DCLC Capping

DCLC Capper

This module closes off the valencies of the input fragments using single atoms. More specifically for each bond A-B, such that atom A is in the fragment, and atom B is not, an atom (default is a hydrogen atom) will be added to the fragment. The new atom will be placed at a distance determined by the average A-X bond in the molecule, where X is the capping atom. If no such bonds exist, then the bond distance is given by the length of the typical A-X bond (i.e. the sum of the atoms’ respective covalent radii).

The inputs to this module are fragments. 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

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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 atom	name : H, atomic number : 1, mass : 1837.289, charge : 1, x : 0, y : 0, z : 0	atom to use as the cap
charge for supersystem	0	N/A
Fragments to cap	N/A	N/A
multiplicity for supersystem	1	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 atom

Description : atom 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

charge for supersystem

Description : N/A
Default Value : 0
Optional? : False
Opaque? : True
Domain Restrictions :
- Type == short

Fragments to cap

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

multiplicity for supersystem

Description : N/A
Default Value : 1
Optional? : False
Opaque? : True
Domain Restrictions :
- Type == unsigned short

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

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