<?php
include_once '/usr/local/lib/openbabel.php';
$obMol = new OBMol();
$obMol->NewAtom();
$numAtoms = $obMol->NumAtoms();
# now 1 atom
$obMol->NewAtom();
$obMol->AddBond(1, 2, 1);
$numBonds = $obMol->NumBonds();
# now 1 bond
$obMol->Clear();
$obConversion = new OBConversion();
$obConversion->SetInAndOutFormats("smi", "svg");
$obConversion->ReadString($obMol, "C1=CC=CS1");
$numAtoms = $obMol->NumAtoms();
# now 5 atoms
$obMol->AddHydrogens();
$numAtoms = $obMol->NumAtoms();
# now 9 atoms
$outMDL = $obConversion->WriteString($obMol);
echo $outMDL;
public function write($format = 'smi', $filename = null, $overwrite = false, $opt = array())
{
$OBConversion = new \OBConversion();
$OBConversion->SetOutFormat($format);
# set options
if (!empty($opt)) {
foreach ($opt as $k => $v) {
if ($v === null) {
$OBConversion->AddOption($k, $OBConversion::OUTOPTIONS, $v);
} else {
$OBConversion->AddOption($k, $OBConversion::OUTOPTIONS);
}
}
}
if (!empty($filename)) {
if (!file_exists($filename) || file_exists($filename) && $overwrite) {
return $OBConversion->WriteFile($this->OBMol, $filename);
}
} else {
return $OBConversion->WriteString($this->OBMol);
}
}
