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));
}
/**
* $outfile will be overwritten.
* $cnit is an array of CNIT codes for the residues that were processed.
*/
function makeSswingKin($pdb1, $pdb2, $outfile, $cnit)
{
if (file_exists($outfile)) {
unlink($outfile);
}
$stats = describePdbStats(pdbstat($pdb1), false);
$h = fopen($outfile, 'a');
fwrite($h, "@text\n");
fwrite($h, "Sidechains have been refit by SSWING. Details of the input file:\n\n");
foreach ($stats as $stat) {
fwrite($h, "[+] {$stat}\n");
}
fwrite($h, "@kinemage 1\n");
// Calculate views for each residue in CNIT
$ctr = computeResCenters($pdb1);
foreach ($cnit as $res) {
$i++;
$c = $ctr[$res];
fwrite($h, "@{$i}viewid {{$res}}\n@{$i}span 12\n@{$i}zslab 100\n@{$i}center {$c['x']} {$c['y']} {$c['z']}\n");
}
fclose($h);
exec("prekin -quiet -append -animate -onegroup -show 'mc,sc(peach),ca,hy,ht,wa' {$pdb1} >> {$outfile}");
exec("phenix.probe -quiet -noticks -nogroup -self 'alta' {$pdb1} >> {$outfile}");
//exec("probe -quiet -noticks -nogroup -self 'alta' $pdb1 >> $outfile");
exec("prekin -quiet -append -animate -onegroup -show 'mc,sc(sky),ca,hy,ht,wa' {$pdb2} >> {$outfile}");
exec("phenix.probe -quiet -noticks -nogroup -self 'alta' {$pdb2} >> {$outfile}");
//exec("probe -quiet -noticks -nogroup -self 'alta' $pdb2 >> $outfile");
}
/**
* $outfile will be overwritten with a data structure suitable for
* sortable_table.php; see that code for documentation.
* $snapfile will be overwritten with an HTML snapshot of the unsorted table;
* if null, this will be skipped.
* $resout is the file name for the table of residue analysis required for horiz
* chart. if null, this will be skipped.
* $clash is the data structure from loadClashlist()
* $rama is the data structure from loadRamachandran()
* $rota is the data structure from loadRotamer()
* $cbdev is the data structure from loadCbetaDev()
* $pperp is the data structure from loadBasePhosPerp()
* $suites is the data structure from loadSuitenameReport()
* Any of them can be set to null if the data is unavailable.
*/
function writeMulticritChart($infile, $outfile, $snapfile, $resout, $clash, $rama, $rota, $cbdev, $pperp, $suites, $bbonds, $bangles, $cablam, $omega, $outliersOnly = false, $doHtmlTable = true, $cleanupAltloc = true)
{
$startTime = time();
//{{{ Process validation data
// Make sure all residues are represented, and in the right order.
$res = listResidues($infile);
//foreach($res as $k => $v)
//{
// echo $k.$v."\n";
//}
$alts = mapAlternates($res);
//foreach($alts as $k => $v)
//{
// foreach($alts[$k] as $i => $j)
// {
// echo $k.$j."\n";
// }
//}
$Bfact = listResidueBfactors($infile);
$Bfact = $Bfact['res'];
$orderIndex = 0;
// used to maintain original PDB order on sorting.
foreach ($res as $k => $v) {
$res[$k] = array('cnit' => $v, 'order' => $orderIndex++, 'resHiB' => $Bfact[$v]);
}
$cell_color_mild = '#ffb3cc';
$cell_color_bad = '#ff76a9';
//this is used for all xxx_isbad not set otherwise
$cell_color_severe = '#ee4d4d';
if (is_array($clash)) {
$with = $clash['clashes-with'];
foreach ($clash['clashes'] as $cnit => $worst) {
$res[$cnit]['clash_val'] = $worst;
$res[$cnit]['clash'] = sprintf("%.2f", $worst) . "Å<br><small>" . $with[$cnit]['srcatom'] . " with " . $with[$cnit]['dstcnit'] . " " . $with[$cnit]['dstatom'] . "</small>";
$res[$cnit]['clash_isbad'] = true;
$res[$cnit]['any_isbad'] = true;
if ($res[$cnit]['clash_val'] < 0.5) {
$res[$cnit]['clash_color'] = $cell_color_mild;
} elseif ($res[$cnit]['clash_val'] > 0.9) {
$res[$cnit]['clash_color'] = $cell_color_severe;
}
//$res[$cnit]['clash_color'] = '#ff3333';
//echo "clash ".$cnit."\n";
}
}
//}}}
if (is_array($rama)) {
foreach ($rama as $item) {
$res[$item['resName']]['rama_val'] = $item['scorePct'];
$phipsi = sprintf("%.1f,%.1f", $item['phi'], $item['psi']);
if (isset($item['type'])) {
if ($item['eval'] == "OUTLIER") {
$res[$item['resName']]['rama'] = "{$item['eval']} ({$item['scorePct']})%)<br><small>{$item['type']} / {$phipsi}</small>";
$res[$item['resName']]['rama_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
// ensures that all outliers sort to the top, b/c 0.2 is a Gly outlier but not a General outlier
$res[$item['resName']]['rama_val'] -= 100.0;
} elseif ($item['eval'] == "Allowed") {
$res[$item['resName']]['rama'] = "{$item['eval']} ({$item['scorePct']}%)<br><small>{$item['type']} / {$phipsi}</small>";
$res[$item['resName']]['rama_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['rama_color'] = $cell_color_mild;
// ensures that all outliers sort to the top, b/c 0.2 is a Gly outlier but not a General outlier
//$res[$item['resName']]['rama_val'] -= 100.0;
$res[$item['resName']]['rama_val'] -= 50.0;
} else {
$res[$item['resName']]['rama'] = "{$item['eval']} ({$item['scorePct']}%)<br><small>{$item['type']} / {$phipsi}</small>";
}
}
}
}
//}}}
if (is_array($rota)) {
foreach ($rota as $item) {
$res[$item['resName']]['rota_val'] = $item['scorePct'];
#if($item['scorePct'] <= 1.0)
if ($item['eval'] == 'OUTLIER') {
$res[$item['resName']]['rota'] = "{$item['eval']} ({$item['scorePct']}%)<br><small>chi angles: " . formatChiAngles($item) . "</small>";
$res[$item['resName']]['rota_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['rota_val'] -= 100.0;
//sorting hack
} elseif ($item['eval'] == 'Allowed') {
$res[$item['resName']]['rota'] = "{$item['eval']} ({$item['scorePct']}%) <i>{$item['rotamer']}</i><br><small>chi angles: " . formatChiAngles($item) . "</small>";
$res[$item['resName']]['rota_color'] = $cell_color_mild;
$res[$item['resName']]['rota_val'] -= 50.0;
//sorting hack
} else {
$res[$item['resName']]['rota'] = "{$item['eval']} ({$item['scorePct']}%) <i>{$item['rotamer']}</i><br><small>chi angles: " . formatChiAngles($item) . "</small>";
}
}
}
//}}}
if (is_array($cablam)) {
//note: sorting keys off of cablam_val
foreach ($cablam as $item) {
$outlierType = trim($item['outlierType']);
if ($outlierType == "CaBLAM Outlier") {
$res[$item['resName']]['cablam'] = "{$item['outlierType']} ({$item['cablamScore']}%)<br><small>{$item['secStruc']}</small>";
$res[$item['resName']]['cablam_val'] = "{$item['cablamScore']}";
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['cablam_isbad'] = true;
//$res[$item['resName']]['cablam_color'] = '#ff6699';
} elseif ($outlierType == "CaBLAM Disfavored") {
$res[$item['resName']]['cablam'] = "{$item['outlierType']} ({$item['cablamScore']}%)<br><small>{$item['secStruc']}</small>";
$res[$item['resName']]['cablam_val'] = "{$item['cablamScore']}";
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['cablam_isbad'] = true;
$res[$item['resName']]['cablam_color'] = $cell_color_mild;
} elseif ($outlierType == "CA Geom Outlier") {
$res[$item['resName']]['cablam'] = "{$item['outlierType']} ({$item['caGeomScore']}%)";
$res[$item['resName']]['cablam_val'] = "{$item['caGeomScore']}";
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['cablam_isbad'] = true;
//$res[$item['resName']]['cablam_color'] = '#999999';//dark grey
$res[$item['resName']]['cablam_color'] = $cell_color_severe;
} else {
$secStruc = ltrim(trim($item['secStruc']), 'try');
$res[$item['resName']]['cablam'] = "Favored ({$item['cablamScore']}%)<br><small>{$secStruc}</small>";
$res[$item['resName']]['cablam_val'] = "{$item['cablamScore']}";
}
}
}
//}}}
if (is_array($cbdev)) {
foreach ($cbdev as $item) {
$res[$item['resName']]['cbdev_val'] = $item['dev'];
if ($item['dev'] >= 0.25) {
$res[$item['resName']]['cbdev'] = sprintf("%.2f", $item['dev']) . "Å";
$res[$item['resName']]['cbdev_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
if ($item['dev'] >= 0.7) {
$res[$item['resName']]['cbdev_color'] = $cell_color_severe;
}
} else {
if ($res[$item['resName']]['cbdev'] == null) {
//for fixing a bug where an ok alt conf dev would get reported instead of the bad dev.
$res[$item['resName']]['cbdev'] = sprintf("%.2f", $item['dev']) . "Å";
}
}
}
}
//}}}
if (is_array($omega)) {
foreach ($omega as $item) {
if ($item['conf'] == 'Cis') {
$res[$item['resName']]['any_isbad'] = true;
if ($item['type'] == 'General') {
$res[$item['resName']]['omega'] = "{$item['conf']} nonPRO<br><small>omega= {$item['omega']}</small>";
$res[$item['resName']]['omega_val'] = "1";
//for column sort
$res[$item['resName']]['omega_isbad'] = true;
} elseif ($item['type'] == 'Pro') {
$res[$item['resName']]['omega'] = "{$item['conf']} PRO<br><small>omega= {$item['omega']}</small>";
$res[$item['resName']]['omega_val'] = "2";
//for column sort
}
} elseif ($item['conf'] == 'Twisted') {
$res[$item['resName']]['any_isbad'] = true;
$res[$item['resName']]['omega_isbad'] = true;
if ($item['type'] == 'General') {
$res[$item['resName']]['omega'] = "{$item['conf']} nonPRO<br><small>omega= {$item['omega']}</small>";
$res[$item['resName']]['omega_val'] = "1";
} elseif ($item['type'] == 'Pro') {
$res[$item['resName']]['omega'] = "{$item['conf']} PRO<br><small>omega= {$item['omega']}</small>";
$res[$item['resName']]['omega_val'] = "1";
}
//for column sort
}
}
}
//}}}
if (is_array($pperp)) {
foreach ($pperp as $item) {
if ($item['outlier']) {
//echo "pperp ".$item['resName']."\n";
$reasons = array();
if ($item['deltaOut'] && $item['epsilonOut']) {
$reasons[] = "δ & ε outlier <br><small>(P-perp distance implies {$item['probpucker']})</small>";
} elseif ($item['deltaOut']) {
$reasons[] = "δ outlier <br><small>(P-perp distance implies {$item['probpucker']})</small>";
} elseif ($item['epsilonOut']) {
$reasons[] = "ε outlier <br><small>(P-perp distance implies {$item['probpucker']})</small>";
}
$res[$item['resName']]['pperp_val'] = 1;
// no way to quantify this
$res[$item['resName']]['pperp'] = "suspect sugar pucker - " . implode(", ", $reasons) . "";
$res[$item['resName']]['pperp_isbad'] = true;
$res[$item['resName']]['any_isbad'] = true;
}
}
}
//}}}
if (is_array($suites)) {
foreach ($suites as $cnit => $item) {
$res[$cnit]['suites_val'] = $item['suiteness'];
$bin = "δ-1δγ {$item['bin']}";
if ($bin == 'δ-1δγ trig') {
$bin = "δ-1δγ none (triaged {$item['triage']} )";
$res[$cnit]['suites_val'] = -1;
// sorts to very top
} elseif ($bin == 'δ-1δγ inc ') {
$bin = 'δ-1δγ none (incomplete)';
$res[$cnit]['suites_val'] = 0.0001;
// sorts just below all outliers
} elseif (preg_match('/7D dist/', $item['triage'])) {
$bin = "{$bin} ( {$item['triage']} )";
}
//echo $cnit."\n";
if ($item['isOutlier']) {
$res[$cnit]['suites'] = "OUTLIER<br><small>{$bin}</small>";
$res[$cnit]['suites_isbad'] = true;
$res[$cnit]['any_isbad'] = true;
} elseif ($item['bin'] == 'inc ') {
$res[$cnit]['suites'] = "conformer: {$item['conformer']}<br><small>{$bin}</small>";
} else {
$res[$cnit]['suites'] = "conformer: {$item['conformer']}<br><small>{$bin}, suiteness = " . sprintf("%.2f", $item[suiteness]) . "</small>";
}
}
}
//}}}
if (is_array($bbonds)) {
//{{{
foreach ($bbonds as $cnit => $item) {
if ($item['isOutlier']) {
$res[$cnit]['bbonds_val'] = abs($item['sigma']);
$res[$cnit]['bbonds'] = "{$item['count']} OUTLIER(S)<br><small>worst is {$item['measure']}: " . sprintf("%.1f", $item[sigma]) . " σ</small>";
$res[$cnit]['bbonds_isbad'] = true;
$res[$cnit]['any_isbad'] = true;
if ($res[$cnit]['bbonds_val'] >= 10) {
$res[$cnit]['bbonds_color'] = $cell_color_severe;
}
}
}
}
//}}}
if (is_array($bangles)) {
//{{{
foreach ($bangles as $cnit => $item) {
if ($item['isOutlier']) {
$res[$cnit]['bangles_val'] = abs($item['sigma']);
$res[$cnit]['bangles'] = "{$item['count']} OUTLIER(S)<br><small>worst is {$item['measure']}: " . sprintf("%.1f", $item[sigma]) . " σ</small>";
$res[$cnit]['bangles_isbad'] = true;
$res[$cnit]['any_isbad'] = true;
if ($res[$cnit]['bangles_val'] >= 10) {
$res[$cnit]['bangles_color'] = $cell_color_severe;
}
}
}
}
//}}}
//}}} Process validation data
//echo "Processing validation data took ".(time() - $startTime)." seconds\n";
//{{{check for alternates
foreach ($res as $cnit => $current) {
$altloc = substr($cnit, 7, 1);
if ($altloc != ' ') {
$b_key = substr($cnit, 0, 7) . ' ' . substr($cnit, 8, 3);
if (isset($res[$b_key])) {
//{{{clash
if (!isset($res[$cnit]['clash'])) {
$res[$cnit]['clash_val'] = $res[$b_key]['clash_val'];
$res[$cnit]['clash'] = $res[$b_key]['clash'];
$res[$cnit]['clash_isbad'] = $res[$b_key]['clash_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
//}}}
//{{{rama
if (!isset($res[$cnit]['rama'])) {
$res[$cnit]['rama_val'] = $res[$b_key]['rama_val'];
$res[$cnit]['rama'] = $res[$b_key]['rama'];
if (isset($res[$b_key]['rama_isbad'])) {
$res[$cnit]['rama_isbad'] = $res[$b_key]['rama_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{rota
if (!isset($res[$cnit]['rota'])) {
$res[$cnit]['rota_val'] = $res[$b_key]['rota_val'];
$res[$cnit]['rota'] = $res[$b_key]['rota'];
if (isset($res[$b_key]['rota_isbad'])) {
$res[$cnit]['rota_isbad'] = $res[$b_key]['rota_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{cbdev
if (!isset($res[$cnit]['cbdev_val'])) {
$res[$cnit]['cbdev_val'] = $res[$b_key]['cbdev_val'];
$res[$cnit]['cbdev'] = $res[$b_key]['cbdev'];
if (isset($res[$b_key]['rama_isbad'])) {
$res[$cnit]['cbdev_isbad'] = $res[$b_key]['cbdev_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{pperp
if (!isset($res[$cnit]['pperp'])) {
if (isset($res[$b_key]['pperp'])) {
$res[$cnit]['pperp_val'] = $res[$b_key]['pperp_val'];
$res[$cnit]['pperp'] = $res[$b_key]['pperp'];
$res[$cnit]['pperp_isbad'] = $res[$b_key]['pperp_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{suites
if (!isset($res[$cnit]['suites'])) {
$res[$cnit]['suites_val'] = $res[$b_key]['suites_val'];
$res[$cnit]['suites'] = $res[$b_key]['suites'];
if (isset($res[$b_key]['suites_isbad'])) {
$res[$cnit]['suites_isbad'] = $res[$b_key]['suites_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{bbonds
if (!isset($res[$cnit]['bbonds'])) {
if (isset($res[$b_key]['bbonds_isbad'])) {
$res[$cnit]['bbonds_val'] = $res[$b_key]['bbonds_val'];
$res[$cnit]['bbonds'] = $res[$b_key]['bbonds'];
$res[$cnit]['bbonds_isbad'] = $res[$b_key]['bbonds_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{bangles
if (!isset($res[$cnit]['bangles'])) {
if (isset($res[$b_key]['bangles_isbad'])) {
$res[$cnit]['bangles_val'] = $res[$b_key]['bangles_val'];
$res[$cnit]['bangles'] = $res[$b_key]['bangles'];
$res[$cnit]['bangles_isbad'] = $res[$b_key]['bangles_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{omega
if (isset($res[$cnit]['omega'])) {
if (isset($res[$b_key]['omega_isbad'])) {
$res[$cnit]['omega_val'] = $res[$b_key]['omega_val'];
$res[$cnit]['omega'] = $res[$b_key]['omega'];
$res[$cnit]['omega_isbad'] = $res[$b_key]['omega_isbad'];
$res[$cnit]['any_isbad'] = $res[$b_key]['any_isbad'];
}
}
//}}}
//{{{Bfactor
if (isset($res[$b_key]['resHiB'])) {
$res[$cnit]['resHiB'] = max($res[$cnit]['resHiB'], $res[$b_key]['resHiB']);
}
//}}}
//{{{CaBLAM
if (isset($res[$cnit]['cablam'])) {
if (isset($res[$b_key]['cablam_isbad'])) {
$res[$cnit]['cablam_val'] = $res[$b_key]['cablam_val'];
$res[$cnit]['cablam'] = $res[$b_key]['cablam'];
$res[$cnit]['cablam_isbad'] = $res[$b_key]['cablam_isbad'];
}
}
//}}}
}
}
}
//}}}
//remove redundant ' ' entries for residues with alternates
if ($cleanupAltloc) {
foreach ($alts as $cnit => $alt) {
foreach ($alts[$cnit] as $i => $j) {
$b_key = substr($cnit, 0, 7) . ' ' . substr($cnit, 8, 3);
unset($res[$b_key]);
}
}
}
//foreach ($bbonds as $cnit => $alt)
//{
// echo $bbonds[$cnit]['resName']."\n";
//}
// $res needs to be saved in raw_data for the horoizontal chart
if ($resout) {
$out = fopen($resout, 'wb');
fwrite($out, mpSerialize($res));
fclose($out);
}
// Set up output data structure
$table = array('prequel' => '', 'headers' => array(), 'rows' => array(), 'footers' => array(), 'sequel' => '');
$startTime = time();
//{{{ Table prequel and headers
// Do summary chart
$pdbstats = pdbstat($infile);
$table['prequel'] = makeSummaryStatsTable($pdbstats['resolution'], $clash, $rama, $rota, $cbdev, $pperp, $suites, $bbonds, $bangles, $cablam, $omega);
if ($doHtmlTable) {
$header1 = array();
$header1[] = array('html' => "<b>#</b>", 'sort' => 1);
$header1[] = array('html' => "<b>Alt</b>", 'sort' => 1);
$header1[] = array('html' => "<b>Res</b>", 'sort' => 1);
$header1[] = array('html' => "<b>High B</b>", 'sort' => -1);
if (is_array($clash)) {
$header1[] = array('html' => "<b>Clash > 0.4Å</b>", 'sort' => -1);
}
if (is_array($rama)) {
$header1[] = array('html' => "<b>Ramachandran</b>", 'sort' => 1);
}
if (is_array($rota)) {
$header1[] = array('html' => "<b>Rotamer</b>", 'sort' => 1);
}
if (is_array($cbdev)) {
$header1[] = array('html' => "<b>Cβ deviation</b>", 'sort' => -1);
}
if (is_array($cablam)) {
$header1[] = array('html' => "<b>CaBLAM</b>", 'sort' => 1);
}
if (is_array($pperp)) {
$header1[] = array('html' => "<b>Base-P perp. dist.</b>", 'sort' => -1);
}
if (is_array($suites)) {
$header1[] = array('html' => "<b>RNA suite conf.</b>", 'sort' => 1);
}
if (is_array($bbonds)) {
$header1[] = array('html' => "<b>Bond lengths</b>", 'sort' => -1);
}
if (is_array($bangles)) {
$header1[] = array('html' => "<b>Bond angles</b>", 'sort' => -1);
}
if (is_array($omega)) {
$header1[] = array('html' => "<b>Cis Peptides</b>", 'sort' => 1);
}
$header2 = array();
$header2[] = array('html' => "");
$header2[] = array('html' => "");
$header2[] = array('html' => "");
$header2[] = array('html' => sprintf("Avg: %.2f", array_sum($Bfact) / count($Bfact)));
if (is_array($clash)) {
$header2[] = array('html' => "Clashscore: {$clash['scoreAll']}");
}
if (is_array($rama)) {
$header2[] = array('html' => "Outliers: " . count(findRamaOutliers($rama)) . " of " . findAltTotal($rama));
}
if (is_array($rota)) {
$header2[] = array('html' => "Poor rotamers: " . count(findRotaOutliers($rota)) . " of " . findAltTotal($rota));
}
if (is_array($cbdev)) {
$header2[] = array('html' => "Outliers: " . count(findCbetaOutliers($cbdev)) . " of " . findAltTotal($cbdev));
}
if (is_array($cablam)) {
$header2[] = array('html' => "Outliers: " . count(findCablamOutliers($cablam)) . " of " . findAltTotal($cablam));
}
if (is_array($pperp)) {
$header2[] = array('html' => "Outliers: " . count(findBasePhosPerpOutliers($pperp)) . " of " . findAltTotal($pperp));
}
if (is_array($suites)) {
$header2[] = array('html' => "Outliers: " . count(findSuitenameOutliers($suites)) . " of " . findAltTotal($suites));
}
if (is_array($bbonds)) {
$header2[] = array('html' => "Outliers: " . count(findGeomOutliers($bbonds)) . " of " . findAltTotal($bbonds));
}
if (is_array($bangles)) {
$header2[] = array('html' => "Outliers: " . count(findGeomOutliers($bangles)) . " of " . findAltTotal($bangles));
}
if (is_array($omega)) {
$header2[] = array('html' => "Non-Trans: " . count(findOmegaOutliers($omega)) . " of " . findAltTotal($omega));
}
$table['headers'] = array($header1, $header2);
}
//}}} Table prequel and headers
//echo "Table prequel and headers took ".(time() - $startTime)." seconds\n";
$startTime = time();
//{{{ Table body
if ($doHtmlTable) {
$rows = array();
foreach ($res as $cnit => $eval) {
if ($outliersOnly && !$eval['any_isbad']) {
continue;
}
if (!$_SESSION['useSEGID']) {
$cni = substr($cnit, 0, 7);
$alt = substr($cnit, 7, 1);
$type = substr($cnit, 8, 3);
} else {
$cni = substr($cnit, 0, 9);
$alt = substr($cnit, 9, 1);
$type = substr($cnit, 10, 3);
}
//$cni = "'".$cni."'";
$row = array();
//$row[] = array('html' => $cnit, 'sort_val' => $eval['order']+0);
$row[] = array('html' => $cni, 'sort_val' => $eval['order'] + 0);
$row[] = array('html' => $alt, 'sort_val' => $alt);
$row[] = array('html' => $type, 'sort_val' => $type);
$row[] = array('html' => $eval['resHiB'], 'sort_val' => $eval['resHiB'] + 0);
foreach (array('clash', 'rama', 'rota', 'cbdev', 'cablam', 'pperp', 'suites', 'bbonds', 'bangles', 'omega') as $type) {
if (is_array(${$type})) {
$cell = array();
if (isset($eval[$type])) {
$cell['html'] = $eval[$type];
} else {
$cell['html'] = "-";
}
if (isset($eval[$type . '_color'])) {
$cell['color'] = $eval[$type . '_color'];
} elseif (isset($eval[$type . '_isbad'])) {
$cell['color'] = $cell_color_bad;
}
if (isset($eval[$type . '_val'])) {
$cell['sort_val'] = $eval[$type . '_val'] + 0;
}
$row[] = $cell;
}
}
/*
if(is_array($clash))
$row[] = array('html' => (isset($eval['clash']) ? $eval['clash'] : "-"), 'sort_val' => $eval['clash_val']+0);
if(is_array($rama))
$row[] = array('html' => (isset($eval['rama']) ? $eval['rama'] : "-"), 'sort_val' => $eval['rama_val']+0);
if(is_array($rota))
$row[] = array('html' => (isset($eval['rota']) ? $eval['rota'] : "-"), 'sort_val' => $eval['rota_val']+0);
if(is_array($cbdev))
$row[] = array('html' => (isset($eval['cbdev']) ? $eval['cbdev'] : "-"), 'sort_val' => $eval['cbdev_val']+0);
if(is_array($pperp))
$row[] = array('html' => (isset($eval['pperp']) ? $eval['pperp'] : "-"), 'sort_val' => $eval['pperp_val']+0);
*/
$rows[] = $row;
}
$table['rows'] = $rows;
}
//}}} Table body
//echo "Table body took ".(time() - $startTime)." seconds\n";
$startTime = time();
$out = fopen($outfile, 'wb');
fwrite($out, mpSerialize($table));
fclose($out);
//echo "Serializing table took ".(time() - $startTime)." seconds\n";
// serialize() and unserialize() screw up floating point numbers sometimes.
// Not only is there a change in precision, but sometimes numbers become INF
// in some versions of PHP 4, like those shipped with Mac OS X.
//
#$tmpfile = $_SESSION['dataDir'].'/'.MP_DIR_RAWDATA.'/table_dump';
#$out = fopen($tmpfile.'1', 'wb');
#fwrite($out, var_export($table, true));
#fclose($out);
#$time = time();
# $out = fopen($tmpfile.'2', 'wb');
# fwrite($out, var_export(unserialize(serialize($table)), true));
# fclose($out);
#echo "Dump+load time for serialize: ".(time() - $time)." seconds\n";
#$time = time();
# $out = fopen($tmpfile.'3', 'wb');
# fwrite($out, var_export(eval("return ".var_export($table, true).";"), true));
# fclose($out);
#echo "Dump+load time for var_export: ".(time() - $time)." seconds\n";
# WAY TOO SLOW (all in PHP, no C code):
#$time = time();
# $json = new Services_JSON();
# $out = fopen($tmpfile.'4', 'wb');
# fwrite($out, var_export($json->decode($json->encode($table)), true));
# fclose($out);
#echo "Dump+load time for JSON: ".(time() - $time)." seconds\n";
if ($snapfile) {
$startTime = time();
$out = fopen($snapfile, 'wb');
//fwrite($out, formatSortableTable($table, 'DUMMY_URL'));
fwrite($out, formatSortableTableJS($table));
fclose($out);
//echo "Formatting sortable table took ".(time() - $startTime)." seconds\n";
}
}
$_SESSION['bgjob']['isRunning'] = false;
# there was an error. Let's see if it is an element type issue.
$errfile = $_SESSION['dataDir'] . "/" . MP_DIR_SYSTEM . "/errors";
$elementerror = is_elementerror($errfile);
if ($elementerror) {
$_SESSION['bgjob']['elementError'] = true;
}
$modelerror = is_modelerror($errfile);
if ($modelerror) {
$_SESSION['bgjob']['modelError'] = true;
} else {
$_SESSION['bgjob']['cctbxError'] = true;
}
die;
}
$minModel['stats'] = pdbstat($outpath2);
$minModel['parent'] = $modelID;
$minModel['modelID_pre_min'] = $newModel['id'];
// for reduce-fix
// transfer mtz to reduced model
if (isset($_SESSION['models'][$modelID]['mtz_file'])) {
$minModel['mtz_file'] = $_SESSION['models'][$modelID]['mtz_file'];
}
if ($reduce_blength == 'ecloud') {
$minModel['history'] = "Derived from {$model['pdb']} by Reduce -build w/ CCTBX side-chain regularization";
} elseif ($reduce_blength == 'nuclear') {
$minModel['history'] = "Derived from {$model['pdb']} by Reduce -build -nuclear w/ CCTBX side-chain regularization";
}
$minModel['isUserSupplied'] = $model['isUserSupplied'];
$minModel['isReduced'] = true;
$minModel['isBuilt'] = true;
/**
* Calling this function creates N new models with hydrogens and then
* reassembles them into one new ensemble with H.
*
* Returns the ID of the newly minted ensemble.
*
* $ensID the ensemble ID for the ensemble to reduce
* $reduceFunc the function to run on ensemble members: one of
* 'reduceBuild', 'reduceNoBuild', or 'reduceTrim'
*/
function reduceEnsemble($ensID, $reduceFunc = 'reduceNoBuild')
{
$ens = $_SESSION['ensembles'][$ensID];
$idList = array();
$pdbList = array();
$reduce_blength = $_SESSION['reduce_blength'];
foreach ($ens['models'] as $modelNum => $modelID) {
$oldModel = $_SESSION['models'][$modelID];
$newModel = createModel($modelID . "H");
$outname = $newModel['pdb'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
if (!file_exists($outpath)) {
mkdir($outpath, 0777);
}
// shouldn't ever happen, but might...
$outpath .= '/' . $outname;
$inpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $oldModel['pdb'];
// FUNKY: calls the function whose name is stored in the variable $reduceFunc
$reduceFunc($inpath, $outpath, $reduce_blength);
$newModel['stats'] = pdbstat($outpath);
$newModel['parent'] = $modelID;
$newModel['history'] = "Derived from {$oldModel['pdb']} by {$reduceFunc}";
$newModel['isUserSupplied'] = $oldModel['isUserSupplied'];
$newModel['isReduced'] = $reduceFunc != 'reduceTrim';
$newModel['isBuilt'] = $reduceFunc == 'reduceBuild';
$_SESSION['models'][$newModel['id']] = $newModel;
$idList[$modelNum] = $newModel['id'];
$pdbList[$modelNum] = $outpath;
}
$ensemble = createEnsemble($ensID . "H");
$ensemble['models'] = $idList;
$ensemble['history'] = "Ensemble of " . count($idList) . " models derived from {$ens['pdb']} by {$reduceFunc}";
//$newModel['isReduced'] = ($reduceFunc != 'reduceTrim');
//$newModel['isBuilt'] = ($reduceFunc == 'reduceBuild');
$ensemble['isReduced'] = $reduceFunc != 'reduceTrim';
$ensemble['isBuilt'] = $reduceFunc == 'reduceBuild';
$ensemble['isUserSupplied'] = $ens['isUserSupplied'];
$joinedModel = joinPdbModels($pdbList);
copy($joinedModel, $_SESSION['dataDir'] . '/' . MP_DIR_MODELS . '/' . $ensemble['pdb']);
unlink($joinedModel);
// Create the ensemble entry
$id = $ensemble['id'];
$_SESSION['ensembles'][$id] = $ensemble;
return $id;
}
function onConvertToBiolUnit()
{
if ($_SESSION['lastUsedModelID']) {
$oldID = $_SESSION['lastUsedModelID'];
$model = $_SESSION['ensembles'][$oldID];
if (!$model) {
return;
}
$modelDir = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
$infile = "{$modelDir}/{$model['pdb']}";
$tmpfile = convertModelsToChains($infile);
$newModel = createModel("{$oldID}-biolunit");
$newID = $newModel['id'];
$newModel['stats'] = pdbstat($tmpfile);
$newModel['history'] = 'Converted from ensemble to biological unit';
$newModel['isUserSupplied'] = $model['isUserSupplied'];
if (!file_exists($modelDir)) {
mkdir($modelDir, 0777);
}
copy($tmpfile, "{$modelDir}/{$newModel['pdb']}");
unlink($tmpfile);
$_SESSION['models'][$newID] = $newModel;
$_SESSION['lastUsedModelID'] = $newID;
}
}
function onelinepack($pdbname, $pdbproberesult)
{
$first = true;
foreach ($pdbname as $pdb) {
$pdbstatresults = pdbstat($pdb);
// call out and figure out how many atoms are in the current model
$numAtoms = $pdbstatresults['heavyatoms'] + $pdbstatresults['hydrogens'];
// call out and get number of residues
$numres = $pdbstatresults['residues'];
//dots numbers
$proberesult = shell_exec("phenix.probe -mc -self 'ALL' -ONELINE {$pdb} ");
//$proberesult = shell_exec("probe -mc -self 'ALL' -ONELINE $pdb ");
//$proberesult = shell_exec("probe -mc -stdbonds -self 'ALL' -ONELINE $pdb ");
// open up the oneline and add in number of atoms and number of residues
$proberesult = trim($proberesult) . $numAtoms . ':' . $numres . "\n";
$out = fopen($pdbproberesult, 'a');
fwrite($out, $proberesult);
fclose($out);
}
}
} elseif ($reduce_blength == 'nuclear') {
$tasks['reduce'] = "Add H with <code>reduce -nobuild9999 -nuclear</code>";
}
$tasks['notebook'] = "Add entry to lab notebook";
setProgress($tasks, 'reduce');
// updates the progress display if running as a background job
$newModel = createModel($modelID . "H");
$outname = $newModel['pdb'];
$outpath = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
if (!file_exists($outpath)) {
mkdir($outpath, 0777);
}
// shouldn't ever happen, but might...
$outpath .= '/' . $outname;
reduceNoBuild($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($tasks, 'notebook');
function makeChartKin($pdbname, $ChartKin)
{
$caption = "caption goes here";
$out = fopen($ChartKin, 'w');
fwrite($out, "@kinemage \n");
fwrite($out, " \n");
fwrite($out, " \n");
fwrite($out, "@onewidth \n");
fwrite($out, "@viewid {Overview} \n");
fwrite($out, "@zoom 1.00 \n");
fwrite($out, "@zslab 200 \n");
fwrite($out, "@ztran 0 \n");
fwrite($out, "@center -16.500 -11.500 0.122 \n");
fwrite($out, "@matrix \n");
fwrite($out, "1.000000 -0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -0.000000 1.000000 \n");
fwrite($out, "@master {Rotamer Outliers} \n");
fwrite($out, "@master {Rotamer % Outliers} \n");
fwrite($out, "@master {Global Measure Chart} \n");
fwrite($out, "@master {Residue Chart} \n");
fwrite($out, "@labellist {label} color= white master= {Global Measure Chart} nobutton \n");
fwrite($out, "{Resolution or Constrains per Residue}100.000 -30.000 0.000 \n");
fwrite($out, "{Value} -30.000 125.000 30.000 \n");
fwrite($out, "@vectorlist {edge} color= gray width= 1 master= {Global Measure Chart} nobutton \n");
fwrite($out, "{plot edge}P 0.000 250.000 0.000 \n");
fwrite($out, "{plot edge}0.000 0.000 0.000 \n");
fwrite($out, "{plot edge}250.000 0.000 0.000 \n");
fwrite($out, "{plot edge}250.000 250.000 0.000 \n");
fwrite($out, "{plot edge}0.000 250.000 0.000 \n");
fwrite($out, "@labellist {label} color= white master= {Residue Chart} nobutton \n");
fwrite($out, "{Model} 30.000 -30.000 -125.000 \n");
fwrite($out, "{Residue Number} -125.000 -30.000 30.000 \n");
fwrite($out, "@vectorlist {edge} color= gray width= 1 master= {Residue Chart} nobutton \n");
fwrite($out, "{plot edge}P -250.000 0.000 -250.000 \n");
fwrite($out, "{plot edge}0.000 0.000 -250.000 \n");
fwrite($out, "{plot edge}0.000 0.000 0.000 \n");
fwrite($out, "{plot edge}-250.000 0.000 0.000 \n");
fwrite($out, "{plot edge}-250.000 0.000 -250.000 \n");
fwrite($out, "@vectorlist {residue} color= gray width= 1 master= {Residue Chart} nobutton \n");
fwrite($out, "{tick}P 0.000 0.000 0.000 \n");
fwrite($out, "{\"}0.000 0.000 10.000 \n");
fwrite($out, "{\"}P -5.000 0.000 0.000 \n");
fwrite($out, "{\"}-5.000 0.000 5.000 \n");
fwrite($out, "{\"}P -10.000 0.000 0.000 \n");
fwrite($out, "{\"}-10.000 0.000 10.000 \n");
fwrite($out, "{\"}P -15.000 0.000 0.000 \n");
fwrite($out, "{\"}-15.000 0.000 5.000 \n");
fwrite($out, "{\"}P -20.000 0.000 0.000 \n");
fwrite($out, "{\"}-20.000 0.000 10.000 \n");
fwrite($out, "{\"}P -25.000 0.000 0.000 \n");
fwrite($out, "{\"}-25.000 0.000 5.000 \n");
fwrite($out, "{\"}P -30.000 0.000 0.000 \n");
fwrite($out, "{\"}-30.000 0.000 10.000 \n");
fwrite($out, "{\"}P -35.000 0.000 0.000 \n");
fwrite($out, "{\"}-35.000 0.000 5.000 \n");
fwrite($out, "{\"}P -40.000 0.000 0.000 \n");
fwrite($out, "{\"}-40.000 0.000 10.000 \n");
fwrite($out, "{\"}P -45.000 0.000 0.000 \n");
fwrite($out, "{\"}-45.000 0.000 5.000 \n");
fwrite($out, "{\"}P -50.000 0.000 0.000 \n");
fwrite($out, "{\"}-50.000 0.000 10.000 \n");
fwrite($out, "{\"}P -55.000 0.000 0.000 \n");
fwrite($out, "{\"}-55.000 0.000 5.000 \n");
fwrite($out, "{\"}P -60.000 0.000 0.000 \n");
fwrite($out, "{\"}-60.000 0.000 10.000 \n");
fwrite($out, "{\"}P -65.000 0.000 0.000 \n");
fwrite($out, "{\"}-65.000 0.000 5.000 \n");
fwrite($out, "{\"}P -70.000 0.000 0.000 \n");
fwrite($out, "{\"}-70.000 0.000 10.000 \n");
fwrite($out, "{\"}P -75.000 0.000 0.000 \n");
fwrite($out, "{\"}-75.000 0.000 5.000 \n");
fwrite($out, "{\"}P -80.000 0.000 0.000 \n");
fwrite($out, "{\"}-80.000 0.000 10.000 \n");
fwrite($out, "{\"}P -85.000 0.000 0.000 \n");
fwrite($out, "{\"}-85.000 0.000 5.000 \n");
fwrite($out, "{\"}P -90.000 0.000 0.000 \n");
fwrite($out, "{\"}-90.000 0.000 10.000 \n");
fwrite($out, "{\"}P -95.000 0.000 0.000 \n");
fwrite($out, "{\"}-95.000 0.000 5.000 \n");
fwrite($out, "{\"}P -100.000 0.000 0.000 \n");
fwrite($out, "{\"}-100.000 0.000 10.000 \n");
fwrite($out, "{\"}P -105.000 0.000 0.000 \n");
fwrite($out, "{\"}-105.000 0.000 5.000 \n");
fwrite($out, "{\"}P -110.000 0.000 0.000 \n");
fwrite($out, "{\"}-110.000 0.000 10.000 \n");
fwrite($out, "{\"}P -115.000 0.000 0.000 \n");
fwrite($out, "{\"}-115.000 0.000 5.000 \n");
fwrite($out, "{\"}P -120.000 0.000 0.000 \n");
fwrite($out, "{\"}-120.000 0.000 10.000 \n");
fwrite($out, "{\"}P -125.000 0.000 0.000 \n");
fwrite($out, "{\"}-125.000 0.000 5.000 \n");
fwrite($out, "{\"}P -130.000 0.000 0.000 \n");
fwrite($out, "{\"}-130.000 0.000 10.000 \n");
fwrite($out, "{\"}P -135.000 0.000 0.000 \n");
fwrite($out, "{\"}-135.000 0.000 5.000 \n");
fwrite($out, "{\"}P -140.000 0.000 0.000 \n");
fwrite($out, "{\"}-140.000 0.000 10.000 \n");
fwrite($out, "{\"}P -145.000 0.000 0.000 \n");
fwrite($out, "{\"}-145.000 0.000 5.000 \n");
fwrite($out, "{\"}P -150.000 0.000 0.000 \n");
fwrite($out, "{\"}-150.000 0.000 10.000 \n");
fwrite($out, "{\"}P -155.000 0.000 0.000 \n");
fwrite($out, "{\"}-155.000 0.000 5.000 \n");
fwrite($out, "{\"}P -160.000 0.000 0.000 \n");
fwrite($out, "{\"}-160.000 0.000 10.000 \n");
fwrite($out, "{\"}P -165.000 0.000 0.000 \n");
fwrite($out, "{\"}-165.000 0.000 5.000 \n");
fwrite($out, "{\"}P -170.000 0.000 0.000 \n");
fwrite($out, "{\"}-170.000 0.000 10.000 \n");
fwrite($out, "{\"}P -175.000 0.000 0.000 \n");
fwrite($out, "{\"}-175.000 0.000 5.000 \n");
fwrite($out, "{\"}P -180.000 0.000 0.000 \n");
fwrite($out, "{\"}-180.000 0.000 10.000 \n");
fwrite($out, "{\"}P -185.000 0.000 0.000 \n");
fwrite($out, "{\"}-185.000 0.000 5.000 \n");
fwrite($out, "{\"}P -190.000 0.000 0.000 \n");
fwrite($out, "{\"}-190.000 0.000 10.000 \n");
fwrite($out, "{\"}P -195.000 0.000 0.000 \n");
fwrite($out, "{\"}-195.000 0.000 5.000 \n");
fwrite($out, "{\"}P -200.000 0.000 0.000 \n");
fwrite($out, "{\"}-200.000 0.000 10.000 \n");
fwrite($out, "{\"}P -205.000 0.000 0.000 \n");
fwrite($out, "{\"}-205.000 0.000 5.000 \n");
fwrite($out, "{\"}P -210.000 0.000 0.000 \n");
fwrite($out, "{\"}-210.000 0.000 10.000 \n");
fwrite($out, "{\"}P -215.000 0.000 0.000 \n");
fwrite($out, "{\"}-215.000 0.000 5.000 \n");
fwrite($out, "{\"}P -220.000 0.000 0.000 \n");
fwrite($out, "{\"}-220.000 0.000 10.000 \n");
fwrite($out, "{\"}P -225.000 0.000 0.000 \n");
fwrite($out, "{\"}-225.000 0.000 5.000 \n");
fwrite($out, "{\"}P -230.000 0.000 0.000 \n");
fwrite($out, "{\"}-230.000 0.000 10.000 \n");
fwrite($out, "{\"}P -235.000 0.000 0.000 \n");
fwrite($out, "{\"}-235.000 0.000 5.000 \n");
fwrite($out, "{\"}P -240.000 0.000 0.000 \n");
fwrite($out, "{\"}-240.000 0.000 10.000 \n");
fwrite($out, "{\"}P -245.000 0.000 0.000 \n");
fwrite($out, "{\"}-245.000 0.000 5.000 \n");
fwrite($out, "{\"}P -250.000 0.000 0.000 \n");
fwrite($out, "{\"}-250.000 0.000 10.000 \n");
fwrite($out, "@vectorlist {Model} color= gray width= 1 master= {Residue Chart} nobutton \n");
fwrite($out, "{tick}P 0.000 0.000 0.000 \n");
fwrite($out, "{\"}10.000 0.000 0.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -10.000 \n");
fwrite($out, "{\"}5.000 0.000 -10.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -20.000 \n");
fwrite($out, "{\"}5.000 0.000 -20.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -30.000 \n");
fwrite($out, "{\"}5.000 0.000 -30.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -40.000 \n");
fwrite($out, "{\"}5.000 0.000 -40.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -50.000 \n");
fwrite($out, "{\"}10.000 0.000 -50.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -60.000 \n");
fwrite($out, "{\"}5.000 0.000 -60.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -70.000 \n");
fwrite($out, "{\"}5.000 0.000 -70.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -80.000 \n");
fwrite($out, "{\"}5.000 0.000 -80.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -90.000 \n");
fwrite($out, "{\"}5.000 0.000 -90.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -100.000 \n");
fwrite($out, "{\"}10.000 0.000 -100.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -110.000 \n");
fwrite($out, "{\"}5.000 0.000 -110.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -120.000 \n");
fwrite($out, "{\"}5.000 0.000 -120.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -130.000 \n");
fwrite($out, "{\"}5.000 0.000 -130.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -140.000 \n");
fwrite($out, "{\"}5.000 0.000 -140.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -150.000 \n");
fwrite($out, "{\"}10.000 0.000 -150.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -160.000 \n");
fwrite($out, "{\"}5.000 0.000 -160.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -170.000 \n");
fwrite($out, "{\"}5.000 0.000 -170.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -180.000 \n");
fwrite($out, "{\"}10.000 0.000 -180.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -190.000 \n");
fwrite($out, "{\"}5.000 0.000 -190.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -200.000 \n");
fwrite($out, "{\"}10.000 0.000 -200.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -210.000 \n");
fwrite($out, "{\"}5.000 0.000 -210.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -220.000 \n");
fwrite($out, "{\"}5.000 0.000 -220.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -230.000 \n");
fwrite($out, "{\"}5.000 0.000 -230.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -240.000 \n");
fwrite($out, "{\"}5.000 0.000 -240.000 \n");
fwrite($out, "{\"}P 0.000 0.000 -250.000 \n");
fwrite($out, "{\"}10.000 0.000 -250.000 \n");
//for each pdb and iterate
//in the beginning.. there was a model!
$modelcounter = 1;
foreach ($pdbname as $pdb) {
//overall stats needed for each pdb file
// crystallographic resolution of the model
$stats = pdbstat($pdb);
$resolution = $stats['resolution'];
/*
$ConstPerRes =
// NMR constraints per Residue in the model
*/
//number of res in the model
$numRes = $stats['residues'];
// plotting of rotamer outliers along for each model along vs. residue number
fwrite($out, "@group {" . basename($pdb, ".pdb") . "} animate dominant \n");
// plot of rotamer outliers
fwrite($out, "@balllist {Rotamer Outliers} color= white radius= 0.5 master= {Rotamer Outliers} nohilite \n");
// create unique temp files in current directory
$tmp1 = tempnam(MP_BASE_DIR . "/tmp", 'graphtemp');
// calculations for rotamer data
runRotamer($pdb, $tmp1);
$rota = loadrotamer($tmp1);
//plotting rotamer outliers, determining the x (res), y (score), and z (model) values
//followed by writing them out in the balllist
$RotaOut = findRotaOutliers($rota);
// $RotaOut is the the list of outliers and their scores
foreach ($RotaOut as $ResName => $score) {
$x = $rota[$ResName]['resNum'] * -1.0;
$y = round($rota[$ResName]['scorePct'], 2);
$z = $modelcounter * -10.0;
// if x = 0, go to next one...
if ($x == 0) {
continue;
}
fwrite($out, "{" . basename($pdb, ".pdb") . " " . $ResName . "}{$x} {$y} {$z} \n");
}
// plotting % rotamer outlier data
// x is what you plot against, resolution / restraints per res etc
// y is the percentage of rotamer outliers in the entire model
// plots the model
$numRotaOut = count(findRotaOutliers($rota));
// can include a factor here
$percentoutlier = round($numRotaOut / $numRes * 100, 2);
// multiplication by 100 is the scaleing 'fudge' factor
$x = $resolution * 100;
// -10.00 another scaling factor
$z = $modelcounter * -10.0;
fwrite($out, "@balllist {Rotamer % Outliers} color= white radius= 1.0 master= {Rotamer % Outliers} nohilite \n");
fwrite($out, "{" . basename($pdb, ".pdb") . " " . $resolution . "A , " . $percentoutlier . "%" . "} {$x} {$percentoutlier} {$z} \n");
unlink($tmp1);
//change the Z number which gets multiplied (and hereafter we added another)
$modelcounter = $modelcounter + 1;
//end of the for each loop going through the PDB files
}
fclose($out);
}
