[Cdk-devel] HIN file reader & writer

[Rajarshi G. <rx...@ps...>]

Hi,
  I've written a HIN file reader and writer class (HINReader.java and
HINWriter.java). I've also modified ReaderFactory.java such that it is
able to guess the format of a HIN file. I've also modified
FileConverter.java to be able to take in HIN format files and output HIN
format files.

Asking FileConverter.java to take in a HIN and output a HIN produces
identical files.

However I tried converting an XYZ format file to HIN. The resultant
output has all the symbols, charges and coordinates correct, but there
is no connection table. Looking at the source for XYZReader.java I see
that no bonds are specified for the molecule. As a result when
HINWriter.java recieves a Molecule it is not able to produce a
connection table in the output file.

My question is: since babel is able to produce a valid HIN file
(including connection table - though all bonds are single) from an XYZ
file is there something that can be done to XYZReader.java (such as
using valencies to guess connections) to make a list of Bond's? Or
should HINWriter.java do the job of trying to generate a connection
table?

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Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net>
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