/**
* $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);
}
/**
* Composites the results of the find___Outliers() functions into a simple,
* non-redundant list of 9-char residues names (keys)
* and counts of outliers (values).
*/
function findAllOutliers($clash, $rama, $rota, $cbdev, $pperp)
{
$worst = array();
#$worst = array_merge($worst, findClashOutliers($clash));
#$worst = array_merge($worst, findRamaOutliers($rama));
#$worst = array_merge($worst, findRotaOutliers($rota));
#$worst = array_merge($worst, findCbetaOutliers($cbdev));
#$worst = array_merge($worst, findBasePhosPerpOutliers($pperp));
foreach (array(findClashOutliers($clash), findRamaOutliers($rama), findRotaOutliers($rota), findCbetaOutliers($cbdev), findBasePhosPerpOutliers($pperp)) as $criterion) {
if (is_array($criterion)) {
foreach ($criterion as $cnit => $dummy) {
$worst[$cnit] += 1;
}
}
}
ksort($worst);
// Put the residues into a sensible order
#return array_keys($worst);
return $worst;
}
