function makeBadRamaKinNMR($infile, $outfile, $rama, $color = 'red')
{
foreach ($rama as $res) {
if ($res['eval'] == 'OUTLIER') {
$worst[] = $res['resName'];
}
}
$mc = resGroupsForPrekin(groupAdjacentRes($worst));
$h = fopen($outfile, 'a');
//changed to @subgroup, added @vectorlist, and changed color to red for rama outliers
fwrite($h, "@subgroup {Rama outliers} \n@vectorlist {Rama outliers} color= red \n");
fclose($h);
foreach ($mc as $mcRange) {
exec("prekin -append -nogroup -listmaster 'Rama Outliers' -scope {$mcRange} -show 'mc({$color})' {$infile} >> {$outfile}");
}
}
/**
* rota is the data from loadRotamer(),
* or null to have it generated on the fly.
*/
function makeBadRotamerKin($infile, $outfile, $rota = null, $color = 'gold', $cutoff = 1.0)
{
if (!$rota) {
$tmp = mpTempfile("tmp_rota_");
runRotamer($infile, $tmp);
$rota = loadRotamer($tmp);
unlink($tmp);
}
foreach ($rota as $res) {
//if($res['scorePct'] <= $cutoff)
if ($res['eval'] == 'OUTLIER') {
//top8000 update uses favored-allowed-outlier eval categories
$worst[] = $res['resName'];
}
}
$sc = resGroupsForPrekin(groupAdjacentRes($worst));
$h = fopen($outfile, 'a');
fwrite($h, "@subgroup {rotamer outliers} dominant\n");
fclose($h);
foreach ($sc as $chainID => $scRange) {
if (!$_SESSION['useSEGID']) {
$opt = "-quiet";
} else {
$opt = "-quiet -segid";
}
//echo("prekin $opt -append -nogroup -nosubgroup -listname 'chain $chainID' -listmaster 'rotamer outliers' -bval -scope $scRange -show 'sc($color)' $infile >> $outfile\n");
/*if( ($chainID[0] == ' ' || $chainID[0] == '_') && $chainID[1] != '_')
{
exec("prekin $opt -append -nogroup -nosubgroup -listname 'chain $chainID[1]' -listmaster 'rotamer outliers' -bval -scope $scRange -show 'sc($color)' $infile >> $outfile");
}
else
{
exec("prekin $opt -append -nogroup -nosubgroup -listname 'chain $chainID' -listmaster 'rotamer outliers' -bval -scope $scRange -show 'sc($color)' $infile >> $outfile");
}*/
exec("prekin {$opt} -append -nogroup -nosubgroup -listname 'chain {$chainID}' -listmaster 'rotamer outliers' -bval -scope {$scRange} -show 'sc({$color})' {$infile} >> {$outfile}");
}
}
