Heavy Atom Partition

Fragmentation by Heavy Atom

For each of the \(N\) heavy atoms (where a heavy atom is defined as any atom, but hydrogen), this fragmentation method creates \(N\) fragments such that the \(i\)-th fragment contains the \(i\)-th heavy atom and all hydrogens bonded to the \(i\)-th heavy atom. In the event that there are hydrogen molecules, (i.e., hydrogen atoms bonded to each other), or lone hydrogen atoms, those are put into their own fragment.

While theoretically usable as a fragmentation method proper, this module is largely envisioned as being used as a pseudoatom submodule, or as the first step in a more involved pseudoatom submodule.

This module will raise an error if there is a hydrogen atom bonded to more than one other atom.

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Property Types

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

  • ghostfragment::pt::FragmentedNuclei

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

System to fragment

N/A

N/A

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.

System to fragment

  • Description : N/A

  • Default Value : N/A

  • Optional? : False

  • Opaque? : True

  • Domain Restrictions :

    • Type == chemist::ChemicalSystemView<chemist::ChemicalSystem const>

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

Fragmented Nuclei

chemist::fragmenting::FragmentedNuclei<chemist::Nuclei>

N/A

Submodules

This section details the full list of submodules that the module uses. For each submodule we have listed:

  • Key : The key used to refer to this particular callback.

  • Property Type : The property type that the submodule must satisfy.

  • Description : How the module will use the submodule.

Key

Property Type

Description

Connectivity

ghostfragment::pt::ConnectivityTable

N/A