StaBeads sets properties for beads using mapping (coarse-graining) scheme for each molecule. More...

#include <sta_beads.h>

Inheritance diagram for StaBeads:

Collaboration diagram for StaBeads:

Public Member Functions
	StaBeads (const ElPtr &el_mols, const Vec< Json > &scheme)
	Constructor of StaBeads class for molecules all of whose `type` property are 1, or molecules all of which do not have the property. More...

	StaBeads (const ElPtr &el_mols, const Map< int, Vec< Json >> &schemes)
	Constructor of StaBeads class for multiple molecular types. More...

Public Member Functions inherited from Starter
	Updater ()=default
	Constructor of Updater class. More...

Public Member Functions inherited from Updater
	Updater ()=default
	Constructor of Updater class. More...

void	compute (const ElPtr &elem, const int elementid, Json &data)
	Managing computation to update Element::data. More...

void	remove_from_skippable_elementids (const int elementid)
	Remove Element::elementid from skippable_elementids. More...

const ShPtr< Generator > &	get_ext_generator ()
	Get ext_generator of this object. More...

Protected Member Functions
virtual void	compute_impl (Json &data, JsonToVoidFunc check_required_keys, JsonToBoolFunc check_optional_keys) override
	This method overrides Updater::compute_impl. More...

Protected Member Functions inherited from Starter
virtual void	compute_body (const ElPtr &elem, Json &data) override
	Compute or parse properties and set them to Element::data given as a mutable reference. More...

Protected Member Functions inherited from Updater
virtual void	compute_common (const ElPtr &elem, Json &data)
	Common part of compute_body. More...

Private Member Functions
std::pair< bool, bool >	check_mol_type_to_abst_beads ()

Private Attributes
Map< int, Vec< Json > >	mol_type_to_abst_beads

Additional Inherited Members
Protected Attributes inherited from Updater
ShPtr< Generator >	ext_generator

Static Protected Attributes inherited from Starter
static const bool	do_sorting_by_id = true

Detailed Description

StaBeads sets properties for beads using mapping (coarse-graining) scheme for each molecule.

An object of this class owns mapping(s) representing coarse-graining scheme(s). Each mapping describes how atoms in a molecule are allocated to beads. Different mapping schemes are acceptable for different molecular types. For each bead, its type and weighting factors of atoms belonging to the bead can be set.

About usage in Python, please see pybind/starters/py_sta_beads.

Definition at line 27 of file sta_beads.h.

Constructor & Destructor Documentation

◆ StaBeads() [1/2]

StaBeads::StaBeads	(	const ElPtr &	el_mols,
		const Vec< Json > &	scheme
	)

Constructor of StaBeads class for molecules all of whose type property are 1, or molecules all of which do not have the property.

Parameters

el_mols

A molecular Element object consisting of beads for which an Element object is created with this constructed object. This parameter is assigned to ext_generator.

Required property

atom-ids : array of integers

scheme List of Json (complex of dictionary and list) objects. Each Json object corresponds to each bead in a molecule, and contains three items: indices-in-mol is an array of zero-based index of atoms in the molecule, type is type of the bead, and weights is an array of floats for weighting factors of atoms. This parameter is stored in mol_type_to_abst_beads as a coarse-graining scheme for molecular type 1.

Definition at line 16 of file sta_beads.cpp.

◆ StaBeads() [2/2]

StaBeads::StaBeads	(	const ElPtr &	el_mols,
		const Map< int, Vec< Json >> &	schemes
	)

Constructor of StaBeads class for multiple molecular types.

Parameters

el_mols

A molecular Element object consisting of beads for which an Element object is created with this constructed object. This parameter is assigned to ext_generator.

Required property

atom-ids : array of integers

schemes Dictionary from molecular type to list of Json (complex of dictionary and list) objects. Each Json object corresponds to each bead in a molecule of that type, and contains three items: indices-in-mol is an array of zero-based index of atoms in the molecule, type is type of the bead, and weights is an array of floats for weighting factors of atoms. This parameter is assigned to mol_type_to_abst_beads.

Definition at line 26 of file sta_beads.cpp.

Member Function Documentation

◆ check_mol_type_to_abst_beads()

std::pair< bool, bool > StaBeads::check_mol_type_to_abst_beads ( )

private

Check if mol_type_to_abst_beads correctly describes coarse-grain mapping schemes.

Returns: A pair of booleans: the first is whether type exists or not, the second is whether weights exists or not. Note that if at least one of Json objects in mol_type_to_abst_beads has type (or weights) property, all the other objects must have that property too.

Definition at line 36 of file sta_beads.cpp.

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◆ compute_impl()

void StaBeads::compute_impl	(	Json &	data,
		JsonToVoidFunc	check_required_keys,
		JsonToBoolFunc	check_optional_keys
	)

overrideprotectedvirtual

This method overrides Updater::compute_impl.

Property to be added

id : integer
mol : integer
atom-ids : array of integers
type : integer (optional)
atom-weights : array of floats (optional)

Implements Updater.

Definition at line 105 of file sta_beads.cpp.

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Member Data Documentation

◆ mol_type_to_abst_beads

Map<int,Vec<Json> > StaBeads::mol_type_to_abst_beads

private

Coarse-grain mapping schemes for each molecular type. Description of coarse-graining is stored in a Map (dictionary) object from molecular type to a Vec (list) object of Json objects. Each Json object corresponds to each bead in a molecule of that type, and contains three items: indices-in-mol is an array of zero-based index of atoms in the molecule, type is type of the bead, and weights is an array of floats for weighting factors of atoms. The last two items are optional. Length of the two arrays, indices-in-mol and weights, should be the same with the number of atoms belonging to the bead.

Definition at line 41 of file sta_beads.h.

The documentation for this class was generated from the following files:

src/starters/sta_beads.h
src/starters/sta_beads.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members