#{{{ a_function_definition - sumary_statement_goes_here
############################################################################
/**
* Documentation for this function.
*/
//function someFunctionName() {}
#}}}########################################################################
# MAIN - the beginning of execution for this page
############################################################################
// Security check on filename
$file = realpath($_REQUEST['file']);
if (!$file || !startsWith($file, realpath($_SESSION['dataDir']))) {
mpLog("security:Attempt to access '{$file}' as '{$_REQUEST['file']}'");
die("Security failure: illegal file request '{$_REQUEST['file']}'");
}
$tmp = mpTempfile('tmp_pdb_trim_');
reduceTrim($file, $tmp);
$name = basename($file);
if (preg_match('/H[0-9]*.pdb$/', $name)) {
// uses preg_split to split the name into an array with the H from the name missing.
$nameArray = preg_split('/H([0-9]*.pdb)$/', $name, -1, PREG_SPLIT_DELIM_CAPTURE);
$name = $nameArray[0] . $nameArray[1];
} elseif (preg_match('/H_reg[0-9]*.pdb$/', $name)) {
// uses preg_split to split the name into an array with the H from the name missing.
$nameArray = preg_split('/H_reg([0-9]*.pdb)$/', $name, -1, PREG_SPLIT_DELIM_CAPTURE);
$name = $nameArray[0] . $nameArray[1];
}
### FUNKY: This turns into a binary file download rather than an HTML page,
### and then calls die(), leaving the user on the original HTML page.
// These lines may be required by Internet Explorer
header("Pragma: public");
/**
* $infiles array of single model PDB files to process
* $outfile will be overwritten with a kinemage
*/
function writeMultimodelChart($infiles, $outfile)
{
$infiles = array_values($infiles);
// re-indexes from 0 ... n-1
$clashes = array();
$clashOuts = array();
$clashCount = array();
$rotas = array();
$rotaOuts = array();
$rotaCount = array();
$ramas = array();
$ramaOuts = array();
$ramaCount = array();
$tmpfile = mpTempfile();
for ($i = 0; $i < count($infiles); $i++) {
runClashlist($infiles[$i], $tmpfile);
$clashes[$i] = loadClashlist($tmpfile);
$clashOuts[$i] = findClashOutliers($clashes[$i]);
foreach ($clashOuts[$i] as $cnit => $junk) {
$clashCount[$cnit] += 1;
}
runRotamer($infiles[$i], $tmpfile);
$rotas[$i] = loadRotamer($tmpfile);
$rotaOuts[$i] = findRotaOutliers($rotas[$i]);
foreach ($rotaOuts[$i] as $cnit => $junk) {
$rotaCount[$cnit] += 1;
}
runRamachandran($infiles[$i], $tmpfile);
$ramas[$i] = loadRamachandran($tmpfile);
$ramaOuts[$i] = findRamaOutliers($ramas[$i]);
foreach ($ramaOuts[$i] as $cnit => $junk) {
$ramaCount[$cnit] += 1;
}
}
$allRes = array_values(listResidues($infiles[0]));
// for now, assume all files have same res
$out = fopen($outfile, 'wb');
fwrite($out, "@kinemage 1\n");
fwrite($out, "@flatland\n");
fwrite($out, "@group {models} animate collapsable\n");
fwrite($out, "@labellist {res names}\n");
for ($j = 0; $j < count($allRes); $j++) {
fwrite($out, "{" . $allRes[$j] . "} 0 -{$j} 0\n");
}
fwrite($out, "@balllist {grid} radius= 0.02 nohighlight color= gray\n");
for ($j = 0; $j < count($allRes); $j++) {
for ($i = 0; $i < count($infiles); $i++) {
fwrite($out, "{} " . (-$i - 1) . " -{$j} 0\n");
}
}
for ($i = 0; $i < count($infiles); $i++) {
fwrite($out, "@subgroup {" . basename($infiles[$i]) . "} dominant\n");
fwrite($out, "@ringlist {clashes} master= {clashes} radius= 0.3 width= 2 color= hotpink\n");
for ($j = 0; $j < count($allRes); $j++) {
if ($clashOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} " . (-$i - 1) . " -{$j} 0\n");
}
}
fwrite($out, "@ringlist {rotamers} master= {rotamers} radius= 0.1 width= 2 color= gold\n");
for ($j = 0; $j < count($allRes); $j++) {
if ($rotaOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} " . (-$i - 1) . " -{$j} 0\n");
}
}
fwrite($out, "@ringlist {Ramachandran} master= {Ramachandran} radius= 0.2 width= 2 color= green\n");
for ($j = 0; $j < count($allRes); $j++) {
if ($ramaOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} " . (-$i - 1) . " -{$j} 0\n");
}
}
}
fwrite($out, "@group {criteria (rings)} animate collapsable\n");
fwrite($out, "@labellist {res names}\n");
for ($j = 0; $j < count($allRes); $j++) {
fwrite($out, "{" . $allRes[$j] . "} 0 -{$j} " . -0.1 * $i . "\n");
}
for ($i = 0; $i < count($infiles); $i++) {
fwrite($out, "@subgroup {" . basename($infiles[$i]) . "} dominant\n");
$xpos = 0;
fwrite($out, "@ringlist {clashes} radius= " . 0.5 * ($i + 1) / count($infiles) . " width= 1 color= hotpink\n");
$xpos -= 1.5;
for ($j = 0; $j < count($allRes); $j++) {
if ($clashOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} {$xpos} -{$j} " . -0.1 * $i . "\n");
}
}
fwrite($out, "@ringlist {rotamers} radius= " . 0.5 * ($i + 1) / count($infiles) . " width= 1 color= gold\n");
$xpos -= 1.5;
for ($j = 0; $j < count($allRes); $j++) {
if ($rotaOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} {$xpos} -{$j} " . -0.1 * $i . "\n");
}
}
fwrite($out, "@ringlist {Ramachandran} radius= " . 0.5 * ($i + 1) / count($infiles) . " width= 1 color= green\n");
$xpos -= 1.5;
for ($j = 0; $j < count($allRes); $j++) {
if ($ramaOuts[$i][$allRes[$j]]) {
fwrite($out, "{" . $allRes[$j] . "} {$xpos} -{$j} " . -0.1 * $i . "\n");
}
}
}
fwrite($out, "@group {criteria (lines)} animate collapsable\n");
fwrite($out, "@labellist {res names}\n");
for ($j = 0; $j < count($allRes); $j++) {
fwrite($out, "{" . $allRes[$j] . "} 0 -{$j} " . -0.1 * $i . "\n");
}
$xpos = 0;
fwrite($out, "@vectorlist {clashes} color= hotpink\n");
$xpos -= 1;
writeMultimodelChart_bars($out, $allRes, $clashCount, count($infiles), $xpos);
fwrite($out, "@vectorlist {rotamers} color= gold\n");
$xpos -= 1;
writeMultimodelChart_bars($out, $allRes, $rotaCount, count($infiles), $xpos);
fwrite($out, "@vectorlist {Ramachandran} color= green\n");
$xpos -= 1;
writeMultimodelChart_bars($out, $allRes, $ramaCount, count($infiles), $xpos);
fwrite($out, "@group {criteria (worms)} animate collapsable\n");
fwrite($out, "@labellist {res names}\n");
for ($j = 0; $j < count($allRes); $j++) {
fwrite($out, "{" . $allRes[$j] . "} 0 -{$j} " . -0.1 * $i . "\n");
}
$xpos = 0;
fwrite($out, "@trianglelist {clashes} color= hotpink\n");
$xpos -= 1;
writeMultimodelChart_boxes($out, $allRes, $clashCount, count($infiles), $xpos);
fwrite($out, "@trianglelist {rotamers} color= gold\n");
$xpos -= 1;
writeMultimodelChart_boxes($out, $allRes, $rotaCount, count($infiles), $xpos);
fwrite($out, "@trianglelist {Ramachandran} color= green\n");
$xpos -= 1;
writeMultimodelChart_boxes($out, $allRes, $ramaCount, count($infiles), $xpos);
fclose($out);
}
/**
* Inserts the given block of text into the named PDB file.
*/
function replacePdbRemark($inpath, $remarkText, $remarkNumber)
{
// Make a copy of the starting PDB file into the tmp dir
$outpath = $inpath;
$inpath = mpTempfile("tmp_remark_");
copy($outpath, $inpath);
// Open input and output streams
$in = fopen($inpath, 'r');
$out = fopen($outpath, 'w');
// Copy headers and remarks that precede ours...
while (!feof($in)) {
$line = fgets($in, 1024);
$start = substr($line, 0, 6);
if ($start == 'REMARK') {
$num = substr($line, 7, 3) + 0;
if ($num >= $remarkNumber) {
if ($num == $remarkNumber) {
$line = null;
}
// mark line as written -- we don't want to write it later!
break;
} else {
fwrite($out, $line);
$line = null;
// mark line as written
}
} elseif ($start == 'USER ' || $start == 'HEADER' || $start == 'OBSLTE' || $start == 'TITLE ' || $start == 'CAVEAT' || $start == 'COMPND' || $start == 'SOURCE' || $start == 'KEYWDS' || $start == 'EXPDTA' || $start == 'AUTHOR' || $start == 'REVDAT' || $start == 'SPRSDE' || $start == 'JRNL ') {
fwrite($out, $line);
$line = null;
// mark line as written
} else {
break;
}
// abort loop for any other type of record
}
// Write our remark
fwrite($out, $remarkText);
// Write the line that made us break, if applicable:
if ($line) {
fwrite($out, $line);
}
// Copy remaining records, skipping any with our same remark number
while (!feof($in)) {
$line = fgets($in, 1024);
$start = substr($line, 0, 6);
if ($start == 'REMARK') {
$num = substr($line, 7, 3) + 0;
if ($num == $remarkNumber) {
continue;
}
}
fwrite($out, $line);
}
// Close streams
fclose($out);
fclose($in);
// Remove duplicate of original file
unlink($inpath);
}
/**
* 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;
}
/**
* Documentation for this function.
*/
function onUploadXray()
{
$req = $_REQUEST;
if ($_REQUEST['cmd'] == "Cancel") {
pageReturn();
} else {
$xrayName = censorFileName($_FILES['uploadFile']['name'], array('mtz'));
// make sure no spaces, etc.
$xrayPath = "{$_SESSION['dataDir']}/" . MP_DIR_XRAYDATA;
if (!file_exists($xrayPath)) {
mkdir($xrayPath, 0777);
}
$xrayPath .= "/{$xrayName}";
$tmpfile = mpTempfile("tmp_mtz");
if (!$_FILES['uploadFile']['error'] && $_FILES['uploadFile']['size'] > 0 && !file_exists($xrayPath) && move_uploaded_file($_FILES['uploadFile']['tmp_name'], $tmpfile)) {
$tf = mtzFormatCorrect($tmpfile);
if ($tf) {
mpLog("mtz-upload:User uploaded an mtz file");
copy($tmpfile, $xrayPath);
$_SESSION['mtzs'][$xrayName] = $xrayName;
pageGoto("upload_other_done.php", array('type' => 'xray', 'xrayName' => $xrayName));
} else {
$this->doUploadError('xray', $xrayPath);
}
} else {
$this->doUploadError('xray', $xrayPath);
}
}
}
/**
* Creates a ZIP archive file containing all the listed files.
* The archive is created as a temporary file and should be unlinked afterwards.
* The name of the temporary file is returned.
* $basepath the ZIP paths will be relative to this folder
* $filelist an array of file paths, specified relative to $basepath
* both directories and files *should* be OK in here
*/
function makeZipForFiles($basepath, $filelist)
{
$outpath = mpTempfile("tmp_zip_");
$cwd = getcwd();
chdir($basepath);
// must compress to stdout b/c otherwise zip wants a .zip ending
exec("zip -qr - " . implode(' ', $filelist) . " > {$outpath}");
chdir($cwd);
// go back to our original working dir
return $outpath;
}