/**
* 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", $_SESSION['bgjob']);
}
}
reduceNoBuild($pdb, $outpath, $reduce_blength);
$newModel['stats'] = pdbstat($outpath);
$newModel['parent'] = $modelID;
if ($reduce_blength == 'ecloud') {
$newModel['history'] = "Derived from {$model['pdb']} by Reduce -nobuild9999";
}
if ($reduce_blength == 'nuclear') {
$newModel['history'] = "Derived from {$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($pdb)) . ").</p>\n";
if ($method == 'build') {
$newEnsID = reduceEnsemble($oldEnsID, 'reduceBuild');
} elseif ($method == 'nobuild') {
$newEnsID = reduceEnsemble($oldEnsID, 'reduceNoBuild');
} else {
$newEnsID = reduceEnsemble($oldEnsID);
}
$newEns = $_SESSION['ensembles'][$newEnsID];
$_SESSION['lastUsedModelID'] = $newEnsID;
// this is now the current model
setProgress($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';
