Identification of rigid segments
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A flexible molecule is treated as a collection of rigid segments. Each segment contains the largest set of adjacent atoms separated by non-rotatable bonds. Segments are separated by rotatable bonds.
The first step in segmentation is ring identification.All bonds within molecular rings are treated as rigid. This classification scheme is a first-order approximation of molecular flexibility, since some amount of flexibility can exist in non-aromatic rings. To treat such phenomenon as sugar puckering and chair-boat hexane conformations, the user will need to supply each ring conformation as a separate input molecule. Additional bonds may be specified as rigid by the user (see Manual Specification of Non-rotatable Bonds).
Identification of Rigid Anchor and Flexible Bonds
The second step is flexible bond identification. Each flexible bond is associated with a label defined in an editable file (see flex.defn). The parameter file is identified with the flex_definition_file parameter. Each label in the file contains a definition based on the atom types (and chemical environment) of the bonded atoms. Each label is also flagged as minimizable. Typically, bonds with some degree of double bond character are excluded from minimization so that planarity is preserved. Each label is also associated with a set of preferred torsion positions. The location of each flexible bond is used to partition the molecule into rigid segments. A segment is the largest local set of atoms that contains only non-flexible bonds.