Bond-Based Fragmenter

This module takes as input a MolecularGraph representation of the molecular system and an integer parameter nbonds, and outputs a FragmentedNuclei object. The fragments are generated by looping over the nodes in MolecularGraph and assembling all nodes a distance of nbonds or less away from the node in question into a fragment. Each distinct fragment will be output exactly once (i.e. no repeats).

Please Cite

No citations

Property Types

The following is a list of property types that this module satisfies.

ghostfragment::pt::NuclearGraphToFragments

Module Inputs

This section details the full list of inputs that the module accepts. Inputs that are not listed as optional must have their value set before the module can be run. Inputs can be set manually by calling the module’s change_input function or by passing arguments to a property type.

Quick Reference

The following table provides a quick summary of the inputs available to this module. The columns are:

Key: The key used to retrieve the option,
Default : The initial value, if one exists, and
Description : A human readable description of what the option is used for.

Key	Default	Description
Molecular Graph	N/A	N/A
nbonds	0	bond width of fragment

Detailed Descriptions

The following subsections provide detailed descriptions of each input recognized by this module. The subsection headings are the name of the input. Within each subsection we list:

Description : A human readable description of what the option is used for.
Default Value : The initial value, if one exists.
Optional? : Whether the value must be set inorder for the module to run.
Opaque? : Does the value of the input influence memoization?.
Domain Restrictions : Criteria a value must obey to be deemed valid.

Molecular Graph

Description : N/A
Default Value : N/A
Optional? : False
Opaque? : True
Domain Restrictions :
- Type == ghostfragment::NuclearGraph

nbonds

Description : bond width of fragment
Default Value : 0
Optional? : False
Opaque? : True
Domain Restrictions :
- Type == unsigned long

Module Results

This section tabulates the full list of results that the module returns. The columns respectively are:

Key: What the result is called
Type: The C++ type of the result
Description: What the result is/how it was computed.

Note

A given property type will only return a subset of the available results. Additional results can be accessed by using other property types or by using the Module class’s advanced API.

Key	Type	Description
Fragments	chemist::fragmenting::FragmentedNuclei<chemist::Nuclei>	N/A

Submodules

The module defines no submodules.