On 10/08/2017 08:16, devw wrote:
The bond detection behavior has been acting up recently and as part of the
problem solving process I've been trying to find any documentation
whatsoever about this "b" option being set in INOPTIONS.
To be more explicit, it's not for a particular format, it has an effect on
how babelbond reads many formats, and that effect is not as stated in the
documentation i could find that mentioned b.

The code that adds bonds is in the functions ConnectTheDots and PerceiveBondOrders in mol.cpp. Look here to see the detail of how they work.

These functions are called from several file formats (xyz is a simple one), depending on the input options b and s. Information on a format and its options can be obtained from, for example, http://open-babel.readthedocs.io/en/latest/FileFormats/XYZ_cartesian_coordinates_format.html
or obabel -L xyz

An overview of the differences between input, output and general options is at http://open-babel.readthedocs.io/en/latest/FileFormats/Overview.html


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