$pepvalid = $pep->validateSequence($sequence) ? 'true' : 'false';
}
if ($nterminus !== '') {
$pep->NTerminus = $nterminus;
}
if ($cterminus !== '') {
$pep->CTerminus = $cterminus;
}
if ($pepvalid === 'true') {
if ($cterminus !== '') {
$ctermmass = strval($pep->getCTerminusMass('monoisotopic'));
}
if ($nterminus !== '') {
$ntermmass = strval($pep->getNTerminusMass('monoisotopic'));
}
$mec = $pep->getMec();
$pepmass = strval($pep->getMass('monoisotopic'));
$pepmcr2 = strval($pep->getTheoreticalMCR('monoisotopic', 2));
$pepmcr3 = strval($pep->getTheoreticalMCR('monoisotopic', 3));
$pepmcr4 = strval($pep->getTheoreticalMCR('monoisotopic', 4));
if (!is_numeric($iccharge)) {
$iccharge = '2';
}
//-- IonCalculator --
$ic = new IonCalculator(array('peptide' => $pep, 'maxcharge' => intval($iccharge), 'weighttype' => 'monoisotopic', 'neutralloss' => array('H2O', 'NH3'), 'customtemplate' => '{ion}{index} {charge}+ {flag}'));
$arrIcRes = array();
foreach ($arrIons as $ion) {
$arrIcRes += $ic->calculateIon($ion);
}
//-- Spectrum --
$validSpec = false;
