/** * $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; }