/**
* Documentation for this function.
*/
function onMakeFinalPDB()
{
$context = getContext();
$newModel = $_SESSION['models'][$context['newModel']];
$oldModel = $_SESSION['models'][$newModel['parent']];
$newPDB = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
$oldPDB = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $oldModel['pdb'];
$url = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
// Put our money where our mouth is and calculate that new PDB file
$all_changes = $context['sswingChanges'];
$usercnit = $_REQUEST['cnit'];
// Remove changes for residues that weren't selected
foreach ($all_changes as $k => $v) {
$res = substr($k, 0, 9);
if (!isset($usercnit[$res])) {
unset($all_changes[$k]);
} else {
$changed_res[$res] = $res;
}
// used below for the lab notebook
}
// Make PDB file
pdbSwapCoords($oldPDB, $newPDB, $all_changes);
// Make up the lab notebook entry
$text = "The following residues were automatically refit by SSWING, creating {$newModel['pdb']} from {$oldModel['pdb']}:\n<ul>\n";
foreach ($changed_res as $res) {
$text .= "<li>{$res}</li>\n";
}
$text .= "</ul>\n";
$text .= "<p>You can now <a href='{$url}'>download the optimized and annotated PDB file</a> (" . formatFilesize(filesize($newPDB)) . ").</p>\n";
$entryNum = addLabbookEntry("Refit sidechains with SSWING to get {$newModel['pdb']}", $text, "{$oldModel['id']}|{$newModel['id']}", 'auto');
$ctx = array('labbookEntry' => $entryNum);
pageGoto("generic_done.php", $ctx);
}
mpSaveSession();
#{{{ a_function_definition - sumary_statement_goes_here
############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
# MAIN - the beginning of execution for this page
############################################################################
$modelID = $_SESSION['bgjob']['modelID'];
$model = $_SESSION['models'][$modelID];
$opts = $_SESSION['bgjob'];
$doAAC = $opts['doKinemage'] && ($opts['kinClashes'] || $opts['kinHbonds'] || $opts['kinContacts']) || $opts['doCharts'] && $opts['chartClashlist'];
$labbookEntry = runAnalysis($modelID, $_SESSION['bgjob']);
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Analysis output: " . ($doAAC ? "all-atom contacts and " : "") . "geometry for {$model['pdb']}", $labbookEntry, $modelID, "auto", $doAAC ? "clash_rama.png" : "ramaplot.png");
/*********************
To compare:
array_diff( array_keys($worst1), array_keys($worst2) ); // things fixed 1->2
array_diff( array_keys($worst2), array_keys($worst1) ); // things broken 1->2
to find residues that are bad in one structure but not the other.
A detailed comparison can then be done between residues in:
array_intersect( array_keys($worst1), array_keys($worst2) ); // things changed but not fixed
**********************
Alternately, you might do
array_unique( array_merge(...keys...) )
function onEditPDB()
{
$req = $_REQUEST;
//if($req['cmd'] == 'Cancel')
if ($req['cmd'] == 'Go back') {
pageGoto("editpdb_setup1.php");
return;
}
// Otherwise, moving forward:
$oldID = $req['modelID'];
$oldModel = $_SESSION['models'][$oldID];
$inpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $oldModel['pdb'];
$newModel = createModel($oldID . "_edit");
$newID = $newModel['id'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
$s = "";
if (is_array($req['removechain']) && count($req['removechain']) > 0) {
removeChains($inpath, $outpath, $req['removechain']);
$s .= "<p>You created {$newModel['pdb']} by removing chain(s) " . implode(', ', $req['removechain']) . " from {$oldModel['pdb']}.\n";
mpLog("editpdb:Removed chains from a PDB file");
} else {
copy($inpath, $outpath);
}
$resolu = $req['resolution'] + 0;
$oldRes = $oldModel['stats']['resolution'] + 0;
if ($resolu && ($oldRes == 0 || $oldRes != $resolu)) {
$remark2 = sprintf("REMARK 2 \nREMARK 2 RESOLUTION. %.2f ANGSTROMS. \n", $resolu);
replacePdbRemark($outpath, $remark2, 2);
$s .= "<p>You manually set the resolution for {$newModel['pdb']}.\n";
mpLog("editpdb:Changed/set resolution for a PDB file");
}
if ($req['removeHs']) {
$newModel = createModel($oldID . "_trimmed");
$newID = $newModel['id'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newModel['pdb'];
reduceTrim($inpath, $outpath);
$s .= "<p>You created {$newModel['pdb']} by removing hydrogens from {$oldModel['pdb']}.\n";
mpLog("editpdb:Removed hydrogens from a PDB file");
}
$newModel['stats'] = pdbstat($outpath);
$newModel['history'] = "Edited {$oldModel['pdb']}";
$newModel['isUserSupplied'] = $oldModel['isUserSupplied'];
$_SESSION['models'][$newID] = $newModel;
$_SESSION['lastUsedModelID'] = $newID;
// this is now the current model
$details = describePdbStats($newModel['stats'], true);
$s .= "<ul>\n";
foreach ($details as $detail) {
$s .= "<li>{$detail}</li>\n";
}
$s .= "</ul>\n";
$entrynum = addLabbookEntry("Created PDB file {$newModel['pdb']}", $s, "{$oldID}|{$newID}", "auto", "scissors.png");
pageGoto("generic_done.php", array('labbookEntry' => $entrynum));
}
# MAIN - the beginning of execution for this page
############################################################################
$modelID = $_SESSION['bgjob']['modelID'];
$model = $_SESSION['models'][$modelID];
$pdbDir = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
$pdb = $pdbDir . '/' . $model['pdb'];
// Set up progress message
$tasks['convert'] = "Convert pdb with <code>remediator -oldout</code>";
$tasks['notebook'] = "Add entry to lab notebook";
setProgress($tasks, 'convert');
// updates the progress display if running as a background job
if (!file_exists($pdbDir)) {
mkdir($pdbDir, 0777);
}
// shouldn't ever happen, but might...
$outpdb = $pdbDir . '/' . $modelID . "v23.pdb";
downgradePDB($pdb, $outpdb);
setProgress($tasks, 'notebook');
$outpdburl = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $modelID . "v23.pdb";
$entry = "remediator was run on {$model['pdb']} to convert its atoms to PDB v2.3 format.\n";
$entry .= "<p>You can now <a href='{$outpdburl}'>download the converted PDB file with hydrogens</a> ";
$entry .= "or <a href='download_trimmed.php?{$_SESSION['sessTag']}&file={$outpdb}'>without hydrogens</a>.</p>\n";
$entry .= $pdbEntries;
//$entry .= "<p>A kinemage of all of the fragments is ready for viewing in KiNG: ".linkKinemage($modelID.'.kin')."</p>\n";
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Converted {$model['pdb']} to {$modelID}" . "v23.pdb.", $entry, "{$modelID}|{$newModel['id']}", "auto", "downgrade.gif");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
// updates the progress display if running as a background job
exec($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);
$entry .= "</pre></p>\n";
}
setProgress($tasks, 'notebook');
// updates the progress display if running as a background job
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Visualized interface contacts for {$model['pdb']}", $entry, $modelID, "auto", "barnase_barstar.png");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
//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;
$newModel['history'] = "Derived from {$model['pdb']} by Reduce -nobuild9999 -nuclear";
}
$newModel['isUserSupplied'] = $model['isUserSupplied'];
$newModel['isReduced'] = true;
$_SESSION['models'][$newModel['id']] = $newModel;
$_SESSION['bgjob']['modelID'] = $newModel['id'];
$_SESSION['lastUsedModelID'] = $newModel['id'];
// this is now the current model
$hcount = countReduceChanges($outpath);
setProgress($tasks, 'notebook');
$pdb = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $outname;
$url = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $outname;
$entry = "Reduce was run on {$model['pdb']} to add and optimize missing hydrogens, resulting in {$newModel['pdb']}.\n";
if ($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";
}
}
$entry .= "Asn/Gln/His flips were not optimized.\n";
$entry .= "<p>You can now <a href='{$url}'>download the annotated PDB file</a> (" . formatFilesize(filesize($pdb)) . ").</p>\n";
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Added H with -nobuild9999 to get {$newModel['pdb']}", $entry, "{$modelID}|{$newModel['id']}", "auto", "add_h.png");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
if ($_SESSION['bgjob']['eds_fofc']) {
setProgress($prog, 'fofc');
$mapName = "{$code}-diff.omap.gz";
$mapPath = "{$mapDir}/{$mapName}";
if (!file_exists($mapPame)) {
$tmpMap = getEdsMap($code, 'omap', 'fofc');
if ($tmpMap && copy($tmpMap, $mapPath)) {
unlink($tmpMap);
$_SESSION['edmaps'][$mapName] = $mapName;
mpLog("edmap-eds:User requested Fo-Fc map for {$code} from the EDS");
$s .= "<p>The Fo-Fc map for {$code} was successfully retrieved from the EDS.</p>\n";
} else {
$s .= "<p><div class='alert'>The Fo-Fc map for {$code} could not be retrieved from the EDS.</div></p>\n";
}
} else {
$s .= "<p><div class='alert'>The Fo-Fc map for {$code} could not be retrieved, because a file of the same name already exists.</div></p>\n";
}
}
} else {
$title = "Failed to retrieve electron density from the EDS";
$s .= "Unable to retrieve maps from the EDS because '{$code}' is not a valid PDB ID.";
}
// I'm too lazy to put it all the hyperlinks by hand :)
$s = preg_replace('/EDS/', "<a href='http://eds.bmc.uu.se/' target='_blank'>EDS</a>", $s);
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry($title, $s, "", "auto", "phe_ed.png");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
$cur = $_SESSION['lastUsedModelID'];
if (isset($_SESSION['ensembles'][$cur])) {
$orig = "the original ensemble (or individual model)";
} else {
foreach ($_SESSION['models'] as $id_m => $model_m) {
if ($_SESSION['lastUsedModelID'] != $id_m) {
$orig = $model_m['pdb'];
}
}
}
$s .= "<p><div class='alert'>The hydrogen atoms from your input model have been removed.<br>\n";
$s .= "You will be able to add hydrogens at either electron cloud positions" . (count($idList) > 1 ? "" : " (default)") . ", which are best for X-ray crystallographic models, <br>";
$s .= "or at nuclear positions, which are best for NMR models, neutron diffraction models, etc.<br>";
$s .= "<br>If you prefer to use the input hydrogen positions, please select {$orig} from the 'Currently working on' list on the next page.</div></p>";
}
if ($model['segmap']) {
$s .= "<p><div class='alert'>Because this model had more segment IDs than chainIDs,\n";
$s .= "the segment IDs were automagically turned into new chain IDs for this model.\n";
$s .= "If you would prefer the original chain IDs, please check the <b>Ignore segID field</b>\n";
$s .= "on the file upload page.</div></p>";
}
$idList[] = $id;
// make sure ensemble ID also appears in notebook
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry($title, $s, implode('|', $idList), "auto", "pdb_icon.png");
setProgress($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", $_SESSION['bgjob']);
}
}
setProgress($tasks, 'notebook');
$pdb = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $newEns['pdb'];
$url = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS . '/' . $newEns['pdb'];
// This should find the line for the first model, at least.
// Some USER MOD records may be munged by the model-joining process.
$hcount = countReduceChanges($pdb);
$entry = "Reduce was run on all models of {$oldEns['pdb']} to add and optimize missing hydrogens, resulting in {$newEns['pdb']}.\n";
if ($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";
}
}
$entry .= "Asn/Gln/His flips were " . ($method == 'build' ? "" : "not") . " optimized.\n";
if ($reduce_blength == 'ecloud') {
$flags = 'electron-cloud';
} else {
$flags = 'nuclear';
}
$entry .= "<p>Reduce placed hydrogens at {$flags} positions.\n";
$entry .= "<p>You can now <a href='{$url}'>download the annotated PDB file</a> (" . formatFilesize(filesize($pdb)) . ").</p>\n";
$_SESSION['bgjob']['labbookEntry'] = addLabbookEntry("Added H with -{$method} to get {$newEns['pdb']}", $entry, "{$oldEnsID}|{$newEnsID}", "auto", "add_h.png");
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
$flag = "-cass";
break;
}
// Do this after file name or it'll get junked up!
if ($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;
