/**
* $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() - $startTime)." seconds\n";
}
}
/**
* This is the uber-validation function that calls everything below.
* It is suited for use from either the web or command line interface.
* This only makes sense in terms of an active session.
* modelID ID code for model to process
* opts has the following keys mapped to boolean flags:
* doKinemage make the multi-criterion kinemage at all?
* kinClashes show clash dots?
* kinHbonds show H-bond dots?
* kinContacts show contact dots?
* kinRama show Rama outliers?
* kinRota show rotamer outliers?
* kinGeom show bond length and angle outliers?
* kinCBdev show C-beta deviations?
* kinBaseP show base-phosphate perpendiculars?
* kinSuite show RNA backbone conformational outliers?
* kinAltConfs show alternate conformations?
* kinBfactor show B-factor color model?
* kinOccupancy show occupancy color model?
* kinRibbons show ribbons?
* kinForceViews force running clashlist, etc to provide @views of bad spots?
* doCharts make the multi-criterion chart and other plots/tables/lists?
* chartClashlist run clashlistcluster?
* chartRama do Rama plots and analysis?
* chartRota do rotamer analysis?
* chartGeom do bond length and angle outliers?
* chartCBdev do CB dev plots and analysis?
* chartBaseP check base-phosphate perpendiculars?
* chartSuite check RNA backbone conformations?
* chartHoriz do horizontal chart?
* chartCoot do coot chart?
* chartMulti do html multi chart?
* chartNotJustOut include residues that have no problems in the list?
* chartAltloc remove redundant residue rows when altlocs present?
* chartImprove compare to reduce -(no)build results to show improvement?
*
* This function returns some HTML suitable for using in a lab notebook entry.
*/
function runAnalysis($modelID, $opts)
{
//{{{ Set up file/directory vars and the task list
// If doKinemage or doCharts is off, turn off all their subordinates
if (!$opts['doKinemage']) {
foreach ($opts as $k => $v) {
if (startsWith($k, 'kin')) {
$opts[$k] = false;
}
}
}
if (!$opts['doCharts']) {
foreach ($opts as $k => $v) {
if (startsWith($k, 'chart')) {
$opts[$k] = false;
}
}
}
if ($opts['kinForceViews']) {
foreach ($opts as $k => $v) {
if (startsWith($k, 'chart')) {
$opts[$k] = true;
}
}
}
$model = $_SESSION['models'][$modelID];
$modelDir = $_SESSION['dataDir'] . '/' . MP_DIR_MODELS;
$modelURL = $_SESSION['dataURL'] . '/' . MP_DIR_MODELS;
$kinDir = $_SESSION['dataDir'] . '/' . MP_DIR_KINS;
$kinURL = $_SESSION['dataURL'] . '/' . MP_DIR_KINS;
if (!file_exists($kinDir)) {
mkdir($kinDir, 0777);
}
$rawDir = $_SESSION['dataDir'] . '/' . MP_DIR_RAWDATA;
if (!file_exists($rawDir)) {
mkdir($rawDir, 0777);
}
$chartDir = $_SESSION['dataDir'] . '/' . MP_DIR_CHARTS;
$chartURL = $_SESSION['dataURL'] . '/' . MP_DIR_CHARTS;
if (!file_exists($chartDir)) {
mkdir($chartDir, 0777);
}
$xrayDir = $_SESSION['dataDir'] . '/' . MP_DIR_XRAYDATA;
$infile = "{$modelDir}/{$model['pdb']}";
$reduce_blength = $_SESSION['reduce_blength'];
if (isset($model['mtz_file'])) {
$mtz_file = $model['mtz_file'];
} else {
$mtz_file = $_SESSION['models'][$model['parent']]['mtz_file'];
}
if ($opts['chartRama']) {
$tasks['rama'] = "Do Ramachandran analysis and make plots (<code>ramalyze</code>)";
}
if ($opts['chartRota']) {
$tasks['rota'] = "Do rotamer analysis (<code>rotalyze</code>)";
}
if ($opts['chartCBdev']) {
$tasks['cbeta'] = "Do Cβ deviation analysis and make kins (<code>cbetadev</code>)";
}
if ($opts['chartOmega']) {
$tasks['omega'] = "Do cis-peptide analysis (<code>omegalyze</code>)";
}
if ($opts['chartCablamLow']) {
$tasks['cablam'] = "Do CaBLAM analysis (<code>cablam_validate</code>)";
}
if ($opts['chartBaseP']) {
$tasks['base-phos'] = "Do RNA sugar pucker analysis";
}
if ($opts['chartSuite']) {
$tasks['suitename'] = "Do RNA backbone conformations analysis";
}
if ($model['stats']['use_cdl']) {
$geomsg = "Using CDL";
} else {
$geomsg = "";
}
if ($opts['chartGeom']) {
$tasks['geomValidation'] = "Do bond length and angle geometry analysis (<code>mp_geo</code>) {$geomsg}";
}
if ($opts['chartClashlist']) {
$tasks['clashlist'] = "Run <code>clashscore</code> to find bad clashes and clashscore";
}
if ($opts['chartImprove']) {
$tasks['improve'] = "Suggest / report on fixes";
}
if ($opts['doCharts'] && !$opts['chartMulti']) {
$tasks['chartsummary'] = "Create summary chart";
}
if ($opts['chartMulti']) {
$tasks['multichart'] = "Create multi-criterion chart";
}
if ($opts['chartHoriz']) {
$tasks['runRSCC'] = "Run real-space correlation";
$tasks['charthoriz'] = "Create horizontal RSCC chart";
}
if ($opts['chartCoot']) {
$tasks['cootchart'] = "Create chart for use in Coot";
}
if ($opts['doKinemage']) {
$tasks['multikin'] = "Create multi-criterion kinemage";
}
//if($opts['doLowRes']) $tasks['lowResKin'] = "Create low-resolution multi-criterion kinemage";
//$doRem40 = $opts['chartClashlist'] || $opts['chartRama'] || $opts['chartRota'];
//if($doRem40) $tasks['remark40'] = "Create REMARK 40 record for the PDB file";
//}}} Set up file/directory vars and the task list
//{{{ Run geometry programs and offer kins to user
//{{{ Ramachandran
if ($opts['chartRama']) {
$startTime = time();
setProgress($tasks, 'rama');
// updates the progress display if running as a background job
$outfile = "{$rawDir}/{$model['prefix']}rama.data";
runRamachandran($infile, $outfile);
$rama = loadRamachandran($outfile);
makeRamachandranKin($infile, "{$kinDir}/{$model['prefix']}rama.kin");
$tasks['rama'] .= " - preview <a href='viewking.php?{$_SESSION['sessTag']}&url={$kinURL}/{$model['prefix']}rama.kin' target='_blank'>kinemage</a>";
setProgress($tasks, 'rama');
// so the preview link is visible
makeRamachandranPDF($infile, "{$chartDir}/{$model['prefix']}rama.pdf");
$tasks['rama'] .= " | <a href='{$chartURL}/{$model['prefix']}rama.pdf' target='_blank'>PDF</a>\n";
setProgress($tasks, 'rama');
// so the preview link is visible
echo "Ramachandran ran for " . (time() - $startTime) . " seconds\n";
}
//}}}
//{{{ Rotamers
if ($opts['chartRota']) {
$startTime = time();
setProgress($tasks, 'rota');
// updates the progress display if running as a background job
$outfile = "{$rawDir}/{$model['prefix']}rota.data";
runRotamer($infile, $outfile);
$rota = loadRotamer($outfile);
echo "Rotamers ran for " . (time() - $startTime) . " seconds\n";
}
//}}}
//{{{ C-beta deviations
if ($opts['chartCBdev']) {
$startTime = time();
setProgress($tasks, 'cbeta');
// updates the progress display if running as a background job
$outfile = "{$rawDir}/{$model['prefix']}cbdev.data";
runCbetaDev($infile, $outfile);
$cbdev = loadCbetaDev($outfile);
makeCbetaDevPlot($infile, "{$kinDir}/{$model['prefix']}cbetadev.kin");
$tasks['cbeta'] .= " - <a href='viewking.php?{$_SESSION['sessTag']}&url={$kinURL}/{$model['prefix']}cbetadev.kin' target='_blank'>preview</a>";
setProgress($tasks, 'cbeta');
// so the preview link is visible
echo "C-beta ran for " . (time() - $startTime) . " seconds\n";
}
//}}}
//{{{ Omega peptides
if ($opts['chartOmega']) {
$startTime = time();
setProgress($tasks, 'omega');
$outfile = "{$rawDir}/{$model['prefix']}omega.data";
//$outfile = "$rawDir/$model[prefix]omega-clashlist.txt";
runOmegalyze($infile, $outfile);
$omega = loadOmegalyze($outfile);
echo "Omegalyze ran for " . (time() - $startTime) . " seconds\n";
}
//}}}
//{{{ CaBLAM
if ($opts['chartCablamLow']) {
setProgress($tasks, 'cablam');
$outfile = "{$rawDir}/{$model['prefix']}cablam.data";
runCablam($infile, $outfile);
$cablam = loadCablam($outfile);
}
//}}}
//{{{ Run nucleic acid geometry programs and offer kins to user
//{{{ Base-phosphate perpendiculars
if ($opts['chartBaseP']) {
setProgress($tasks, 'base-phos');
// updates the progress display if running as a background job
$outfile = "{$rawDir}/{$model['prefix']}pperp.data";
runBasePhosPerp($infile, $outfile);
$pperp = loadBasePhosPerp($outfile);
}
//}}}
//{{{ Suitename
if ($opts['chartSuite']) {
setProgress($tasks, 'suitename');
// updates the progress display if running as a background job
$outfile = "{$chartDir}/{$model['prefix']}suitename.txt";
runSuitenameReport($infile, $outfile);
$suites = loadSuitenameReport($outfile);
$tasks['suitename'] .= " - <a href='viewtext.php?{$_SESSION['sessTag']}&file={$outfile}&mode=plain' target='_blank'>preview</a>\n";
setProgress($tasks, 'suitename');
// so the preview link is visible
$outfile = "{$chartDir}/{$model['prefix']}suitestring.txt";
runSuitenameString($infile, $outfile);
makeSuitenameKin($infile, "{$kinDir}/{$model['prefix']}suitename.kin");
}
//}}}
//}}} Run nucleic acid geometry programs and offer kins to user
//{{{ Bonds and Angles
if ($opts['chartGeom']) {
setProgress($tasks, 'geomValidation');
// updates the progress display if running as a background job
$geomfile = "{$rawDir}/{$model['prefix']}geomvalidation.data";
runValidationReport($infile, $geomfile, $model['stats']['use_cdl']);
//$protfile = "$rawDir/$model[prefix]protvalidation.data";
//runValidationReport($infile, $protfile, "protein");
//$rnafile = "$rawDir/$model[prefix]rnavalidation.data";
//runValidationReport($infile, $rnafile, "rna");
//$validate_bond = loadValidationBondReport($protfile,"protein");
//if (is_array($validate_bond))
$validate_bond = array_merge(loadValidationBondReport($geomfile, "protein"), loadValidationBondReport($geomfile, "rna"));
if (count($validate_bond) == 0) {
$validate_bond = null;
}
$validate_angle = array_merge(loadValidationAngleReport($geomfile, "protein"), loadValidationAngleReport($geomfile, "rna"));
if (count($validate_angle) == 0) {
$validate_angle = null;
}
}
//}}}
//}}} Run programs and offer kins to user
//{{{ Run all-atom contact programs and offer kins to user
// Clashes
if ($opts['chartClashlist']) {
$startTime = time();
setProgress($tasks, 'clashlist');
// updates the progress display if running as a background job
$outfile = "{$chartDir}/{$model['prefix']}clashlist.txt";
#runClashlist($infile, $outfile, $reduce_blength);
runClashscore($infile, $outfile, $reduce_blength);
#$clash = loadClashlist($outfile);
$clash = loadClashscore($outfile);
//$clashPct = runClashStats($model['stats']['resolution'], $clash['scoreAll'], $clash['scoreBlt40']);
$tasks['clashlist'] .= " - <a href='viewtext.php?{$_SESSION['sessTag']}&file={$outfile}&mode=plain' target='_blank'>preview</a>\n";
setProgress($tasks, 'clashlist');
// so the preview link is visible
echo "chartClashlist ran for " . (time() - $startTime) . " seconds\n";
}
//}}} Run all-atom contact programs and offer kins to user
//{{{ Run real-space correlation
$model['raw_rscc_name'] = "{$model['parent']}_raw.rscc";
$model['rscc_name'] = "{$model['parent']}.rscc";
$rscc_out = "{$xrayDir}/{$model['parent']}.rscc";
$rscc_prequel_out = "{$xrayDir}/{$model['parent']}_prequel.rscc";
if ($opts['chartHoriz']) {
$startTime = time();
setProgress($tasks, 'runRSCC');
runRscc($infile, $mtz_file, $rscc_out, $rscc_prequel_out);
echo "runRscc ran for " . (time() - $startTime) . " seconds\n";
echo $mtz_file;
echo isset($mtz_file);
}
//}}}
//{{{ Report on improvements (that could be) made by MolProbity
$improveText = "";
if ($opts['chartImprove'] && ($clash || $rota)) {
$startTime = time();
setProgress($tasks, 'improve');
// updates the progress display if running as a background job
$altpdb = mpTempfile("tmp_altH_pdb_");
$mainClashscore = $clash ? $clash['scoreAll'] : 0;
$mainRotaCount = $rota ? count(findRotaOutliers($rota)) : 0;
$improvementList = array();
if ($model['isBuilt']) {
$altInpath = $modelDir . '/' . $_SESSION['models'][$model['parent']]['pdb'];
reduceNoBuild($altInpath, $altpdb, $reduce_blength);
// Rotamers
$outfile = mpTempfile("tmp_rotamer_");
runRotamer($altpdb, $outfile);
$altrota = loadRotamer($outfile);
$altRotaCount = count(findRotaOutliers($altrota));
if ($altRotaCount > $mainRotaCount) {
if ($altRotaCount - $mainRotaCount > 1) {
$improvementList[] = "fixed " . ($altRotaCount - $mainRotaCount) . " bad rotamers";
} else {
$improvementList[] = "fixed " . ($altRotaCount - $mainRotaCount) . " bad rotamer";
}
}
unlink($outfile);
// Clashes
$outfile = mpTempfile("tmp_clashlist_");
#runClashlist($altpdb, $outfile, $reduce_blength);
runClashscore($altpdb, $outfile, $reduce_blength);
#$altclash = loadClashlist($outfile);
$altclash = loadClashscore($outfile);
if ($altclash['scoreAll'] - $mainClashscore >= 0.005) {
//0.005 is the smallest change that will still be reported by the sprintf("%.2f") below
$improvementList[] = "improved your clashscore by " . sprintf("%.2f", $altclash['scoreAll'] - $mainClashscore) . " points";
}
unlink($outfile);
if (count($improvementList) > 0) {
$improveText .= "<div class='feature'>By adding H to this model and allowing Asn/Gln/His flips, you have already ";
$improveText .= implode(" and ", $improvementList);
$improveText .= ". <br /><b>Make sure you download the modified PDB to take advantage of these improvements! <br />NOTE: Atom positions have changed, so refinement to idealize geometry is necessary.</b></div>\n";
}
} elseif ($mainClashscore > 0 || $mainRotaCount > 0) {
if ($model['parent']) {
$altInpath = $_SESSION['models'][$model['parent']]['pdb'];
} else {
$altInpath = $model['pdb'];
}
$altInpath = "{$modelDir}/{$altInpath}";
reduceBuild($altInpath, $altpdb, $reduce_blength);
if ($mainRotaCount > 0) {
$outfile = mpTempfile("tmp_rotamer_");
runRotamer($altpdb, $outfile);
$altrota = loadRotamer($outfile);
$altRotaCount = count(findRotaOutliers($altrota));
if ($altRotaCount < $mainRotaCount) {
$improvementList[] = "fix " . ($mainRotaCount - $altRotaCount) . " bad rotamers";
}
unlink($outfile);
}
if ($mainClashscore > 0) {
$outfile = mpTempfile("tmp_clashlist_");
#runClashlist($altpdb, $outfile, $reduce_blength);
runClashscore($altpdb, $outfile, $reduce_blength);
#$altclash = loadClashlist($outfile);
$altclash = loadClashscore($outfile);
if ($mainClashscore - $altclash['scoreAll'] >= 0.005) {
//0.005 is the smallest change that will still be reported by the sprintf("%.2f") below
$improvementList[] = "improve your clashscore by " . sprintf("%.2f", $mainClashscore - $altclash['scoreAll']) . " points";
}
unlink($outfile);
}
if (count($improvementList) > 0) {
$improveText .= "<div class='feature'>By adding H to this model and allowing Asn/Gln/His flips, we could <i>automatically</i> ";
$improveText .= implode(" and ", $improvementList);
$improveText .= ".</div>\n";
}
}
unlink($altpdb);
echo "chart Improve ran for " . (time() - $startTime) . " seconds\n";
}
//}}} Report on improvements (that could be) made by by MolProbity
//{{{ Build multi-criterion chart, kinemage, horizontal, chart
if ($opts['doCharts']) {
$startTime = time();
if ($opts['chartMulti']) {
setProgress($tasks, 'multichart');
// updates the progress display if running as a background job
} else {
setProgress($tasks, 'chartsummary');
}
$outfile = "{$rawDir}/{$model['prefix']}multi.table";
$snapfile = "{$chartDir}/{$model['prefix']}multi.html";
$resout = "{$rawDir}/{$model['prefix']}multi_res.table";
writeMulticritChart($infile, $outfile, $snapfile, $resout, $clash, $rama, $rota, $cbdev, $pperp, $suites, $validate_bond, $validate_angle, $cablam, $omega, !$opts['chartNotJustOut'], $opts['chartMulti'], $opts['chartAltloc']);
if ($opts['chartMulti']) {
$tasks['multichart'] .= " - <a href='viewtable.php?{$_SESSION['sessTag']}&file={$outfile}' target='_blank'>preview</a>\n";
setProgress($tasks, 'multichart');
// so the preview link is visible
} else {
$tasks['chartsummary'] .= " - <a href='viewtable.php?{$_SESSION['sessTag']}&file={$outfile}' target='_blank'>preview</a>\n";
setProgress($tasks, 'chartsummary');
// so the preview link is visible
}
if ($opts['chartHoriz']) {
setProgress($tasks, 'charthoriz');
$horiz_table_file = "{$rawDir}/{$model['prefix']}horiz.table";
writeHorizontalChart($resout, $rscc_out, $outfile, $horiz_table_file, $rscc_prequel_out);
}
if ($opts['chartCoot']) {
setProgress($tasks, 'cootchart');
$outfile = "{$chartDir}/{$model['prefix']}multi-coot.scm";
$outfile_py = "{$chartDir}/{$model['prefix']}multi-coot.py";
#makeCootMulticritChart($infile, $outfile, $clash, $rama, $rota, $cbdev, $pperp);
makeCootClusteredChart($infile, $outfile, $outfile_py, $clash, $rama, $rota, $cbdev, $pperp);
}
echo "do Charts ran for " . (time() - $startTime) . " seconds\n";
}
if ($opts['doKinemage']) {
$startTime = time();
setProgress($tasks, 'multikin');
// updates the progress display if running as a background job
$mcKinOpts = array('ribbons' => $opts['kinRibbons'], 'Bscale' => $opts['kinBfactor'], 'Qscale' => $opts['kinOccupancy'], 'altconf' => $opts['kinAltConfs'], 'rama' => $opts['kinRama'], 'rota' => $opts['kinRota'], 'geom' => $opts['kinGeom'], 'cbdev' => $opts['kinCBdev'], 'omega' => $opts['kinOmega'], 'cablam' => $opts['kinCablamLow'], 'pperp' => $opts['kinBaseP'], 'clashdots' => $opts['kinClashes'], 'hbdots' => $opts['kinHbonds'], 'vdwdots' => $opts['kinContacts']);
$outfile = "{$kinDir}/{$model['prefix']}multi.kin";
$viewRes = array();
//echo "kinForceViews = ".$opts['kinForceViews']."\n";
if ($opts['kinForceViews']) {
//echo "Ran calcLocalBadness\n";
$viewRes = array_keys(calcLocalBadness($infile, 10, $clash, $rama, $rota, $cbdev, $pperp));
}
makeMulticritKin2(array($infile), $outfile, $mcKinOpts, $viewRes);
// EXPERIMENTAL: gzip compress large multikins
if (filesize($outfile) > MP_KIN_GZIP_THRESHOLD) {
destructiveGZipFile($outfile);
}
echo "do Kinemage ran for " . (time() - $startTime) . " seconds\n";
}
//}}} Build multi-criterion chart, kinemage
//{{{ Low-resolution-specific analyses
//Low-res kinemage is being simplified and merged into main kinemage
//if($opts['doLowRes'])
//{
// if($opts['kinCablamLow'] || $opts['other'])
// {
// $startTime = time();
// setProgress($tasks, 'lowResKin');
// $lowResKinOpts = array(//first column is opts, second column sets true-false
// 'ribbons' => $opts['kinRibbons'],//pass pdb w/HELIX+SHEET for this
// 'rama' => $opts['kinRama'],
// 'geom' => $opts['kinGeom'],
// 'cbdev' => $opts['kinCBdev'],
// 'omega' => $opts['kinOmega'],
// 'cablam' => $opts['kinCablamLow'],
// 'clashdots' => $opts['kinClashes']
// );
// $outfile = "$kinDir/$model[prefix]low_multi.kin";
// $cablamSecStrucFile = "$modelDir/$model[prefix]cablam_sec_struc_records.pdb";
// //$viewRes = array(); //Used with opts[kinForceViews], not necessary argument for makeMulticritKin2
// makeMulticritKinLowRes(array($infile), $outfile, $cablamSecStrucFile, $lowResKinOpts);
// if(filesize($outfile) > MP_KIN_GZIP_THRESHOLD) destructiveGZipFile($outfile);
// echo "do low-res Kinemage ran for ".(time() - $startTime)." seconds\n";
// }
//}
//}}}
//{{{ Create REMARK 40 and insert into PDB file
//if(is_array($clash) || is_array($rama) || is_array($rota))
//{
// setProgress($tasks, 'remark40'); // updates the progress display if running as a background job
// $remark40 = makeRemark40($clash, $rama, $rota);
// replacePdbRemark($infile, $remark40, 40);
//}
//}}} Create REMARK 40 and insert into PDB file
//{{{ Create lab notebook entry
$entry = "";
if (is_array($clash) || is_array($rama) || is_array($rota) || is_array($cbdev) || is_array($pperp) || is_array($suites)) {
$entry .= "<h3>Summary statistics</h3>\n";
$entry .= makeSummaryStatsTable($model['stats']['resolution'], $clash, $rama, $rota, $cbdev, $pperp, $suites, $validate_bond, $validate_angle, $cablam, $omega);
}
$entry .= $improveText;
if ($opts['doKinemage'] || $opts['doCharts']) {
$entry .= "<h3>Multi-criterion visualizations</h3>\n";
$entry .= "<div class='indent'>\n";
$entry .= "<table width='100%' border='0'><tr valign='top'>\n";
if ($opts['doKinemage']) {
$entry .= "<td>" . linkAnyFile("{$model['prefix']}multi.kin", "Kinemage", "img/multikin.jpg") . "</td>\n";
}
if ($opts['doCharts']) {
$entry .= "<td>" . linkAnyFile("{$model['prefix']}multi.table", "Chart", "img/multichart.jpg") . "</td>\n";
if ($opts['chartCoot']) {
$entry .= "<td>" . linkAnyFile("{$model['prefix']}multi-coot.scm", "To-do list for Coot", "img/multichart-coot.jpg") . "<br><small><i>Open this in Coot 0.1.2 or later using Calculate | Run Script...</i></small></td>\n";
#$entry .= "<td>".linkAnyFile("$model[prefix]multi-coot.py", "To-do list for Coot Python", "img/multichart-coot.jpg")."<br><small><i>Open this in Coot 0.1.2 or later using Calculate | Run Script...</i></small></td>\n";
}
if ($opts['chartHoriz']) {
$entry .= "<td>" . linkAnyFile("{$model['prefix']}horiz.table", "Horizontal Chart", "img/multichart_horiz.jpg") . "</td>\n";
}
}
//if($opts['doLowRes']) {
// if($opts['kinCablamLow'] || $opts['other']) {
// $entry .= "<td>".linkAnyFile("$model[prefix]low_multi.kin", "LowRes MultiKin", "img/low_multikin.jpg")."</td>\n";
// }
//}
$entry .= "</tr></table>\n";
$entry .= "</div>\n";
}
if ($opts['chartClashlist'] || $opts['chartRama'] || $opts['chartCBdev'] || $opts['chartSuite']) {
$entry .= "<h3>Single-criterion visualizations</h3>";
$entry .= "<ul>\n";
if ($opts['chartClashlist']) {
$entry .= "<li>" . linkAnyFile("{$model['prefix']}clashlist.txt", "Clash list") . "</li>\n";
}
if ($opts['chartRama']) {
$entry .= "<li>" . linkAnyFile("{$model['prefix']}rama.kin", "Ramachandran plot kinemage") . "</li>\n";
$entry .= "<li>" . linkAnyFile("{$model['prefix']}rama.pdf", "Ramachandran plot PDF") . "</li>\n";
}
if ($opts['chartCBdev']) {
$entry .= "<li>" . linkAnyFile("{$model['prefix']}cbetadev.kin", "Cβ deviation scatter plot") . "</li>\n";
}
if ($opts['chartSuite']) {
$entry .= "<li>" . linkAnyFile("{$model['prefix']}suitename.txt", "RNA backbone report") . "</li>\n";
$entry .= "<li>" . linkAnyFile("{$model['prefix']}suitestring.txt", "RNA backbone conformation \"sequence\"") . "</li>\n";
$entry .= "<li>" . linkAnyFile("{$model['prefix']}suitename.kin", "RNA backbone multi-D plot of conformations") . "</li>\n";
}
$entry .= "</ul>\n";
}
if ($remark40) {
$entry .= "<h3>REMARK 40</h3>";
$url = "{$modelURL}/{$model['pdb']}";
$entry .= "You can <a href='{$url}'>download your PDB file with REMARK 40</a> inserted, or the same <a href='download_trimmed.php?{$_SESSION['sessTag']}&file={$infile}'> without hydrogens</a>.\n";
$entry .= "<p><pre>{$remark40}</pre></p>";
}
//}}} Create lab notebook entry
setProgress($tasks, null);
// everything is finished
return $entry;
}
