mpLog("new-session:New session started by calling MolProbity directly with " . $pdbCode);
mpLog("browser-detect:" . $_SERVER['HTTP_USER_AGENT']);
mpLog("refered-by:" . $_SERVER['HTTP_REFERER']);
if (strlen($pdbCode) > 10) {
mpLog("bad-pdb:Invalid PDB code detected.");
$pdbCode = "";
}
$_SESSION['bgjob']['pdbCode'] = $pdbCode;
$_SESSION['bgjob']['isCnsFormat'] = false;
$_SESSION['bgjob']['ignoreSegID'] = false;
$_SESSION['bgjob']['biolunit'] = false;
$_SESSION['bgjob']['eds_2fofc'] = false;
$_SESSION['bgjob']['eds_fofc'] = false;
// launch background job
pageCall("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/addmodel.php", "upload_pdb_done.php", 3);
} else {
mpLog("new-session:New interactive user session started on the web");
mpLog("browser-detect:" . $_SERVER['HTTP_USER_AGENT']);
mpLog("refered-by:" . $_SERVER['HTTP_REFERER']);
}
} elseif (isset($_REQUEST['eventID'])) {
$eid = $_REQUEST['eventID'] + 0;
if (isset($page['handlers'][$eid])) {
$funcName = $page['handlers'][$eid]['funcName'];
$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()
/**
* 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);
}
}
/**
* 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);
}
}
/**
* 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);
}
/**
* 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);
}
}
/**
* 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);
}
}
/**
* 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);
}
/**
* 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);
}
}
}
/**
* 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 onFetchEdsMap()
{
$req = $_REQUEST;
if ($req['cmd'] == "Cancel") {
pageReturn();
return;
}
unset($_SESSION['bgjob']);
// Clean up any old data
$_SESSION['bgjob']['pdbCode'] = $req['pdbCode'];
$_SESSION['bgjob']['eds_2fofc'] = $req['eds_2fofc'];
$_SESSION['bgjob']['eds_fofc'] = $req['eds_fofc'];
// logging is done is background job
// launch background job
pageGoto("job_progress.php");
launchBackground(MP_BASE_DIR . "/jobs/fetch-edsmap.php", "generic_done.php", 3);
}
/**
* 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 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);
}
}