/**
* 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", $ctx);
}
foreach ($cnit as $res) {
$tasks[$res] = "Process {$res} with SSWING";
}
$tasks["combine"] = "Combine all changes and create kinemage";
$tmpdir = $_SESSION['dataDir'] . '/' . MP_DIR_WORK;
if (!file_exists($tmpdir)) {
mkdir($tmpdir, 0777);
}
$all_changes = array();
foreach ($cnit as $res) {
setProgress($tasks, $res);
$changes = runSswing($pdbin, $map, $tmpdir, $res, $_SESSION['bgjob']['fastSearch'] ? true : false);
$all_changes = array_merge($all_changes, $changes);
}
setProgress($tasks, "combine");
pdbSwapCoords($pdbin, $pdbout, $all_changes);
$kindir = $_SESSION['dataDir'] . '/' . MP_DIR_KINS;
if (!file_exists($kindir)) {
mkdir($kindir, 0777);
}
makeSswingKin($pdbin, $pdbout, "{$kindir}/{$newModel['prefix']}sswing.kin", $cnit);
$_SESSION['bgjob']['newModel'] = $newModel['id'];
$_SESSION['lastUsedModelID'] = $newModel['id'];
// this is now the current model
$_SESSION['bgjob']['sswingChanges'] = $all_changes;
setProgress($tasks, null);
############################################################################
// Clean up and go home
unset($_SESSION['bgjob']['processID']);
$_SESSION['bgjob']['endTime'] = time();
$_SESSION['bgjob']['isRunning'] = false;
