function displayKin($context)
{
echo $this->pageHeader("Kinemage {$context['kinName']} added");
echo "Your kinemage has been uploaded. You may now view it in KiNG:\n";
echo "<ul><li>" . linkKinemage($context['kinName']) . "</li></ul>\n";
echo "<p>" . makeEventForm("onReturn");
echo "<input type='submit' name='cmd' value='Continue >'>\n</form></p>\n";
echo $this->pageFooter();
}
/**
* Context must contain the following keys:
* newModel the ID of the model just added
* cnit a set of CNIT codes for residues that were processed
* sswingChanges the changes for pdbSwapCoords() produced by SSWING
*/
function display($context)
{
echo $this->pageHeader("Review SSwing changes");
$modelID = $context['newModel'];
$model = $_SESSION['models'][$modelID];
$cnit = $context['cnit'];
?>
<p>
Please examine the kinemage below to see the effects of changes made by SSWING.
Afterwards, please select which of the changes you would like to accept as-is.
Residues that are not selected will be restored to their original conformation.
</p><?php
echo "<p>" . linkKinemage("{$model['prefix']}sswing.kin") . "</p>\n";
echo makeEventForm("onMakeFinalPDB") . "<p>";
foreach ($cnit as $res) {
echo "<br><input type='checkbox' name='cnit[{$res}]' value='{$res}' checked> {$res}\n";
}
echo "</p><p><input type='submit' name='cmd' value='Generate modified PDB file >'></p>\n";
echo "</form>\n";
echo $this->pageFooter();
}
$tasks['dots'] = "Calculate contact dots using Probe";
}
if ($doList) {
$tasks['list'] = "List atomic contacts found by Probe";
}
$tasks['notebook'] = "Make lab notebook entry";
// Actually run things
$entry = "";
if ($doProbe) {
setProgress($tasks, 'kin');
// updates the progress display if running as a background job
exec($prekin_cmd1);
setProgress($tasks, 'dots');
// updates the progress display if running as a background job
exec($probe_cmd1);
$entry .= "<p>Your kinemage is ready for viewing in KiNG: " . linkKinemage($outname) . "</p>\n";
$entry .= "<p>The actual commands used were as follows:\n<ul>\n";
$entry .= "<li><code>prekin -lots {$model['pdb']} > {$outname}</code></li>\n";
$entry .= "<li><code>probe {$flags} {$model['pdb']} >> {$outname}</code></li>\n";
$entry .= "</ul>\n";
}
if ($doList) {
setProgress($tasks, 'list');
// updates the progress display if running as a background job
exec($probe_cmd2);
$entry .= "Types of contacts include the following:";
$entry .= "<p><code>hb</code> = hydrogen bond; <code>wc</code> = wide contact; <code>cc</code> = close contact; <code>so</code> = small overlap; <code>bo</code> = big overlap";
$entry .= "<p>The list of contacts is as follows:</p>\n";
$entry .= "<p><pre>\n";
$entry .= @file_get_contents($list_out);
$entry .= "</pre></p>\n";
//echo "For $pdbName\n";
if (preg_match("/" . $modelID . ".*\\.[0-9]*-[0-9]*\\.pdb/", $pdbName)) {
//echo "Found $pdbName\n";
$filledPdbFile = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $pdbName;
$pdburl = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $pdbName;
$pdbEntries .= "<p>File <a href='{$pdburl}'>{$pdbName}</a> (" . formatFilesize(filesize($filledPdbFile)) . ").</p>\n";
$gapCount += 1;
} else {
if (preg_match("/.kin/", $pdbName)) {
// because JiffiLoop puts all output files in one directory, this moves the output kin to the kin directory.
//echo "kin file name: ".$pdbName."\n";
$origKinFile = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $pdbName;
$newKinFile = $kinDir . '/' . $pdbName;
rename($origKinFile, $newKinFile);
$jiffiKin = $pdbName;
}
}
}
//$pdbout = $_SESSION['dataDir'].'/'.MP_DIR_MODELS.'/'.$pdbpath;
//$pdburl = $_SESSION['dataURL'].'/'.MP_DIR_MODELS.'/'.$pdbpath;
$entry = "Jiffiloop was run on {$model['pdb']}; {$gapCount} JiffiLoop PDB files were found. If there are no files shown here, JiffiLoop likely crashed; please contact the developers.\n";
//$entry .= "<p>You can now <a href='$pdburl'>download the annotated PDB file</a> (".formatFilesize(filesize($pdb)).").</p>\n";
$entry .= $pdbEntries;
$entry .= "<p>A kinemage of the fragments from this run is ready for viewing in KiNG: " . linkKinemage($jiffiKin) . "</p>\n";
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Filled gaps in {$modelID}.", $entry, "{$modelID}|{$newModel['id']}", "auto", "add_h.png");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
/**
* Documentation for this function.
*/
function onRerunReduce()
{
$req = $_REQUEST;
$doflip = $req['doflip'];
$modelID = $req['modelID'];
$model = $_SESSION['models'][$modelID];
$pdb = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $model['pdb'];
$url = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $model['pdb'];
// If all changes were accepted, we will not need to re-run Reduce.
// We're going to construct a lab notebook entry at the same time.
$changes = decodeReduceUsermods($pdb);
$rerun = false;
$flags = '';
$n = count($changes[0]);
// How many changes are in the table?
$autoflip = "<p>The following residues were flipped automatically by Reduce:\n<ul>\n";
$userflip = "<p>The following residues were flipped manually by the user:\n<ul>\n";
$userkeep = "<p>The following residues were NOT flipped, though Reduce recommended doing so:\n<ul>\n";
for ($c = 0; $c < $n; $c++) {
// Expect checks for ones flipped originally; expect no check for ones not flipped.
$expected = $changes[4][$c] == "FLIP" || $changes[4][$c] == "CLS-FL";
if ($expected) {
if ($doflip[$c]) {
$autoflip .= "<li>{$changes[1][$c]} {$changes[2][$c]} {$changes[3][$c]} {$changes[13][$c]}</li>\n";
} else {
$userkeep .= "<li>{$changes[1][$c]} {$changes[2][$c]} {$changes[3][$c]} {$changes[13][$c]}</li>\n";
$rerun = true;
}
} elseif ($doflip[$c]) {
$userflip .= "<li>{$changes[1][$c]} {$changes[2][$c]} {$changes[3][$c]} {$changes[13][$c]}</li>\n";
}
}
$autoflip .= "</ul>\n</p>\n";
$userflip .= "</ul>\n</p>\n";
$userkeep .= "</ul>\n</p>\n";
$hcount = countReduceChanges($pdb);
$parent = $_SESSION['models'][$model['parent']];
$entry = "Reduce was run on {$parent['pdb']} to add and optimize hydrogens, and optimize Asn, Gln, and His flips, yielding {$model['pdb']}.\n";
if ($hcount) {
$entry .= "{$hcount['found']} hydrogens were found in the original model, and {$hcount['add']} hydrogens were added.\n";
if ($hcount['std']) {
$entry .= "{$hcount['std']} H were repositioned to standardize bond lengths.\n";
}
if ($hcount['adj']) {
$entry .= "The positions of {$hcount['adj']} hydrogens were adjusted to optimize H-bonding.\n";
}
}
if ($_SESSION['reduce_blength'] == 'ecloud') {
$flags = 'electron-cloud';
} else {
$flags = 'nuclear';
}
$entry .= "<p>Reduce placed hydrogens at {$flags} positions.\n";
$entry .= "<p>Reduce used <a href=http://kinemage.biochem.duke.edu/software/reduce.php> reduce_wwPDB_het_dict.txt </a> as the het dictonary.\n";
if ($doflip && $n > 0) {
$entry .= "<p>You can now download this atom-shifted and annotated <a href='{$url}'>PDB file with hydrogens</a>";
$entry .= " or <a href='download_trimmed.php?{$_SESSION['sessTag']}&file={$pdb}'>without hydrogens (flips only)</a> <b>which should be re-refined before deposition.</b></p>\n";
} else {
$entry .= "<p>You can now download the optimized and annotated <a href='{$url}'>PDB file with hydrogens</a>";
$entry .= " or <a href='download_trimmed.php?{$_SESSION['sessTag']}&file={$pdb}'>without hydrogens (flips only)</a>.</p>\n";
}
$nqkin = $_SESSION['dataDir'] . '/' . MP_DIR_KINS . "/{$model['prefix']}flipnq.kin";
$hiskin = $_SESSION['dataDir'] . '/' . MP_DIR_KINS . "/{$model['prefix']}fliphis.kin";
if (file_exists($nqkin) && file_exists($hiskin)) {
$entry .= "<p>These Flipkin kinemages illustrate both flip states for all Asn/Gln/His.\n";
$entry .= "Residues that Reduce <i>suggested</i> flipping are marked with stars (*) in the Views menu.\n";
$entry .= "<ul>\n";
$entry .= "<li>" . linkKinemage("{$model['prefix']}flipnq.kin") . "</li>\n";
$entry .= "<li>" . linkKinemage("{$model['prefix']}fliphis.kin") . "</li>\n";
$entry .= "</ul></p>\n";
}
if (strpos($autoflip, "<li>") !== false) {
$entry .= $autoflip;
}
if (strpos($userflip, "<li>") !== false) {
$entry .= $userflip;
}
if (strpos($userkeep, "<li>") !== false) {
$entry .= $userkeep;
}
// Go ahead and make the notebook entry inline -- this can't take more than 1-2 sec.
if ($_SESSION['reduce_blength'] == 'ecloud') {
$flags = '-build';
} else {
$flags = '-build -nuclear';
}
if ($rerun) {
$title = "Added H with {$flags} and user overrides to get {$model['pdb']}";
} else {
$title = "Added H with {$flags} to get {$model['pdb']}";
}
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry($title, $entry, "{$parent['id']}|{$modelID}", "auto", "add_h.png");
$_SESSION['bgjob']['modelID'] = $_REQUEST['modelID'];
$_SESSION['bgjob']['doflip'] = $_REQUEST['doflip'];
// User requested changes; re-launch Reduce
if ($rerun) {
mpLog("reduce-custom:User made changes to flips suggested by Reduce -build");
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/reduce-fix.php", "reduce_done.php", 5);
} else {
mpLog("reduce-accept:User accepted all flips proposed by Reduce -build as-is");
pageGoto("reduce_done.php", $_SESSION['bgjob']);
}
}
$flag = "-cass";
break;
}
// Do this after file name or it'll get junked up!
if ($rainbow) {
$flag .= " -colornc";
}
// Color ramp N --> C ?
if ($cpkballs) {
$flag .= " -show 'mc,sc,ht,at'";
}
$tasks['kin'] = "Make kinemage using <code>Prekin {$flag}</code>";
setProgress($tasks, 'kin');
// updates the progress display if running as a background job
$outfile = "{$kinDir}/{$model['prefix']}{$scriptName}.kin";
if ($scriptName == "halfbonds") {
$cmd = "prekin {$flag} {$infile} | php -f " . MP_BASE_DIR . "/lib/halfbonds.php > {$outfile}";
} else {
$cmd = "prekin {$flag} {$infile} > {$outfile}";
}
exec($cmd);
// Lab notebook entry / results page
$entry = "";
$entry .= "<p>Your kinemage is ready for viewing in KiNG: " . linkKinemage("{$model['prefix']}{$scriptName}.kin") . "</p>\n";
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Made simple kinemage of {$model['pdb']}", $entry, $modelID, "auto", "porin_barrel.png");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
makeRamachandranPDF($infile, $outfile);
$labbookEntry .= "<h3>Multi-model Ramachandran plot</h3>\n";
$labbookEntry .= "<p>" . linkAnyFile("{$ensemble['prefix']}rama.pdf", "Ramachandran plot PDF") . "</p>\n";
}
if ($opts['doMultiGraph']) {
setProgress($tasks, 'multigraph');
// updates the progress display if running as a background job
$outfile = "{$kinDir}/{$ensemble['prefix']}multigraph.kin";
makeChartKin($infiles, $outfile);
$labbookEntry .= "<div class='alert'>\n<center><h3>ALPHA TEST</h3></center>\n";
$labbookEntry .= "Not suitable for use by the general public: " . linkKinemage("{$ensemble['prefix']}multigraph.kin", "Multi-criterion graph");
$labbookEntry .= "</div>\n";
}
if ($opts['doMultiModelChart']) {
setProgress($tasks, 'multichart');
// updates the progress display if running as a background job
$outfile = "{$kinDir}/{$ensemble['prefix']}mmmcc.kin";
// Multi-Model Multi-Criterion Chart
writeMultimodelChart($infiles, $outfile);
$labbookEntry .= "<div class='alert'>\n<center><h3>ALPHA TEST</h3></center>\n";
$labbookEntry .= "Not suitable for use by the general public: " . linkKinemage("{$ensemble['prefix']}mmmcc.kin", "Multi-chart mockup");
$labbookEntry .= "</div>\n";
}
setProgress($tasks, null);
//-----------------------------------------------------------------
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Analysis output: all-atom contacts and geometry for {$ensemble['pdb']}", $labbookEntry, $ensID, "auto", "clash_rama.png");
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
