Is RXN format is still supported

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Is RXN format is still supported

Charlie Zhu
Hi,

I have tested a few RXN files on Openbabel GUI on Windows but 0 result has been output. One of the RXN file is attached.
I temporarily have to use Regexp to parse the RXN format to SDF as C# code as pasted below. It is even not trusted by myself.

                f = Regex.Replace(f, "\\$RXN(.*?)\\$MOL\\r?\\n", "", RegexOptions.Singleline);
                f = Regex.Replace(f, "\\$MOL", "$$$$$$$$", RegexOptions.Singleline);
                f = f + "$$$$\r\n";

Anyone knows what's the matter?
Thanks,

Charlie

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rxn-2.rxn (1K) Download Attachment
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Re: Is RXN format is still supported

Geoffrey Hutchison
> I have tested a few RXN files on Openbabel GUI on Windows but 0 result has been output. One of the RXN file is attached.

RXN format is definitely supported for reaction conversion (e.g., to CML reaction formats). What exactly are you trying to do in the GUI?

Thanks,
-Geoff
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Re: Is RXN format is still supported

Chris Morley-3
In reply to this post by Charlie Zhu
Charlie Zhu wrote:

> I have tested a few RXN files on Openbabel GUI on Windows but 0 result
> has been output. One of the RXN file is attached.
> I temporarily have to use Regexp to parse the RXN format to SDF as C#
> code as pasted below. It is even not trusted by myself.
>
>                 f = Regex.Replace(f, "\\$RXN(.*?)\\$MOL\\r?\\n", "",
> RegexOptions.Singleline);
>                 f = Regex.Replace(f, "\\$MOL", "$$$$$$$$",
> RegexOptions.Singleline);
>                 f = f + "$$$$\r\n";
>
> Anyone knows what's the matter?

I think there are two issues here.

RXN format seems to be working ok for converting to and from
reactions. What you seem to want is to convert from rxn to sdf -
converting from a reaction to molecules. This reasonable request is
not currently supported, but I have just written some code that will
allow it to happen from all reaction formats to most molecular
formats. I will commit it to the development code soon.

In the meantime in v2.2.3 you can already convert from a reaction in
cml to molecules in sdf, say. So, in the GUI, convert from rxn to cml,
Copy Output to Input (File menu) and convert to sdf.

The other issue is that your example file contains two lines in a mol
file part which are not interpreted by OpenBabel and are ignored. One
is in the bond block:
   4 F    4   9  17  35  53

I don't understand it, but Marvin seems to like it.

The other is:
M  ALS   4  4 F F   Cl  Br  I

an Atom List, which is for queries in the MDL documentation,
equivalent, I think, to SMARTS [F,Cl,Br,I]. Marvin seems to use it as
a Markush structure. Currently the target atom is converted to an
unspecified * atom, which is compatible but too general.  As far as I
know, OpenBabel currently does not have any support for Markush
structures, but it might be something of interest for the future.

Chris


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Fwd: Is RXN format is still supported

Charlie Zhu

Hi Chris,

You gave me the point. My task is just to extract all reactant and product from the reaction. I have thought it is a nature feature for Open Babel to convert from Reaction to Molecules because I have do it successfully against CDX files.

By the way the RXN and CDX files are all exported by Chemdraw 8.0.

Thank you.

Charlie


On Wed, Nov 11, 2009 at 11:03 PM, Chris Morley <[hidden email]> wrote:
Charlie Zhu wrote:

> I have tested a few RXN files on Openbabel GUI on Windows but 0 result
> has been output. One of the RXN file is attached.
> I temporarily have to use Regexp to parse the RXN format to SDF as C#
> code as pasted below. It is even not trusted by myself.
>
>                 f = Regex.Replace(f, "\\$RXN(.*?)\\$MOL\\r?\\n", "",
> RegexOptions.Singleline);
>                 f = Regex.Replace(f, "\\$MOL", "$$$$$$$$",
> RegexOptions.Singleline);
>                 f = f + "$$$$\r\n";
>
> Anyone knows what's the matter?

I think there are two issues here.

RXN format seems to be working ok for converting to and from
reactions. What you seem to want is to convert from rxn to sdf -
converting from a reaction to molecules. This reasonable request is
not currently supported, but I have just written some code that will
allow it to happen from all reaction formats to most molecular
formats. I will commit it to the development code soon.

In the meantime in v2.2.3 you can already convert from a reaction in
cml to molecules in sdf, say. So, in the GUI, convert from rxn to cml,
Copy Output to Input (File menu) and convert to sdf.

The other issue is that your example file contains two lines in a mol
file part which are not interpreted by OpenBabel and are ignored. One
is in the bond block:
  4 F    4   9  17  35  53

I don't understand it, but Marvin seems to like it.

The other is:
M  ALS   4  4 F F   Cl  Br  I

an Atom List, which is for queries in the MDL documentation,
equivalent, I think, to SMARTS [F,Cl,Br,I]. Marvin seems to use it as
a Markush structure. Currently the target atom is converted to an
unspecified * atom, which is compatible but too general.  As far as I
know, OpenBabel currently does not have any support for Markush
structures, but it might be something of interest for the future.

Chris


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