioVP(); + proMat[5] = atanHalfTheta; + proMat[10] = (zFar + zNear) / (zNear - zFar); + proMat[14] = (-2.0f * zFar * zNear) / (zFar - zNear); + proMat[15] = 0.0f; + proMat[11] = -1.0f; + } + gl.glMultMatrixf(FloatBuffer.wrap(proMat)); + gl.glMatrixMode(GL.GL_MODELVIEW); gl.glLoadIdentity(); + projectionChanged = false; + } + + /* + * Change boolean 'perspective' to indicate the projection matrix + * needs to be changed. + */ + public void changeProjection(){ + perspective = !perspective; + prefs.putBoolean(Defines.PERSPECTIVE_PROJECTION, perspective); + projectionChanged = true; } *************** *** 185,189 **** * @return the reference */ ! public GLDrawable getDrawable() { return drawable; } --- 243,247 ---- * @return the reference */ ! public GLAutoDrawable getDrawable() { return drawable; } |
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From: swinnen <sw...@us...> - 2006-02-22 15:44:20
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Update of /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9453/src/org/nanodesigner/g3d Modified Files: OGLInit.java Log Message: Added debug info on videocard opengl support Index: OGLInit.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/OGLInit.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** OGLInit.java 29 Jul 2005 13:56:18 -0000 1.6 --- OGLInit.java 22 Feb 2006 15:43:36 -0000 1.7 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Jul 29, 2005 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1.2 ! * @date Jan 30, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 27,31 **** import java.util.prefs.PreferenceChangeEvent; ! import net.java.games.jogl.*; import org.nanodesigner.core.*; --- 27,32 ---- import java.util.prefs.PreferenceChangeEvent; ! import javax.media.opengl.*; ! import javax.media.opengl.glu.*; import org.nanodesigner.core.*; *************** *** 36,40 **** public class OGLInit { private Preferences prefs; ! private GLDrawable drawable; private GLU glu; private GL gl; --- 37,41 ---- public class OGLInit { private Preferences prefs; ! private GLAutoDrawable drawable; private GLU glu; private GL gl; *************** *** 47,51 **** /** Creates a new instance of OGLInit */ ! public OGLInit() { OGLInitListener listener = new OGLInitListener(); prefs = Preference.getG3DPrefs(); --- 48,53 ---- /** Creates a new instance of OGLInit */ ! public OGLInit(GLU glu) { ! this.glu = glu; OGLInitListener listener = new OGLInitListener(); prefs = Preference.getG3DPrefs(); *************** *** 58,65 **** * @param quadratic the quadric object */ ! public void initialize(GLDrawable drawable, GLUquadric quadratic) { this.drawable = drawable; gl = drawable.getGL(); - glu = drawable.getGLU(); // Anti-aliasing --- 60,66 ---- * @param quadratic the quadric object */ ! public void initialize(GLAutoDrawable drawable, GLUquadric quadratic) { this.drawable = drawable; gl = drawable.getGL(); // Anti-aliasing *************** *** 76,82 **** --- 77,85 ---- // Set background colour setBackgroundColour(bgColour); + gl.glClearDepth(1.0f); // Depth buffer setup gl.glEnable(GL.GL_DEPTH_TEST); // Enables depth testing gl.glDepthFunc(GL.GL_LEQUAL); // The type of depth testing to do + gl.glHint(GL.GL_PERSPECTIVE_CORRECTION_HINT, GL.GL_NICEST);// Really Nice Perspective Calculations gl.glEnable(GL.GL_CULL_FACE); // Do not display back sides *************** *** 92,98 **** gl.glEnable(GL.GL_COLOR_MATERIAL); ! gl.glLightfv(GL.GL_LIGHT0, GL.GL_AMBIENT, ambientLight); // Setup ambient light ! gl.glLightfv(GL.GL_LIGHT0, GL.GL_DIFFUSE, diffuseLight); // Setup diffuse light ! gl.glLightfv(GL.GL_LIGHT0, GL.GL_POSITION, lightPosition); // Position the light gl.glEnable(GL.GL_LIGHT0); --- 95,101 ---- gl.glEnable(GL.GL_COLOR_MATERIAL); ! gl.glLightfv(GL.GL_LIGHT0, GL.GL_AMBIENT, ambientLight, 0); // Setup ambient light ! gl.glLightfv(GL.GL_LIGHT0, GL.GL_DIFFUSE, diffuseLight, 0); // Setup diffuse light ! gl.glLightfv(GL.GL_LIGHT0, GL.GL_POSITION, lightPosition, 0); // Position the light gl.glEnable(GL.GL_LIGHT0); *************** *** 101,105 **** System.out.println("Videocard brand name: " + gl.glGetString(GL.GL_RENDERER)); System.out.println("Videocard supports OpenGL v" + gl.glGetString(GL.GL_VERSION)); ! System.out.println("Supported OpenGL extensions: " + gl.glGetString(GL.GL_EXTENSIONS)); } } --- 104,112 ---- System.out.println("Videocard brand name: " + gl.glGetString(GL.GL_RENDERER)); System.out.println("Videocard supports OpenGL v" + gl.glGetString(GL.GL_VERSION)); ! ! String[] result = gl.glGetString(GL.GL_EXTENSIONS).split("\\s"); ! System.out.println("Supported OpenGL extensions: "); ! for (int i = 0; i < result.length; i++) ! System.out.println("\t" + result[i]); } } |
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From: swinnen <sw...@us...> - 2006-02-22 15:24:11
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Update of /cvsroot/nanodesigner/org.nanodesigner.core/src/org/nanodesigner/core In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31124/src/org/nanodesigner/core Modified Files: Defines.java Log Message: Added projection property. Index: Defines.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.core/src/org/nanodesigner/core/Defines.java,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** Defines.java 14 May 2005 07:20:49 -0000 1.2 --- Defines.java 22 Feb 2006 15:23:45 -0000 1.3 *************** *** 1,8 **** /* * @author Valère Swinnen ! * @version 0.0.1 ! * @date Feb 24, 2004 * ! * Copyright © 2004-2005, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify --- 1,8 ---- /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jan 9, 2006 * ! * Copyright © 2004-2006, The Nanodesigner Development Team * * This program is free software; you can redistribute it and/or modify *************** *** 50,52 **** --- 50,55 ---- public static final String COLOURMAP = "colourmap"; public static final int COLOURMAP_DEF = 0; + + public static final String PERSPECTIVE_PROJECTION = "perspective_projection"; + public static final boolean PERSPECTIVE_PROJECTION_DEF = false; } |
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From: swinnen <sw...@us...> - 2006-02-22 15:22:24
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Update of /cvsroot/nanodesigner/org.nanodesigner.core/src/org/nanodesigner/core In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30202/src/org/nanodesigner/core Modified Files: nanodesigner.png Log Message: Index: nanodesigner.png =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.core/src/org/nanodesigner/core/nanodesigner.png,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 Binary files /tmp/cvslsIJfY and /tmp/cvssdx1Nt differ |
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From: swinnen <sw...@us...> - 2005-07-29 13:56:26
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Update of /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv556/src/org/nanodesigner/g3d Modified Files: OGLInit.java Log Message: Shows videocard info when -debug option is used Index: OGLInit.java =================================================================== RCS file: /cvsroot/nanodesigner/org.nanodesigner.g3d/src/org/nanodesigner/g3d/OGLInit.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** OGLInit.java 21 Jul 2005 16:51:41 -0000 1.5 --- OGLInit.java 29 Jul 2005 13:56:18 -0000 1.6 *************** *** 1,6 **** /* * @author Valère Swinnen ! * @version 0.1 ! * @date Jul 20, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team --- 1,6 ---- /* * @author Valère Swinnen ! * @version 0.1.1 ! * @date Jul 29, 2005 * * Copyright © 2004-2005, The Nanodesigner Development Team *************** *** 96,99 **** --- 96,106 ---- gl.glLightfv(GL.GL_LIGHT0, GL.GL_POSITION, lightPosition); // Position the light gl.glEnable(GL.GL_LIGHT0); + + if(Globals.debug) { + System.out.println("Videocard vendor: " + gl.glGetString(GL.GL_VENDOR)); + System.out.println("Videocard brand name: " + gl.glGetString(GL.GL_RENDERER)); + System.out.println("Videocard supports OpenGL v" + gl.glGetString(GL.GL_VERSION)); + System.out.println("Supported OpenGL extensions: " + gl.glGetString(GL.GL_EXTENSIONS)); + } } |
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From: swinnen <sw...@us...> - 2005-07-26 17:07:12
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Update of /cvsroot/nanodesigner In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15517 Added Files: Installation notes.html Log Message: --- NEW FILE: Installation notes.html --- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <style type="text/css"> <!-- A:link {text-decoration: none} A:visited {text-decoration: none} A:active {text-decoration: none} h2 { font-size: 14px; font-weight: bold; border-bottom: 1px solid #808080; margin-top: 5px; margin-bottom: 5px; color: #D20005; background: #ffffff } p.center { text-align: center } p.centerbold { text-align: center; font-weight: bold } p.small-bold { font-family: serif; font-size: 11px; font-weight: bold } ul.text { list-style-type: none } --> </style> <title>Nanodesigner version 0.1.1 installation notes.</title> </head> <body> <p class="centerbold">Nanodesigner</p> <p class="centerbold">Installation notes version 0.1.1.</p> <p class="center">Last revised: July 21, 2005.</p> <h2>Contents.</h2> <blockquote> <dl> <dt><a href="#install">Installation</a></dt> <dt><a href="#compile">Compilation</a></dt> <dt><a href="#documentation">Documentation</a></dt> <dt><a href="#information">More information</a></dt> </dl> </blockquote> <h2><a name="install"><b>Installation.</b></a></h2> <ul class="text"> <li>You will need to have the following software packages installed:<br /> <ul> <li><a href="http://java.sun.com/j2se/1.5.0/download.jsp">J2SE v1.5 or higher</a></li> <li><a href="http://ant.apache.org/bindownload.cgi">A recent version of Ant</a> (if you are not using an IDE that is)</li> <li><a href="http://java.sun.com/products/javahelp/download_binary.html">JavaHelp 2.x</a></li> <li><a href="https://jogl.dev.java.net/servlets/ProjectDocumentList?folderID=2869&expandFolder=2869&folderID=0">JOGL 1.1 beta 10</a> or higher. <p><b>Windows:</b><br /> Install JOGL by downloading jogl.jar and jogl-natives-win32.jar. Copy jogl.jar to the directory jdk1.5.x\jre\lib\ext. Copy the content of jogl-natives-win32.jar, i.e. the files libjogl.so and libjogl_cg.so, to the directory jdk1.5.x\jre\lib\i386.</p> <p><b>Linux:</b><br /> Install JOGL by downloading jogl.jar and jogl-natives-linux.jar. Copy jogl.jar to the directory jdk1.5.x/jre/lib/ext. Copy the content of jogl-natives-linux.jar, i.e. the files libjogl.so and libjogl_cg.so, to the /usr/lib directory.</p></li> <li><a href="https://java3d.dev.java.net/binary-builds.html">Vecmath 1.3 library</a> <p><b>Windows:</b><br /> Extract vecmath.jar from the file java3d-1_3_x-windows-i586.zip. Inside this zip file you will find a file j3d-13x-win.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory jdk1.5.x\jre\lib\ext.</p> <p><b>Linux:</b><br /> Extract vecmath.jar from the file java3d-1_3_x-linux-i586.zip. Inside this zip file you will find a file j3d-13x-linux.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory jdk1.5.x/jre/lib/ext.</p></li> </ul> <p>Make sure that you update your path environment variable so that the programs can run (javac, javadoc, ant and jhindexer).</p> </ul> <h2><a name="compile"><b>Compilation.</b></a></h2> <ul class="text"> <li><a name="windows"><b>Windows</b></a> <ul> <li>Open a dos window and run 'ant' in the Nanodesigner-0.1.1 directory. This command will create three jar files called core.jar, g3d.jar and gui.jar and will put thes files in Nanodesigner-0.1.1\jars. <li>Go to the Nanodesigner-0.1.1\HelpDocs directory and run 'jhindexer help'. This command will create the JavaHelpSearch directory. <li>While still in the Helpdocs directory create a jar file with the help documents by running the command 'jar -cvf nd_help.jar *'. <li>Copy nd_help.jar to the Nanodesigner-0.1.1\jars directory <li>Copy jh.jar from the JavaHelp directory (jh2.0\javahelp\lib) to the Nanodesigner-0.1.1\jars directory </ul> <p><a name="linux"><b>Linux</b></a></p> <ul> <li>Open a terminal window and run 'ant' in the Nanodesigner-0.1.1 directory. This command will create three jar files called core.jar, g3d.jar and gui.jar and put these files in the Nanodesigner-0.1.1/jars directory. <li>Go to the Nanodesigner-0.1.1/HelpDocs directory and run 'jhindexer help'. This command will create the JavaHelpSearch directory. <li>While still in the Helpdocs directory create a jar file with the help documents by running the command 'jar -cvf nd_help.jar *'. <li>Copy nd_help.jar to the Nanodesigner-0.1.1/jars directory <li>Copy jh.jar from the JavaHelp directory (jh2.0/javahelp/lib) to the Nanodesigner-0.1.1/jars directory </ul> </ul> <h2><a name="documentation"><b>Documentation.</b></a></h2> <p>The Nanodesigner API documents can be generated by running the command 'ant doc' in a dos (windows) or terminal (linux) window in the Nanodesigner-0.1.1 directory. A directory called 'api-doc' will be created with all API documentation in html format.</p> <h2><a name="information"><b>More information.</b></a></h2> <p>For more information, visit our website at <a href="http://www.nanodesigner.org/">www.nanodesigner.org</a>.</p> <hr> <p class="small-bold">The Nanodesigner development team.</p> </body> </html> |
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From: swinnen <sw...@us...> - 2005-07-26 17:07:02
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Update of /cvsroot/nanodesigner In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15452 Added Files: Release notes.html Log Message: --- NEW FILE: Release notes.html --- <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <style type="text/css"> <!-- A:link {text-decoration: none} A:visited {text-decoration: none} A:active {text-decoration: none} h2 { font-size: 14px; font-weight: bold; border-bottom: 1px solid #808080; margin-top: 5px; margin-bottom: 5px; color: #D20005; background: #ffffff } p.center { text-align: center } p.centerbold { text-align: center; font-weight: bold } p.small-bold { font-family: serif; font-size: 11px; font-weight: bold } ul.text { list-style-type: none } --> </style> <title>Nanodesigner release notes 0.1.1.</title> </head> <body> <p class="centerbold">Nanodesigner</p> <p class="centerbold">Release notes version 0.1.1.</p> <p class="center">Last revised: July 21, 2005.</p> <h2>Contents.</h2> <blockquote> <dl> <dt><a href="#intro">Introduction</a></dt> <dt><a href="#requirements">System requirements</a></dt> <dd><a href="#hardware">Recommended hardware</a></dd> <dd><a href="#software">Software</a></dd> <dt><a href="#installation">Installation</a></dt> <dd><a href="#windows">Windows OS</a></dd> <dd><a href="#linux">Linux distributions</a></dd> <dt><a href="#issues">Known issues</a></dt> <dt><a href="#documentation">Documentation</a></dt> <dt><a href="#information">More information</a></dt> </dl> </blockquote> <h2><a name="intro"><b>Introduction.</b></a></h2> <p>Nanodesigner is a free, open source, software tools platform intended for the design of atomic structures from the ground up, atom-by-atom, molecule by molecule. Nanodesigner is written in the Java programming language.</p> <h2><a name="requirements"><b>System requirements.</b></a></h2> <ul> <li><a name="hardware"><b>Recommended hardware</b></a><br /> <ul class="text"> <li><b>Processor</b>: 1 GHz or higher<br> <b>Memory</b>: 256 megabytes or more<br> <b>Video card</b>: supporting OpenGL v1.2 or higher<br> <b>Virtual memory</b>: 500 megabytes or more<br> <b>Disk space</b>: 10 megabytes of free space</li> </ul> <p><a name="software"><b>Software</b></a></p> <ul> <li>Nanodesigner needs Java v1.5 or higher to run: <ul class="text"> <li>1. Use the <a href="http://java.sun.com/j2se/1.5.0/download.jsp">Java runtime environment (JRE) v1.5 or higher</a>, or<br> 2. Use the <a href="http://java.sun.com/j2se/1.5.0/download.jsp">Java development environment (J2SE) v1.5 or higher</a></li> </ul><br> <li>Nanodesigner uses the vecmath.jar library which is part of Java3D.<br> The latest releases can be found at <a href="https://java3d.dev.java.net/binary-builds.html">this location.</a><br /> </li> <li>Nanodesigner also needs Java bindings for OpenGL (JOGL) to run.<br> This release will only run using <a href="https://jogl.dev.java.net/servlets/ProjectDocumentList?folderID=2869&expandFolder=2869&folderID=0">JOGL v1.1 beta 10</a> or higher.</li> </ul> </ul> <h2><a name="installation"><b>Installation.</b></a></h2> <ul class="text"> <li><p><a name="windows"><b>Windows</b></a></p> <p>Nanodesigner has been tested on Windows2000 and WindowsXP.<br />The installation is fairly straightforward:</p> <ul> <li>Install a Java environment v1.5 or higher, if not already available on your system, by downloading JRE or JDK v1.5 or higher (see <a href="#software">System requirements/Software</a> above). Remember the directory where the Java environment is located. Set JAVA_HOME in case of the installation of a JDK. The JRE version is normally installed in the directory C:\Program Files\Java.<br /> </li> <li>Install JOGL by downloading jogl.jar and jogl-natives-win32.jar from the location mentioned in <a href="#software">System requirements/Software</a> above. <ul> <li>Copy jogl.jar to the directory jre1.5.x\lib\ext (or jdk1.5.x\jre\lib\ext in case only the JDK is installed).</li> <li>Copy the content of jogl-natives-win32.jar, i.e. the files jogl.dll and jogl_cg.dll, to the directory jre1.5.x\bin (or jdk1.5.x\jre\bin in case only the JDK is installed).</li> </ul><br /></li> <li>Extract vecmath.jar from the file java3d-1_3_x-windows-i586.zip. Inside this zip file you will find a file j3d-13x-win.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory jre1.5.x\lib\ext (or jdk1.5.x\jre\lib\ext in case only the JDK is installed).<br /> </li> <li>Choose a directory on the hard disk and unzip the content of Nanodesigner-0.1.1-bin.zip into this directory.</li> </ul><br /></li> <li><a name="linux"><b>Linux</b></a> <p>Nanodesigner has been tested on RedHat Fedora 2.</p> <ul> <li>Install a Java environment v1.5 or higher, if not already available on your system, by downloading JRE or JDK v1.5 or higher (see <a href="#software">System requirements/Software</a> above). Remember the directory where the Java environment is located.<br /> </li> <li>Install JOGL by downloading jogl.jar and jogl-natives-linux.jar from the location mentioned in <a href="#software">System requirements/Software</a> above. <ul> <li>Copy jogl.jar to the directory jre1.5.x/lib/ext (or jdk1.5.x/jre/lib/ext in case JDK is installed instead).</li> <li>Copy the content of jogl-natives-linux.jar, i.e. the files libjogl.so and libjogl_cg.so, to the directory /usr/lib.</li> </ul><br /></li> <li>Extract vecmath.jar from the file java3d-1_3_x-linux-i586.zip. Inside this zip file you will find a file j3d-13x-linux.zip. Inside this zip file you will find vecmath.jar. Copy this file to the directory jre1.5.x/lib/ext (or jdk1.5.x/jre/lib/ext in case a JDK is installed).<br /> </li> <li>Choose a directory on the hard disk and unzip the content of Nanodesigner-0.1.1-bin.zip into this directory.</li> </ul> </ul> <h2><a name="issues"><b>Known Issues.</b></a></h2> <ul class="text"> <li><b>Performance</b> <ul class="text"> <li>Performance largely depends on the hardware the program is running. No attempt is made yet to optimize the creation of the display lists so the size of the molecules that can be displayed is limited. Small molecules up to 1000 atoms can be displayed without a problem. Performance is best in wireframe display mode which is the default display mode. In general performance seems a bit slower on Linux than on Windows systems.</li> </ul> </ul> <h2><a name="documentation"><b>Documentation.</b></a></h2> <p>A full-featured build-in help system is included in the program starting this release. <h2><a name="information"><b>More information.</b></a></h2> <p>For more information, visit our website at <a href="http://www.nanodesigner.org/">www.nanodesigner.org</a>.</p> <hr> <p class="small-bold">The Nanodesigner development team.</p> </body> </html> |