openbabel 生成smiles的sdf文件

打开sdf文件下载地址：http://pan.baidu.com/s/1kUWGTJT 

linux下生成sdf。

<?php  
header("Content-Type:text/html;charset=utf-8");  
ini\_set('memory\_limit', '140000M'); // 设置文件上传大小  
ini\_set("max\_execution\_time", 0);  
require\_once './functions.php';  
include './configDB.php';  
$starTime = microtime\_float();  
$dsn = "mysql:host={$dbHost};dbname={$dbName};charset=utf8";  
$dbObj = new \\PDO ( $dsn, $dbUser, $dbPass);

$tbName = "sci\_data";  
$mol\_field = 'smiles';  
$query = "SELECT id as name ,smiles FROM \`{$tbName}\` where smiles!=''";

$sdfName = "./sdf/indexs117";

$sdf = \[\];  
$i = 0;  
$j = 0;  
$buffer = "";

$resource = $dbObj->query ( $query );

while($data = $resource->fetch ( \\PDO::FETCH\_ASSOC )){  
    $j++;  
    $array = \[\];  
    $string = OBABLE\_PATH." -:\\"{$data\['smiles'\]}\\" --property ";  
    foreach($data as $k=>$v){  
        if($k=='smiles')  
            continue;  
        $k = str\_replace(\["(",")"\], \["\\\\(","\\\\)"\], $k);  
        $string .= $k."=\\"".$v."\\"\\\\;";  
    }  
    $string .= "  -osdf --gen2d \\n";  
    //echo $string."<br/>";  
    exec($string,$array);  
    if(!isset($array\[1\])){  
        file\_put\_contents($sdfName."StringErr.txt", $string,FILE\_APPEND);  
        file\_put\_contents($sdfName."err.txt", var\_export($data,1),FILE\_APPEND);  
        continue;  
    }  
    if(!preg\_match("/OpenBabel\*/", $array\[1\])){  
        file\_put\_contents($sdfName."StringErr.txt", $string,FILE\_APPEND);  
        file\_put\_contents($sdfName."err.txt", var\_export($data,1),FILE\_APPEND);  
        continue;  
    }  
    $i++;  
    $buffer .= implode("\\r\\n", $array) . PHP\_EOL;  
    if(is\_int($i/1000)){  
        file\_put\_contents($sdfName.".sdf", $buffer,FILE\_APPEND);  
        $buffer = "";  
    }  
}

if($buffer){  
    file\_put\_contents($sdfName.".sdf", $buffer,FILE\_APPEND);  
}

$endTime = microtime\_float();  
echo "using time :".($endTime-$starTime)."<br/>";  
echo $i;exit;  
exit;  
?>

windows下生成sdf

<?php  
ini\_set('memory\_limit', '-1'); // 设置文件上传大小  
ini\_set("max\_execution\_time", 0);  
include "functions.php";  
$start = microtime\_float ();  
$dsn = 'mysql:host=locahost;dbname=xxxx;charset=utf8';  
$dbObj = new \\PDO ( $dsn, "root", "xxxxx" );  
$query = 'SELECT id,smiles FROM \`xxx\` ';  
$res = $dbObj->query($query);  
while(($data = $res->fetch ( \\PDO::FETCH\_ASSOC ))!==false){  
        $datas\[\] = $data;  
}  
// p($datas);die();

$sdfName = "t4";  
// p($datas);  
// /usr/local/bin/obabel -:"\[Na+\].\[O-\]S(=O)(=O)c1ccc(cc1)C(\[\*\])C\[\*\]" --property CAS="25704-18-1"\\;Catalog ID="111"\\;Compound Name="Poly(sodium-p-styrenesulfonate)"\\;M.F.=C8H7NaO3S\\; M.W.=206.194\\;MDL=MFCD00084449\\; Website address="1111"\\;-osdf --gen2d  
// /usr/local/bin/obabel -:"O=C1Oc2c(C1)cc(cc2)Br" --property hello=world\\;Catalog ID=123 \\;web size=http://www.baidu.com \\;Compound Name="Poly(sodium-p-styrenesulfonate)" -osdf --gen2d  
$sdf = \[ \];  
$i = 0;  
$buffer = "";  
foreach ( $datas as $data ) {  
    $string = '';  
    $array = \[\];  
    $string = OBABLE\_PATH . " -:\\"{$data\['smiles'\]}\\" --property ";  
    foreach ( $data as $k => $v ) {  
        if ($k == 'smiles')  
            continue;  
        //$k = str\_replace ( \[ "(",")" \], \[ "\\\\(","\\\\)" \], $k );  
        $string .= $k . "=\\"" . addslashes(html\_entity\_decode($v)) . "\\";";  
    }  
    $string .= "  -osdf --gen2d \\n";  
    exec ( $string, $array );  
    // var\_dump($array);die();  
    if (! isset ( $array \[1\] )) {  
        file\_put\_contents ( $sdfName . "StringErr.txt", $string."\\r\\n", FILE\_APPEND );  
        file\_put\_contents ( $sdfName . "err.txt", var\_export ( $data, 1 )."\\r\\n", FILE\_APPEND );  
        continue;  
    }  
    if (! preg\_match ( "/OpenBabel\*/", $array \[1\] )) {  
        file\_put\_contents ( $sdfName . "StringErr.txt", $string."\\r\\n", FILE\_APPEND );  
        file\_put\_contents ( $sdfName . "err.txt", var\_export ( $data, 1 )."\\r\\n", FILE\_APPEND );  
        continue;  
    }  
    $i ++;  
    $buffer .= implode ( "\\r\\n", $array ) . PHP\_EOL;  
    // var\_dump($buffer);  
    if ($i % 100 == 0) {  
        file\_put\_contents ( $sdfName . ".sdf", $buffer, FILE\_APPEND );  
        $buffer = "";  
        //break;  
    }  
}  
// p($buffer);  
if ($buffer) {  
    file\_put\_contents ( $sdfName . ".sdf", $buffer, FILE\_APPEND );  
}  
$end = microtime\_float ();  
echo "using time :" . ($end - $start) . "<br/>";  
echo $i;  
exit ();