Atomic Capping

Single Atom Capper

This module closes off the valencies of the input fragments using single nuclei. More specifically for each bond A-B, such that atom A is in the fragment, and atom B is not, a nucleus (default is a hydrogen nucleus) will be added to the fragment. By default the added nucleus will be placed at the location of B.

The inputs to this module are fragments and the . In general these inputs are non-disjoint, for this reason we choose to establish connectivity at an atomic level.

Generate atomic connectivity
Determine caps we need
Pair each fragment with its set of caps

Please Cite

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Property Types

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

ghostfragment::pt::CappedFragments

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
capping nucleus	name : H, atomic number : 1, mass : 1837.289, charge : 1, x : 0, y : 0, z : 0	nucleus to use as the cap
Fragments to cap	N/A	N/A
System connectivity	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.

capping nucleus

Description : nucleus to use as the cap
Default Value : name : H,

atomic number : 1, mass : 1837.289, charge : 1, x : 0, y : 0, z : 0 - Optional? : False - Opaque? : True - Domain Restrictions :

Type == chemist::Nucleus

Fragments to cap

Description : N/A
Default Value : N/A
Optional? : False
Opaque? : True
Domain Restrictions :
- Type == chemist::fragmenting::FragmentedNuclei<chemist::Nuclei>

System connectivity

Description : N/A
Default Value : N/A
Optional? : False
Opaque? : True
Domain Restrictions :
- Type == std::set<std::pair<unsigned long, unsigned long>, std::less<std::pair<unsigned long, unsigned long>>, std::allocator<std::pair<unsigned long, 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
Capped Fragments	chemist::fragmenting::FragmentedNuclei<chemist::Nuclei>	N/A

Submodules

The module defines no submodules.