This subroutine guess the connectivity of the system from the coordinates and the atomic number of its atoms. It is based on distances and atomic radii, so it can easily fail on distorted geometries. It should be used only when the the bonds of the molecule are not availble in any other way; it is often used to assign connectivity to a QM part that does not have any. H B C N O F Si P S Cl As Se Br Te I
Type | Intent | Optional | Attributes | Name | ||
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type(ommp_topology_type), | intent(inout) | :: | top |
Topology for which connectivity should be guessed. |
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integer(kind=ip), | intent(in), | optional | :: | exclude_list(:) |
List of atoms that should not be connected when guessing the topology, this is used for LA that could have an ambiguous or not defined position. |