/**
* Context is an array containing:
* newModel the ID of the model just added, or null on failure
* labbookEntry the labbook entry number for adding this new model
* errorMsg an error diagnosis from failed PDB upload
*/
function display($context)
{
$labbook = openLabbook();
if (!$context['newModel']) {
if (isset($context['errorMsg'])) {
echo $this->pageHeader("Model upload failed");
echo "For some reason, your file could not be uploaded.\n<ul>\n";
echo "<li>{$context['errorMsg']}</li>\n";
echo "</ul>\n";
} else {
echo $this->pageHeader("Model retrieval failed");
echo "For some reason, your file could not be pulled from the network.\n<ul>\n";
echo "<li>Check the PDB/NDB identifier code and try again.</li>\n";
echo "<li>Check the PDB/NDB web site - their server may be down.</li>\n";
echo "</ul>\n";
}
echo "<p>" . makeEventForm("onTryAgain");
echo "<table border='0' width='100%'><tr>\n";
echo "<td align='left'><input type='submit' name='cmd' value='< Try again'></td>\n";
echo "<td align='right'><input type='submit' name='cmd' value='Cancel'></td>\n";
echo "</tr></table>\n</form></p>\n";
} else {
$num = $context['labbookEntry'];
// Start the page: produces <HTML>, <HEAD>, <BODY> tags
echo $this->pageHeader($labbook[$num]['title']);
//echo formatLabbookEntry($labbook[$num]);
echo $labbook[$num]['entry'];
// avoid date stamp, title clutter
//echo "<p><a href='".makeEventURL('onEditNotebook', $num)."'>Edit notebook entry</a></p>\n";
echo "<p>" . makeEventForm("onReturn");
echo "<input type='submit' name='cmd' value='Continue >'>\n</form></p>\n";
}
echo $this->pageFooter();
}
/**
* Context is not used.
*/
function display($context)
{
mpLog("notebook-view:User visited Lab Notebook page");
$labbook = openLabbook();
echo $this->pageHeader("Lab notebook", "notebook");
// Set time zone form
echo makeEventForm("onSetTimezone");
echo "<table border='0' width='100%'><tr>\n";
echo "<td>Current time: " . formatTime(time()) . "</td>\n";
echo "<td>" . timeZonePicker('timezone', $_SESSION['timeZone']);
echo "<input type='submit' name='cmd' value='Set time zone'></td>\n";
echo "</tr></table></form>\n";
echo "</div>\n<br>\n<div class='pagecontent'>\n";
// Notebook table of contents
echo "<h3><a name='top'</a>Table of contents:</h3>\n";
echo "<div class='indent'>\n";
$this->printTOC($labbook);
//onNotebookEdit removed for security reasons (probably nobody was using it)
//echo makeEventForm("onNotebookEdit");
//echo "<input type='submit' name='cmd' value='Create new entry'>\n</form>\n";
echo "</div>\n";
// Actual notebook entries
foreach ($labbook as $num => $entry) {
$this->printEntry($num, $entry);
}
echo $this->pageFooter();
}
/**
* Context is an array containing:
* labbookEntry the labbook entry number
*/
function display($context)
{
$labbook = openLabbook();
$num = $context['labbookEntry'];
echo $this->pageHeader($labbook[$num]['title']);
//echo formatLabbookEntry($labbook[$num]);
echo $labbook[$num]['entry'];
// avoid date stamp, title clutter
//echo "<p><a href='".makeEventURL('onEditNotebook', $num)."'>Edit notebook entry</a></p>\n";
echo "<p>" . makeEventForm("onReturn");
echo "<input type='submit' name='cmd' value='Continue >'>\n</form></p>\n";
echo $this->pageFooter();
}
/**
* If the user requested to save changes, make sure we do that before returning.
*/
function onSaveEntry()
{
$req = $_REQUEST;
// Did we get an edit request?
if ($req['labbookEditCmd'] == "Save") {
$labbook = openLabbook();
if (isset($req['entryNumber'])) {
$entryNum = $req['entryNumber'];
$labbook[$entryNum] = $req['labbookEntry'];
mpLog("notebook-edit:User modified existing lab notebook entry");
} else {
$entryNum = count($labbook);
$labbook[$entryNum] = $req['labbookEntry'];
mpLog("notebook-add:User added a new entry to the lab notebook");
}
saveLabbook($labbook);
}
pageReturn();
}
/**
* Make sure you say what $context is here. For example:
*
* Context is an array containing:
* labbookEntry the labbook entry number for adding this new model
*/
function display($context)
{
echo $this->pageHeader("NAME OF YOUR PAGE GOES HERE");
// Here's a sample page that displays a notebook entry.
// The notebook entry number was specified in $context['labbookEntry']
// This is a common way to display results of a background job.
// Load and format the notebook entry:
$labbook = openLabbook();
$num = $context['labbookEntry'];
echo formatLabbookEntry($labbook[$num]);
// This line makes a URL that, when clicked, will cause the onEditNotebook()
// function to be called. It's declared below...
echo "<p><a href='" . makeEventURL('onEditNotebook', $num) . "'>Edit notebook entry</a></p>\n";
// These lines create an HTML form that will call onReturn() to be called
// when the user clicks the Continue > button. onReturn() is declared below.
echo "<p>" . makeEventForm("onReturn");
echo "<input type='submit' name='cmd' value='Continue >'>\n</form></p>\n";
// Note the explicit </form> to end the form!
echo $this->pageFooter();
}
/**
* Context is an array containing:
* labbookEntry the labbook entry number
* modelID the ID of the new Reduced model
*/
function display($context)
{
$labbook = openLabbook();
$num = $context['labbookEntry'];
echo $this->pageHeader($labbook[$num]['title']);
//echo formatLabbookEntry($labbook[$num]);
echo $labbook[$num]['entry'];
// avoid date stamp, title clutter
//echo "<p><a href='".makeEventURL('onEditNotebook', $num)."'>Edit notebook entry</a></p>\n";
echo "<p>" . makeEventForm("onReturn");
echo "<input type='submit' name='cmd' value='Continue >'>\n</form></p>\n";
$modelID = $context['modelID'];
$model = $_SESSION['models'][$modelID];
if ($modelID && $model && $model['isReduced'] && $model['isUserSupplied']) {
$url = makeEventURL('onDownload', $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $model['pdb']);
?>
<script language='JavaScript'>
function confirmPdbDownload()
{
if(window.confirm("Your PDB file has been changed. Would you like to download the new coordinates now?"))
window.location.href = "<?php
echo $url;
?>
"
}
// This nifty function means we won't override other ONLOAD handlers
function windowOnload(f)
{
var prev = window.onload;
window.onload = function() { if(prev) prev(); f(); }
}
windowOnload(confirmPdbDownload)
</script>
<?php
}
echo $this->pageFooter();
}
/**
* Context is not used.
*/
function display($context)
{
echo $this->pageHeader("Main page", "welcome");
// echo mpSerialize($_SESSION['models']);
if (count($_SESSION['models']) > 0 && $_SESSION['lastUsedModelID']) {
echo "<h5 class='welcome'>Suggested Tools (<a href='" . makeEventURL("onGoto", "sitemap.php") . "'>all tools</a>)</h5>\n";
echo "<div class='indent'>\n";
echo makeEventForm("onSetWorkingModel") . "\n";
$this->displayModels($context);
echo "</form>\n";
if (isset($_SESSION['ensembles'][$_SESSION['lastUsedModelID']])) {
$this->displayEnsembleTools($context);
} else {
$this->displayModelTools($context);
}
echo "</div></div>\n<br>\n<div class='pagecontent'>\n";
}
// Entries / files should display if we have any entries.
// We can have entries with no models -- e.g., uploading a het dictionary first thing.
$labbook = openLabbook();
if (count($labbook) > 0) {
$this->displayEntries($context, $labbook);
echo "<br>\n";
//echo "</div>\n<br>\n<div class='pagecontent'>\n";
//$this->displayFiles($context);
//$this->displayFilesJS($context);
$this->displayAllFiles($context);
echo "</div>\n<br>\n<div class='pagecontent'>\n";
}
$this->displayUpload($context);
echo "</div>\n<br>\n<div class='pagecontent'>\n";
?>
<table border='0' width='100%'><tr valign='top'><td width='45%'>
<h3>Walkthroughs, tutorials, and usage FAQs:</h3>
<p><b><?php
echo "<a href='" . makeEventURL("onGoto", "helper_xray.php") . "'>Evaluate X-ray structure</a>";
?>
:</b>
Typical steps for a published X-ray crystal structure
or one still undergoing refinement.</p>
<p><b><?php
echo "<a href='" . makeEventURL("onGoto", "helper_nmr.php") . "'>Evaluate NMR structure</a>";
?>
:</b>
Typical steps for a published NMR ensemble
or one still undergoing refinement.</p>
<p><b><?php
echo "<a href='" . makeEventURL("onGoto", "helper_rebuild.php") . "'>Fix up structure</a>";
?>
:</b>
Rebuild the model to remove outliers
as part of the refinement cycle.</p>
<p><b><?php
echo "<a href='" . makeEventURL("onGoto", "helper_kinemage.php") . "'>Work with kinemages</a>";
?>
:</b>
Create and view interactive 3-D graphics
from your web browser.</p>
<p><b><a target="_blank" href="help/validation_options/validation_options.html">Guide to validation options</a>:</b>
Choose validations appropriate to a structure.</p>
<?php
// <h3>What's new in 4.0:</h3><ul>
// <li>Updated Reduce-added hydrogen lengths to be more consistent with other crystallography software.</li>
// <li>New <a href='http://kinemage.biochem.duke.edu/databases/top8000.php' target='_blank'>Top8000</a> Ramachandran validation information.</li>
// <li>Allows use of both electron cloud and nuclear x-H bond-lengths. Read more about this change <a href='".makeEventURL("onGoto", "helper_hydrogens.php")."'>here</a>.</li>
// <li>Full support for 2-character CHAINIDs added. 4-character SEGIDs also supported in place of CHAINIDs.</li>
// </ul>
echo "<h3>What's new in 4.2:</h3><ul>\n <li>Cis-peptide identification, markup and statistics now available.</li>\n <li>CaBLAM Cα-based validation of protein backbone and secondary structure now available.</li>\n <li>Rotamer validation now uses <a href='http://kinemage.biochem.duke.edu/databases/top8000.php' target='_blank'>Top8000</a> rotamer distributions. Favored vs Allowed distinction introduced for rotamers.</li>\n <li>New coloring scheme in multicriterion chart encodes outlier severity at a glance.</li>\n <li><a target='_blank' href='help/validation_options/validation_options.html'>Online tutorial</a> explaining markup and methods</li>\n <li>We now use a conformation-dependent library (CDL) from Dunbrack and Karplus for geometry analysis if requested.\n </ul>\n <h3>What's new in 4.1:</h3><ul>\n <li>Validation analysis now powered by CCTBX. Also adds geometry regularization for N/Q/H flip corrections. Read more about this change <a href='" . makeEventURL("onGoto", "helper_cctbx.php") . "'>here</a>.</li>\n <li>Alternate conformations now handled for validation analysis.</li>\n </ul>\n </td><td width='10%'><!-- horizontal spacer --></td><td width=='45%'>";
?>
<h3>Citations, science, and technical FAQs:</h3>
<p><b><a href='help/about.html' target='_blank'>Cite MolProbity</a></b>:
<small>Chen et al. (2010)
<a href="http://kinemage.biochem.duke.edu/lab/papers.php" target="_blank">MolProbity:
all-atom structure validation for macromolecular crystallography.</a>
Acta Crystallographica D66:12-21.
</p>
<center>and/or</center>
<p>Davis et al. (2007)
<a href="http://kinemage.biochem.duke.edu/lab/papers.php" target="_blank">MolProbity:
all-atom contacts and structure validation for proteins and nucleic acids.</a>
Nucleic Acids Research 35:W375-W383.
</small></p>
<p><b><a href='help/about.html' target='_blank'>Cite KiNG</a></b>:
<small>Chen et al. (2009)
<a href="http://kinemage.biochem.duke.edu/lab/papers.php" target="_blank">KiNG (Kinemage, Next Generation):
A versatile interactive molecular and scientific visualization program.</a>
Protein Science 18:2403-2409.
</small></p>
<p><b><a href='help/about.html' target='_blank'>Cite CCTBX</a></b>:
<small>Grosse-Kunstleve et al. (2002)
<a href="http://scripts.iucr.org/cgi-bin/paper?ks0118" target="_blank">The Computational Crystallography Toolbox:
crystallographic algorithms in a reusable software framework.</a>
J. Appl. Cryst. 35:126-136.
</small></p>
<p><b><?php
echo "<a href='" . makeEventURL("onGoto", "helper_hydrogens.php") . "'>About hydrogens</a>";
?>
:</b>
Why have the hydrogen bondlengths changed?</p>
<p><b><a href='help/java.html' target='_blank'>Installing Java</a></b>: how to make kinemage graphics work in your browser.</p>
<p><b><?php
echo "<a href='" . makeEventURL("onGoto", "get_molprobity.php") . "'>Download MolProbity</a>";
?>
</b>: how can I run a private MolProbity server, or run from the command line?</p>
<p><small><i>NB: the back button doesn't work inside MolProbity</i></small></p><!-- by request of DCR -->
</td></tr></table>
<?php
// These are too annoying to have at the top all the time
$this->displayWarnings($context);
echo $this->pageFooter();
}
/**
* Returns the entry number of the new entry.
*/
function addLabbookEntry($title, $text, $model = "", $keywords = "", $thumbnail = null)
{
$labbook = openLabbook();
$entry = newLabbookEntry($model, $keywords);
$entry['title'] = $title;
$entry['entry'] = $text;
if ($thumbnail) {
$entry['thumbnail'] = $thumbnail;
}
// else it stays the default
$entryNum = count($labbook);
$labbook[$entryNum] = $entry;
saveLabbook($labbook);
return $entryNum;
}
// Pages in subdirectories of lib/ or public_html/ will need more "/.." 's.
if (!defined('MP_BASE_DIR')) {
define('MP_BASE_DIR', realpath(dirname(__FILE__) . '/..'));
}
// 2. Include core functionality - defines constants, etc.
require_once MP_BASE_DIR . '/lib/core.php';
require_once MP_BASE_DIR . '/lib/labbook.php';
// 3. Restore session data. If you don't want to access the session
// data for some reason, you must call mpInitEnvirons() instead.
mpStartSession();
// 4. For pages that want to see the session but not change it, such as
// pages that are refreshing periodically to monitor a background job.
mpSessReadOnly();
# MAIN - the beginning of execution for this page
############################################################################
$labbook = openLabbook();
$entry = $labbook[$_REQUEST['entry_num']];
// Start the page: produces <HTML>, <HEAD>, <BODY> tags
echo mpPageHeader("{$entry['title']}");
?>
<form>
<table border='0' width='100%'><tr>
<td align='left'><small>
When finished, you should
<input type="button" value="close this window"
language="JavaScript" onclick="self.close();">.
</small></td><td align='right'><small><i>
Hint: Use File | Save As... to save a copy of this page.
</i></small></td>
</tr></table>
</form>
