Compute Bonds

Description

Compute atomic bonds.

Input Ports

structure_in MoleculeType Molecular structure data. If it already has bonds defined, the module offers the choice to keep or recompute them.

Parameters

H bonds toggle Enable computation of H bonds.
Force recomp. toggle Recompute bonds even if they are present in the input structure.
Use alt. dist. toggle Use bonding distances from the current info set.
Freeze bonds toggle Don't recompute bonds even if interatomic distances change.
Greedy bonding toggle Disregard the maximum bonds per atom limit.
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 distance to form 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 the newly computed bonds added.
Return to index