Remove Border Atoms

Description

Removes atoms that have bonds with atoms outside the unit cell. This is needed to normalize the coordination computation for a structure.

Input Ports

structure_in MoleculeType Molecular structure data. It must contains unit cell definition data.

Parameters

H bonds toggle Enable computation of H bonds.
Greedy bonding toggle Ignore the maximum number of bonds for each atom.
Bonding Range Adjustment slider Percentage of variation of the maximum distance between atoms to form a bond.
H Bonding Range Adjustment slider Percentage of variation of the maximum distance between H and an atom to form a bond.
H Bond Max Distance slider Maximum lenght of an H bond.
H Bond Max Angle slider Maximum angle HXY (in X__H..Y where .. is the H bond) to form an H bond.

Output Ports

structure_out MoleculeType Molecular structure data with border atoms removed.
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