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The MDL .mol file format is a ``de facto'' standard file format
for representing small molecules used by MDL Information Systems, of
San Leandro, California. This file format is traditionally used to
represent discrete molecules, however it also contains addition atom
and bond fields used to represent substructure queries. These query
files are used by MDL's MACCS and ISIS/Host products to specify the
substructure pattern to be used for the search.
An MDL mol file/connection table consists of five parts; a three line line ``header block'', a one line ``counts block'', an ``atom block'' containing a single line for each atom, a ``bond block'' containing a single line for each bond, and finally a trailing ``properties block'' that contains optional additional information. This file format is based upon a regular ASCII text file, each line consisting of upto 80 charcters delimited by a usual line terminator (either carrige return/linefeed or just a linefeed character). Almost all information (with the exception of some fields in the properties block) uses a fixed width encoding, such that whitespace is significant and that values must reside in their dictated columns.
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