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Molecular dynamics by NMR data analysis

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Fix for the atom_connect() method and the creation of the CONECT record.

The atom_connect() method was modified to only append the atom index if it wasn't already in the
bonded list. The CONECT record now uses the atom numbers and not atom indecies.

Authored by: bugman 2008-07-04

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Molecular dynamics by NMR data analysis

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