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_sources/module_api/All_nmers.rst.txt

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+..   This page is autogenerated by pluginplay::document_module. Any changes made
+..   to this document will be overwritten the next time it is generated.
+
+#########
+All nmers
+#########
+
+
+.. |n| replace:: :math:`n`
+
+NMers
+=====
+
+Given a set of input fragments, this module will take all |n|-way unions of the
+input fragments. This module works with both disjoint and intersecting
+fragments. For intersecting fragments, this module will ensure that the
+resulting set of |n|-mers are such that no |n|-mer is a subset of another
+|n|-mer (notably this also guarantees their uniqueness).
+
+
+***********
+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                    |
++-----------------+---------+------------------------+
+| n               | 1       | The maximum n-mer size |
++-----------------+---------+------------------------+
+
+
+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
+
+n
+-
+
+- Description : The maximum n-mer size
+- Default Value : 1
+- Optional? : False
+- Opaque? : True
+- Domain Restrictions :
+
+  - Type == unsigned short
+
+
+**************
+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
+**********
+
+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 |
++===============+============================================+=============+
+| Monomer maker | ghostfragment::pt::NuclearGraphToFragments | N/A         |
++---------------+--------------------------------------------+-------------+

_sources/module_api/Atomic_Capping.rst.txt

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+..   This page is autogenerated by pluginplay::document_module. Any changes made
+..   to this document will be overwritten the next time it is generated.
+
+##############
+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
+***********
+
+No citations
+
+**************
+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,          | nucleus to use as the cap |
+|                     | atomic number : 1, |                           |
+|                     | mass : 1837.289,   |                           |
+|                     | charge : 1,        |                           |
+|                     | x : 0,             |                           |
+|                     | y : 0,             |                           |
+|                     | z : 0              |                           |
++---------------------+--------------------+---------------------------+
+| 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.
+