Hi Chris,
I don't think java would be suitable to manipulate the information
would you have in your data file. Perl possibly could handle it, but
a high level programming language, such as C or C++, would be a
better choice. You could also use Basic, Fortran or a number of
others.
As far as determining incorrect information in your data file, you
would probably need to recreate the molecules to see what atoms are
attached to something. One of the proteins I loaded into a program
had the atoms in the correct locations, but some were not connected
properly. I have to edit the bonds manually before I could
manipulate the molecule. Your data file could have the same problem
and doesn't really have any stray atoms.
Lance

--- In ChemistrySoftware@yahoogroups.com, "cjthorley"
<cjthorley@y...> wrote:
>
> Dear All,
> I wonder is anyone can help me. I want to find away of coding a
> small program that will clean up and SDF file. When I say clean up
I
> mean remove entires that don't have a connection table or indeed
> don't have the correct format and therefore not a valid MOL file.
So
> in short lets say that I have an SDF file that I have been told
> contains 100 structures but inorder for these structures to be
> enetered into a database they must have valid MOL file
> representations. I know there are various commercial tool
available
> to do this but I want to have ago at writing my own personal
program
> that can do this. I have a little java experience but perhaps Perl
> or Python scripting might produce the desired result. If anyone
has
> any suggestions on how I could do this would be fantastic. Im a
> little unsure how its possible to validate a segment of a text
file
> (ie fractions of the SDF file) against a known format. The mains
> issues would be that the lengths and formats of each MOL file
entry
> in the SDF file might not have the same information.
> Anyway any tips would be great.
> Thanks
> Chris Thorley
>