Re: [OpenBabel-scripting] MOL file as string by parameter and JME

[kohai.raul <koh...@gm...>]

Oops,

pasted wrong version of perl script:

>From PERL (OBConverter.pl):

#!/usr/bin/perl

use Chemistry::OpenBabel;

 $chemdata = shift;
 $serviceIn = shift;
 $serviceOut = shift;

  my $obMolIn = new Chemistry::OpenBabel::OBMol;
  my $obConv = new Chemistry::OpenBabel::OBConversion;

  $obConv->SetInAndOutFormats($serviceIn, $serviceOut);
  $obConv->ReadString($obMolIn, $chemdata);
  my $obOut=$obConv->WriteString($obMolIn);

  print ("$obOut");


2011/1/25 kohai.raul [via Open Babel] <
ml-...@n4...<ml-node%2B3...@n4...>
>

> Hi all,
>
> problem Solved! ... if it could to help someone:
>
> From PHP:
>
>
>
>   public function largeDataConverter($chemData,$inFormat,$outFormat){
>
>     $file="OBConverter.pl @'$chemData' '$inFormat' '$outFormat'";
>     $myVar = "";
>
>     ob_start();
>     passthru("$file");
>     $myVar = ob_get_contents();
>     ob_end_clean ();
>
>     if (substr_count(strtolower($myVar), 'error')>0)
>       $myVar="";
>
>     return $myVar;
>
>   //$myVar contains the conversion result from perl script.
>
>   }
>
>
>
> From PERL (OBConverter.pl):
>
>
> #!/usr/bin/perl
>
> use Chemistry::OpenBabel;
>
>  @chemdata = shift;
>  $serviceIn = shift;
>  $serviceOut = shift;
>
>   my $obMolIn = new Chemistry::OpenBabel::OBMol;
>   my $obConv = new Chemistry::OpenBabel::OBConversion;
>
>   $obConv->SetInAndOutFormats($serviceIn, $serviceOut);
>   $obConv->Read($obMolIn, @chemdata);
>   my $obOut=$obConv->WriteString($obMolIn);
>
>   print ("$obOut");
>
>
> This way, Perl admits $chemdata as SMI or MOL, all in string format, no
> external files needed.
>
> Thanks to this, I found that   JME-SMI->MOL / or CML / or VMOL, etc.. have
> not the same results as JME-MOL->CML / or VMOL, etc ... because to spatial
> data??... maybe...  as I said, I'm not chemist, but now I understand that
> SMI doesn't express the same information such as MOL, and there will be more
> resulting data in MOL->CML than SMI->CML
>
> Now, I can not only make use of JME.smiles() (from javascript), but
> JME.molFile() and obtain via "php-ob-bridge" conversions to CML, VMOL, INCHI
> .... through the flux:
>
> Web-Client (JME ->javascript molFile -> AJAX ) -> SERVER ( php +
> "ob-bridge" -> chem results available on php -> to DB or anything ) ->
> callback (JSON) -> javascript (on web client)
>
> Best Regards,
>
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-- 
--
Raúl Cruz
foro.fuentedepermacultura.org
"pro-curando..."

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