/**
* 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();
}
/**
* Documentation for this function.
*/
function onStartSSwing()
{
$req = $_REQUEST;
if ($req['cmd'] == 'Go back') {
$c = getContext();
$ctx['modelID'] = $c['modelID'];
$ctx['map'] = $c['map'];
pageGoto("sswing_setup1.php", $ctx);
return;
}
$ctx = getContext();
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob']['modelID'] = $ctx['modelID'];
$_SESSION['bgjob']['edmap'] = $ctx['map'];
$_SESSION['bgjob']['cnit'] = $req['cnit'];
$_SESSION['bgjob']['fastSearch'] = $req['fastSearch'];
mpLog("sswing:Launched SSWING to refit " . count($_req['cnit']) . " residue(s)");
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/sswing.php", "sswing_choose.php", 5);
}
/**
* Launches Prekin when the user submits the form.
*/
function onRunProbe()
{
$req = $_REQUEST;
//if($req['cmd'] == 'Cancel')
if ($req['cmd'] == 'Go back') {
pageGoto("interface_setup1.php");
return;
}
// Otherwise, moving forward:
$_SESSION['lastUsedModelID'] = $req['modelID'];
// this is now the current model
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob'] = $req;
mpLog("interface:Visualizing interface contacts with complex Probe run");
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/interface-vis.php", "generic_done.php", 5);
}
/**
* This function calls the notebook editor so the user can modify the notebook
* entry. Control is transfered to another page, namely, notebook_edit.php.
* When that page is done, it will call pageReturn(), and control will return
* to this class--display() will be called again to show the entry.
*
* This function gets called when the user clicks the link made by display()
*
* $arg contains the entry number of the notebook entry to edit. It was specified
* by the call to makeEventURL() that occurs in display(), above.
* $req is filled in with the usually info from the form submission, but
* we don't need to use it for anything here.
*/
function onPdbConvert()
{
$req = $_REQUEST;
if ($req['cmd'] == 'Cancel') {
pageReturn();
return;
}
if (isset($req['modelID'])) {
$_SESSION['lastUsedModelID'] = $req['modelID'];
// this is now the current model
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob'] = $req;
mpLog("convertPdb:Converted '{$req['modelID']}' to PDBv2.3");
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/pdb_convert.php", "generic_done.php", 3);
} else {
$context = getContext();
if (isset($req['modelID'])) {
$context['modelID'] = $req['modelID'];
}
//if(isset($req['scriptName'])) $context['scriptName'] = $req['scriptName'];
setContext($context);
}
}
*****************************************************************************/
// EVERY *top-level* page must start this way:
// 1. Define it's relationship to the root of the MolProbity installation.
// 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';
// 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();
mpLog("king:User opened a kinemage file in KiNG");
#{{{ a_function_definition - sumary_statement_goes_here
############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
# MAIN - the beginning of execution for this page
############################################################################
// Note that changing size breaks the "Close" button, at least in Safari, b/c the page reloads.
if (isset($_REQUEST['size'])) {
$kingSize = $_REQUEST['size'];
setcookie('viewking_kingSize', $kingSize);
// You could get in trouble if a background job was running (hence the check here)
// or if you somehow hit the size-change link while another page was loading (unlikely),
/**
* Documentation for this function.
*/
function onFeedbackSend()
{
$req = $_REQUEST;
$subject = "MolProbity feedback: {$req['inRegardTo']}";
$msg_text = "\n" . "User name : {$req['senderName']}\n" . "User email : {$req['senderEmail']}\n" . "Subject : {$req['inRegardTo']}\n" . "\n\n" . wordwrap($req['feedbackText'], 76);
// Write a local copy of the email in case sendmail isn't working
$tmpfile = tempnam(MP_BASE_DIR . '/feedback', 'email_');
chmod($tmpfile, 0666 & ~MP_UMASK);
// tempnam gets wrong permissions sometimes?
$h = fopen($tmpfile, 'wb');
fwrite($h, $msg_text);
fclose($h);
$ok = mpSendEmail($req['senderName'], $req['senderEmail'], $subject, $msg_text);
mpLog("feedback:Sent with subject {$req['inRegardTo']}; success={$ok}");
pageGoto("feedback_done.php", $msg_text);
}
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));
}
/**
* Documentation for this function.
*/
function onAddH()
{
$req = $_REQUEST;
if ($req['cmd'] == 'Cancel') {
pageReturn();
return;
}
// Otherwise, moving forward:
if (isset($req['modelID']) && isset($req['method']) && isset($req['blength'])) {
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob']['modelID'] = $req['modelID'];
$_SESSION['bgjob']['makeFlipkin'] = $req['makeFlipkin'];
$_SESSION['bgjob']['nqh_regularize'] = $req['nqh_regularize'];
$_SESSION['bgjob']['reduce_blength'] = $req['blength'];
$_SESSION['reduce_blength'] = $_SESSION['bgjob']['reduce_blength'];
if ($req['method'] == 'build') {
if ($_SESSION['bgjob']['reduce_blength'] == 'ecloud') {
mpLog("reduce-build:User ran default Reduce -build job; flipkins=" . $_REQUEST['makeFlipkin']);
} else {
mpLog("reduce-build:User ran default Reduce -build -nuclear job; flipkins=" . $_REQUEST['makeFlipkin']);
}
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/reduce-build.php", "reduce_choose.php", 5);
} elseif ($req['method'] == 'nobuild') {
if ($_SESSION['bgjob']['reduce_blength'] == 'ecloud') {
mpLog("reduce-nobuild:User ran Reduce with -nobuild9999 flag");
} else {
mpLog("reduce-nobuild:User ran Reduce with -nobuild9999 -nuclear flag");
}
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/reduce-nobuild.php", "generic_done.php", 5);
}
} else {
$context = getContext();
if (isset($req['modelID'])) {
$context['modelID'] = $req['modelID'];
}
if (isset($req['method'])) {
$context['method'] = $req['method'];
}
if (isset($req['blength'])) {
$context['blength'] = $req['blength'];
}
setContext($context);
}
}
/**
* Launches Prekin when the user submits the form.
*/
function onRunPrekin()
{
$req = $_REQUEST;
if ($req['cmd'] == 'Cancel') {
pageReturn();
return;
}
// Otherwise, moving forward:
if (isset($req['modelID']) && isset($req['scriptName'])) {
$_SESSION['lastUsedModelID'] = $req['modelID'];
// this is now the current model
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob'] = $req;
mpLog("makekin:Creating simple kinemages from built-in Prekin script '{$req['scriptName']}'");
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/makekin.php", "generic_done.php", 3);
} else {
$context = getContext();
if (isset($req['modelID'])) {
$context['modelID'] = $req['modelID'];
}
if (isset($req['scriptName'])) {
$context['scriptName'] = $req['scriptName'];
}
setContext($context);
}
}
function getMaps($code)
{
global $map_notebook_msg;
$map_notebook_msg = "";
$prog = getProgressTasks();
if ($_SESSION['bgjob']['eds_2fofc']) {
$prog['2fofc'] = "Download 2Fo-Fc map from the EDS";
}
if ($_SESSION['bgjob']['eds_fofc']) {
$prog['fofc'] = "Download Fo-Fc (difference) map from the EDS";
}
$mapDir = "{$_SESSION['dataDir']}/" . MP_DIR_EDMAPS;
if (!file_exists($mapDir)) {
mkdir($mapDir, 0777);
}
if ($_SESSION['bgjob']['eds_2fofc']) {
setProgress($prog, '2fofc');
$mapName = "{$code}.omap.gz";
$mapPath = "{$mapDir}/{$mapName}";
if (!file_exists($mapPame)) {
$tmpMap = getEdsMap($code, 'omap', '2fofc');
if ($tmpMap && copy($tmpMap, $mapPath)) {
unlink($tmpMap);
$_SESSION['edmaps'][$mapName] = $mapName;
mpLog("edmap-eds:User requested 2Fo-Fc map for {$code} from the EDS");
$map_notebook_msg .= "<p>The 2Fo-Fc map for {$code} was successfully retrieved from the EDS.</p>\n";
} else {
$map_notebook_msg .= "<p><div class='alert'>The 2Fo-Fc map for {$code} could not be retrieved from the EDS.</div></p>\n";
}
} else {
echo "Map file already exists";
}
}
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");
$map_notebook_msg .= "<p>The Fo-Fc map for {$code} was successfully retrieved from the EDS.</p>\n";
} else {
$map_notebook_msg .= "<p><div class='alert'>The Fo-Fc map for {$code} could not be retrieved from the EDS.</div></p>\n";
}
}
}
setProgress($prog, null);
}
/**
* 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']);
}
}
/**
* Documentation for this function.
*/
function onSetTimezone()
{
$req = $_REQUEST;
if (isset($req['timezone'])) {
$_SESSION['timeZone'] = $req['timezone'];
mpLog("timezone:User specified timezone as " . $req['timezone']);
}
}
/**
* Documentation for this function.
*/
function onUploadHetDictFile()
{
if ($_REQUEST['cmd'] == "Cancel") {
pageReturn();
} else {
// Remove the old het dictionary:
if (isset($_SESSION['hetdict'])) {
unlink($_SESSION['hetdict']);
unset($_SESSION['hetdict']);
}
$dictName = "user_het_dict.txt";
$dictPath = "{$_SESSION['dataDir']}/" . MP_DIR_TOPPAR;
if (!file_exists($dictPath)) {
mkdir($dictPath, 0777);
}
$dictPath .= "/{$dictName}";
if (!$_FILES['uploadFile']['error'] && $_FILES['uploadFile']['size'] > 0 && move_uploaded_file($_FILES['uploadFile']['tmp_name'], $dictPath)) {
// Uploaded file probably has restrictive permissions
chmod($dictPath, 0666 & ~MP_UMASK);
exec("echo >> {$dictPath}");
// adds a blank line
exec("cat " . MP_REDUCE_HET_DICT . " >> {$dictPath}");
// appends the std dict
$_SESSION['hetdict'] = $dictName;
mpLog("hetdict-upload:User uploaded an custom het dictionary file");
pageGoto("upload_other_done.php", array('type' => 'hetdict'));
} else {
$this->doUploadError('hetdict');
}
}
}
/**
* This function calls the notebook editor so the user can modify the notebook
* entry. Control is transfered to another page, namely, notebook_edit.php.
* When that page is done, it will call pageReturn(), and control will return
* to this class--display() will be called again to show the entry.
*
* This function gets called when the user clicks the link made by display()
*
* $arg contains the entry number of the notebook entry to edit. It was specified
* by the call to makeEventURL() that occurs in display(), above.
* $req is filled in with the usually info from the form submission, but
* we don't need to use it for anything here.
*/
function onFillGaps()
{
$req = $_REQUEST;
if ($req['cmd'] == 'Cancel') {
pageReturn();
return;
}
if (isset($req['modelID'])) {
$_SESSION['lastUsedModelID'] = $req['modelID'];
// this is now the current model
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob'] = $req;
mpLog("makekin:Filling fragments in: '{$req['modelID']}'");
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/fillfragments.php", "generic_done.php", 3);
} else {
$context = getContext();
if (isset($req['modelID'])) {
$context['modelID'] = $req['modelID'];
}
//if(isset($req['scriptName'])) $context['scriptName'] = $req['scriptName'];
setContext($context);
}
}
############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
# MAIN - the beginning of execution for this page
############################################################################
if (!isset($_REQUEST['fileName']) || !isset($_REQUEST['fileContents'])) {
die("This page for file uploads only");
}
// First make sure this is a legal file name with no weird chars, ending in .kin
$outname = censorFileName($_REQUEST['fileName'], "kin");
// Now make sure we have a directory to put it in
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_KINS;
if (!file_exists($outpath)) {
mkdir($outpath, 0777);
}
// Finally, make sure we don't overwrite anything already in existance!
while (file_exists("{$outpath}/{$outname}" . $serial)) {
$serial++;
}
$outpath = "{$outpath}/{$outname}" . $serial;
$h = fopen($outpath, 'wb');
fwrite($h, $_REQUEST['fileContents']);
fclose($h);
$size = strlen($_REQUEST['fileContents']);
echo "OK name={$outpath}; size={$size}\n";
// msg for KiNG
mpLog("savekin:User saved a modified kinemage under {$outpath}; size={$size}");
/**
* Documentation for this function.
*/
function onRunAnalysis()
{
$req = $_REQUEST;
if ($req['cmd'] == 'Cancel') {
pageReturn();
return;
}
// Otherwise, moving forward:
if (isset($req['ensID'])) {
$_SESSION['lastUsedModelID'] = $req['ensID'];
// this is now the current "model"
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob'] = $req;
mpLog("aacgeom:Running all-atom contact and geometric analyses");
// The chartXXX vars aren't defined in this interface (yet), but they don't hurt anything...
if ($req['kinClashes'] || $req['kinHbonds'] || $req['kinContacts'] || $req['chartClashlist']) {
mpLog("aacgeom-aac:Generataing all-atom contact data of some type");
}
if ($req['kinRama'] || $req['chartRama']) {
mpLog("aacgeom-rama:Doing Ramachandran analysis");
}
if ($req['kinRota'] || $req['chartRota']) {
mpLog("aacgeom-rota:Doing rotamer analysis");
}
if ($req['kinCBdev'] || $req['chartCBdev']) {
mpLog("aacgeom-cbdev:Doing C-beta deviation analysis");
}
if ($req['kinBaseP'] || $req['chartBaseP']) {
mpLog("aacgeom-basep:Validating base-phosphate distances vs sugar puckers");
}
// doMultiGraph hasn't been renamed to doCharts yet...
if ($req['doKinemage']) {
mpLog("aacgeom-mkin:Multi-criterion validation kinemage");
}
//if($req['doCharts']) mpLog("aacgeom-mchart:Multi-criterion validation chart");
if ($req['doMultiGraph']) {
mpLog("aacgeom-mchart:Multi-criterion validation chart");
}
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/ens_aacgeom.php", "generic_done.php", 5);
}
}
/** Returns true if a new session was created, false otherwise. */
function mpStartSession($createIfNeeded = false)
{
// First set up constants, env. variables, etc.
mpInitEnvirons();
// Cookies cause more trouble than they're worth
ini_set("session.use_cookies", 0);
ini_set("session.use_only_cookies", 0);
// We want to control garbage collection more carefully
// (MP_SESSION_LIFETIME is a dummy -- lifetime is determined per-session)
ini_set("session.gc_maxlifetime", MP_SESSION_LIFETIME);
#ini_set("session.gc_probability", 100);
// Set up our session name
session_name(MP_SESSION_NAME);
// Establish custom routines for persisting session data
session_set_save_handler("mpSessOpen", "mpSessClose", "mpSessRead", "mpSessWrite", "mpSessDestroy", "mpSessGC");
// Restore the session data
@session_start();
// we get meaningless error msgs when used from a script env.
mpCheckSessionID(session_id());
// just in case
// Check to make sure we have a working directory for this user.
//$dataDir = MP_BASE_DIR."/public_html/data/".session_id();
$dataDir = MP_JOB_DATA_DIR . session_id();
if (!file_exists($dataDir)) {
if ($createIfNeeded) {
// Always do cleanup before starting a new session
// (MP_SESSION_LIFETIME is a dummy -- lifetime is determined per-session)
mpSessGC(MP_SESSION_LIFETIME);
// Main data directories
mkdir($dataDir, 0770);
// Default mode; is modified by UMASK too.
mkdir("{$dataDir}/" . MP_DIR_SYSTEM, 0770);
mkdir("{$dataDir}/tmp", 0770);
// Others specified in config.php must be created on demand.
// Set up some session variables. See docs for explanation.
$_SESSION['dataDir'] = $dataDir;
$_SESSION['dataURL'] = "data/" . session_id();
$_SESSION['sessTag'] = session_name() . "=" . session_id();
$_SESSION['userIP'] = getVisitorIP();
$_SESSION['timeZone'] = MP_DEFAULT_TIMEZONE;
$_SESSION['kingSize'] = "default";
$_SESSION['currEventID'] = 1;
// used by (optional) MVC/event architecture
$_SESSION['models'] = array();
// no models to start with
$_SESSION['ensembles'] = array();
// no ensembles to start with
$_SESSION['reduce_blength'] = "ecloud";
// x-H distance
$_SESSION['useSEGID'] = false;
// TODO: perform other tasks to start a session
// Create databases, etc, etc.
//mpLog("new-session:New user session started");
$sessionCreated = true;
} else {
mpLog("badsession:Unknown session with ID '" . session_id() . "'");
die("Specified session '" . session_id() . "' does not exist.");
}
} else {
$sessionCreated = false;
}
// Mark the lifetime of this session
mpSessSetTTL(session_id(), MP_SESSION_LIFETIME);
// Also set location of Reduce's heterogen dictionary,
// overriding the value set up by mpInitEnvirons().
// Better here than on command line b/c it affects e.g. flipkin too
if (isset($_SESSION['hetdict'])) {
putenv("REDUCE_HET_DICT=" . $_SESSION['hetdict']);
} else {
putenv("REDUCE_HET_DICT=" . MP_REDUCE_HET_DICT);
}
return $sessionCreated;
}
// 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();
#{{{ a_function_definition - sumary_statement_goes_here
############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
# MAIN - the beginning of execution for this page
############################################################################
// Security check on filename
$file = realpath($_REQUEST['file']);
if (!$file || !startsWith($file, realpath($_SESSION['dataDir']))) {
mpLog("security:Attempt to access '{$file}' as '{$_REQUEST['file']}'");
die("Security failure: illegal file request '{$_REQUEST['file']}'");
}
$tmp = mpTempfile('tmp_pdb_trim_');
reduceTrim($file, $tmp);
$name = basename($file);
if (preg_match('/H[0-9]*.pdb$/', $name)) {
// uses preg_split to split the name into an array with the H from the name missing.
$nameArray = preg_split('/H([0-9]*.pdb)$/', $name, -1, PREG_SPLIT_DELIM_CAPTURE);
$name = $nameArray[0] . $nameArray[1];
} elseif (preg_match('/H_reg[0-9]*.pdb$/', $name)) {
// uses preg_split to split the name into an array with the H from the name missing.
$nameArray = preg_split('/H_reg([0-9]*.pdb)$/', $name, -1, PREG_SPLIT_DELIM_CAPTURE);
$name = $nameArray[0] . $nameArray[1];
}
### FUNKY: This turns into a binary file download rather than an HTML page,
$s .= "<p><div class='alert'>The 2Fo-Fc map for {$code} could not be retrieved from the EDS.</div></p>\n";
}
} else {
$s .= "<p><div class='alert'>The 2Fo-Fc map for {$code} could not be retrieved, because a file of the same name already exists.</div></p>\n";
}
}
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");
$funcArgs = $page['handlers'][$eid]['funcArgs'];
// We use a variable function name here to call the handler.
//$delegate->$funcName($funcArg, $_REQUEST);
// Now this is *real* voodoo:
call_user_func_array(array(&$delegate, $funcName), $funcArgs);
// In case we changed $_SESSION but display() calls mpSessReadOnly()
// This save won't stop the session from being automatically saved again
// after display() and the end of the page.
// (Though display() shouldn't write to $_SESSION anyway, except events!)
// However: this can truncate the session file just as a background job
// is starting, so launchBackground() makes the session read-only,
// so this call does nothing in that case.
mpSaveSession();
} else {
$GLOBALS['badEventOccurred'] = true;
mpLog("bad-event:Event ID '{$eid}' is unknown for page {$page['delegate']}. No action taken.");
}
}
// Clean up from event processing //////////////////////////////////////////////
clearEventHandlers();
// events defined by previous display() are not valid
// Handle a return from a called page //////////////////////////////////////////
// This should now be possible but has not been implemented yet.
// pageReturn() should set global variables ($page_return_callback and _argument)
// and there should be a while() loop here to process multi-level returns.
// Display user interface //////////////////////////////////////////////////////
$page = end($_SESSION['pages']);
// not a ref; read only
$delegate = makeDelegateObject();
// Can't call mpSessReadOnly() or we won't be able to create events.
// Other than events, display() shouldn't write to the session though.
/**
* Documentation for this function.
*/
function onRunAnalysis()
{
$req = $_REQUEST;
if ($req['cmd'] == 'Cancel') {
pageReturn();
return;
}
// Otherwise, moving forward:
if (isset($req['modelID'])) {
$_SESSION['lastUsedModelID'] = $req['modelID'];
// this is now the current model
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob'] = $req;
mpLog("aacgeom:Running all-atom contact and geometric analyses");
if ($req['kinClashes'] || $req['kinHbonds'] || $req['kinContacts'] || $req['chartClashlist']) {
mpLog("aacgeom-aac:Generataing all-atom contact data of some type");
}
if ($req['kinRama'] || $req['chartRama']) {
mpLog("aacgeom-rama:Doing Ramachandran analysis");
}
if ($req['kinRota'] || $req['chartRota']) {
mpLog("aacgeom-rota:Doing rotamer analysis");
}
if ($req['kinGeom'] || $req['chartGeom']) {
mpLog("aacgeom-geom:Doing geometry analysis");
}
if ($req['kinCBdev'] || $req['chartCBdev']) {
mpLog("aacgeom-cbdev:Doing C-beta deviation analysis");
}
if ($req['kinBaseP'] || $req['chartBaseP']) {
mpLog("aacgeom-basep:Validating base-phosphate distances vs sugar puckers");
}
if ($req['kinSuite'] || $req['chartSuite']) {
mpLog("aacgeom-suite:Validating RNA backbone conformations");
}
if ($req['doKinemage']) {
mpLog("aacgeom-mkin:Multi-criterion validation kinemage");
}
if ($req['doCharts']) {
mpLog("aacgeom-mchart:Multi-criterion validation chart");
}
$modelID = $_SESSION['bgjob']['modelID'];
// $model = $_SESSION['models'][$modelID];
if ($req['chartHoriz'] and !isset($_SESSION['models'][$modelID]['mtz_file'])) {
// check to see if there is one mtz. If so, then link it to the
// model being analyzed automatically
$xrayDir = $_SESSION['dataDir'] . '/' . MP_DIR_XRAYDATA;
if (file_exists($xrayDir)) {
$mtzs = array();
$handle = opendir($xrayDir);
while (false !== ($entry = readdir($handle))) {
if (substr($entry, -4) != ".mtz") {
continue;
}
$mtzs[] = $entry;
}
if (count($mtzs) == 1) {
$_SESSION['models'][$modelID]['mtz_file'] = $xrayDir . '/' . $mtzs[0];
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/aacgeom.php", "generic_done.php", 5);
} else {
pageCall("link_model_2_mtz.php", array('modelID' => $modelID));
}
} else {
pageCall("link_model_2_mtz.php", array('modelID' => $modelID));
}
} else {
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/aacgeom.php", "generic_done.php", 5);
}
}
}
if (!defined('MP_BASE_DIR')) {
define('MP_BASE_DIR', realpath(dirname(__FILE__) . '/..'));
}
// 2. Include core functionality - defines constants, etc.
require_once MP_BASE_DIR . '/lib/core.php';
// 3. Restore session data. If you don't want to access the session
// data for some reason, you must call mpInitEnvirons() instead.
mpStartSession();
// 4. For pages that want to see the session but not change it, such as
// pages that are refreshing periodically to monitor a background job.
#mpSessReadOnly();
# MAIN - the beginning of execution for this page
############################################################################
if ($_POST['confirm']) {
// Must log first or we lose our session ID for the log!
mpLog("logout-session:User cleaned up all session files and left the site");
mpDestroySession();
}
// Start the page: produces <HTML>, <HEAD>, <BODY> tags
echo mpPageHeader("Thanks!");
############################################################################
?>
<center>
Thanks for using MolProbity!
All your data files have been erased.
<br>
<br>
<br>
<br>
<a href="index.php"><img src="img/mplogo_clear.png"><br>Start another MolProbity session</a>
<br>
/**
* Documentation for this function.
*/
function onAddH()
{
$req = $_REQUEST;
if ($req['cmd'] == 'Cancel') {
pageReturn();
return;
}
// Otherwise, moving forward:
if (isset($req['ensID']) && isset($req['method']) && isset($req['blength'])) {
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob']['ensID'] = $req['ensID'];
$_SESSION['bgjob']['method'] = $req['method'];
$_SESSION['bgjob']['reduce_blength'] = $req['blength'];
mpLog("reduce-ensemble:User ran default Reduce -{$req['method']} job on an ensemble");
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/ens_reduce.php", "generic_done.php", 5);
} else {
$context = getContext();
if (isset($req['ensID'])) {
$context['ensID'] = $req['ensID'];
}
if (isset($req['method'])) {
$context['method'] = $req['method'];
}
if (isset($req['blength'])) {
$context['blength'] = $req['blength'];
}
setContext($context);
}
}