From owner-chemistry@ccl.net Mon Nov 21 00:11:01 2005
From: "Geoffrey Hutchison grh25^cornell.edu" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: info about .MOL files needed
Message-Id: <-30017-051120021929-443-pn+ZGqAgxEFDqIVJSDK/rA{}server.ccl.net>
X-Original-From: Geoffrey Hutchison <grh25%x%cornell.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed
Date: Sat, 19 Nov 2005 20:27:00 -0500
Mime-Version: 1.0 (Apple Message framework v746.2)


Sent to CCL by: Geoffrey Hutchison [grh25^cornell.edu]
Well, MDL Molfiles have a published specification:
http://www.mdl.com/downloads/public/ctfile/ctfile.jsp

If you're looking for an open package to parse MDL Molfiles, there  
are several (off the top of my head), depending on what you want. For  
example Open Babel is a flexible converter for a wide range of  
chemistry file formats:
Open Babel http://openbabel.sourceforge.net/
CDK        http://cdk.sourceforge.net/
JOELib     http://joelib.sourceforge.net/
Rosetta    http://octetsource.org/

Of course in practice, there are Molfiles which don't adhere to the  
standard, so if you're writing a parser, you might want to be  
flexible about what files you accept.

Cheers,
-Geoff

--
-Dr. Geoffrey Hutchison        <grh25(-)cornell.edu>
Cornell University, Department of Chemistry and Chemical Biology
Abruņa Group                http://abruna.chem.cornell.edu/

On Nov 19, 2005, at 5:30 PM, Roman Garcia nykros]|[gmail.com wrote:

> Sent to CCL by: Roman Garcia [nykros|,|gmail.com]
> ------=_Part_15806_31969803.1132417002248
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> Hi,
>   I=B4m new to CCL, sorry if this question has been previously  
> answered, bu=
> t
> CCL search capabilities seems to be disabled. I would like to know  
> if anyon=
> e
> can help me: I need the specification of .MOL files to build a  
> parser to
> extract molecule information. Is there a free parser available?
>  Any usefull information will be apreciated.
>   Thank you in advance. Roman Garcia.
>
> ------=_Part_15806_31969803.1132417002248
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> <div>Hi,</div>
> <div>&nbsp;</div>
> <div>&nbsp; I=B4m new to CCL, sorry if this question has been  
> previously an=
> swered, but CCL search capabilities seems to  
> be&nbsp;disabled.&nbsp;I would=
>  like&nbsp;to know if anyone can&nbsp;help me: I&nbsp;need the  
> specificatio=
> n of .MOL files to build a parser to extract molecule information.  
> Is there=
>  a free parser available?
> </div>
> <div>&nbsp; Any usefull information will be apreciated.</div>
> <div>&nbsp;</div>
> <div>&nbsp; Thank you in advance. Roman Garcia.</div>
> <div>&nbsp;</div>
>
> ------=_Part_15806_31969803.1132417002248--
>
>
>
> -= This is automatically added to each message by the mailing  
> script =-
> To recover the email address of the author of the message, please  
> change>
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- 
> +-+-+
>
>
>