.. index:: pair: namespace; pntToPnt
.. _doxid-namespacepnt_to_pnt:

namespace pntToPnt
==================

.. toctree::
	:hidden:

Overview
~~~~~~~~




.. ref-code-block:: cpp
	:class: doxyrest-overview-code-block

	
	namespace pntToPnt {

	// global functions

	Eigen::MatrixXd :ref:`getPointSetRefRing<doxid-namespacepnt_to_pnt_1a5b2c3bd3984c707965b6cc5ec03ff1da>`(int n, int axialDim);
	Eigen::MatrixXd :ref:`createPrismBlock<doxid-namespacepnt_to_pnt_1ab2aaa39d1afd5e2b9a2f23d26323d339>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const Eigen::MatrixXd& refPoints, int ringSize, const std::vector<int>& basal1, const std::vector<int>& basal2);
	double :ref:`getRadiusFromRings<doxid-namespacepnt_to_pnt_1a318a49881fa85f0f239778cd6c7a33f9>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2);
	double :ref:`getAvgHeightPrismBlock<doxid-namespacepnt_to_pnt_1af0adb2c86725daa33e7553c7456b1260>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2);
	int :ref:`relOrderPrismBlock<doxid-namespacepnt_to_pnt_1aaa5adb93aab9c04dae3b0dd82255113b>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, const std::vector<std::vector<int>>& nList, std::vector<int>& outBasal1, std::vector<int>& outBasal2);
	int :ref:`relOrderPrismBlock<doxid-namespacepnt_to_pnt_1ad35ccbeea04f34625242accc1af6d6f8>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, std::vector<int>& outBasal1, std::vector<int>& outBasal2);
	Eigen::MatrixXd :ref:`fillPointSetPrismRing<doxid-namespacepnt_to_pnt_1add7f31e0a4e17beae5c3ded8752e9259>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basalRing, int startingIndex);
	Eigen::MatrixXd :ref:`fillPointSetPrismBlock<doxid-namespacepnt_to_pnt_1ad9d450912979a4c05acb3e1f7829a55f>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, int startingIndex);
	Eigen::MatrixXd :ref:`getPointSetCage<doxid-namespacepnt_to_pnt_1a332141ec965df89d231a1def4dc3f5d7>`(:ref:`ring::strucType<doxid-group__ring_1ga301cfdc88452cfe51bd4f745d223a7e1>` type);
	int :ref:`relOrderHC<doxid-namespacepnt_to_pnt_1ae91f374f024840f0e75795a5b6c5f2ee>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, const std::vector<std::vector<int>>& nList, std::vector<int>& matchedBasal1, std::vector<int>& matchedBasal2);
	std::vector<int> :ref:`relOrderDDC<doxid-namespacepnt_to_pnt_1afa4d01264e49ab06b2828332e961c8f4>`(int index, const std::vector<std::vector<int>>& rings, const std::vector<:ref:`cage::Cage<doxid-structcage_1_1_cage>`>& cageList);
	std::vector<int> :ref:`relOrderDDC<doxid-namespacepnt_to_pnt_1a104a9978a1cec40aeb76f2dbb5afa277>`(const std::vector<int>& equatorial, int index, const std::vector<std::vector<int>>& rings, const std::vector<:ref:`cage::Cage<doxid-structcage_1_1_cage>`>& cageList);
	Eigen::MatrixXd :ref:`changeHexCageOrder<doxid-namespacepnt_to_pnt_1a640219c17f532aa11fe3269cd5d3a4e8>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, int startingIndex = 0);
	Eigen::MatrixXd :ref:`changeDiaCageOrder<doxid-namespacepnt_to_pnt_1a76f40693a1710a7a2d065a211de8b033>`(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& ddcOrder, int startingIndex = 0);

	} // namespace pntToPnt
.. _details-namespacepnt_to_pnt:

Detailed Documentation
~~~~~~~~~~~~~~~~~~~~~~



Global Functions
----------------

.. index:: pair: function; getPointSetRefRing
.. _doxid-namespacepnt_to_pnt_1a5b2c3bd3984c707965b6cc5ec03ff1da:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	Eigen::MatrixXd getPointSetRefRing(int n, int axialDim)

Fills up an eigen matrix point set a reference ring, which is a regular n-gonal polygon; where n is the number of nodes in the ring.

.. index:: pair: function; createPrismBlock
.. _doxid-namespacepnt_to_pnt_1ab2aaa39d1afd5e2b9a2f23d26323d339:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	Eigen::MatrixXd createPrismBlock(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const Eigen::MatrixXd& refPoints, int ringSize, const std::vector<int>& basal1, const std::vector<int>& basal2)

Creates an eigen matrix for the points of a prism block, constructed from the points of a perfect polygon of radius 1, given the basal rings and axial dimension.

.. index:: pair: function; getRadiusFromRings
.. _doxid-namespacepnt_to_pnt_1a318a49881fa85f0f239778cd6c7a33f9:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	double getRadiusFromRings(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2)

Calculate the average radial distance for the basal rings, calculated from the centroid of each basal ring.

.. index:: pair: function; getAvgHeightPrismBlock
.. _doxid-namespacepnt_to_pnt_1af0adb2c86725daa33e7553c7456b1260:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	double getAvgHeightPrismBlock(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2)

Calculate the average height of the prism block, calculated using the basal rings of the prism and the axial dimension.

.. index:: pair: function; relOrderPrismBlock
.. _doxid-namespacepnt_to_pnt_1aaa5adb93aab9c04dae3b0dd82255113b:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	int relOrderPrismBlock(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, const std::vector<std::vector<int>>& nList, std::vector<int>& outBasal1, std::vector<int>& outBasal2)

Get the relative ordering of a pair of basal rings for a deformed prism/perfect prism.

Outputs a vector of vectors of indices, such that the first vector is for the first basal ring, and the second vector is for the second basal ring. The input neighbour list is with respect to indices, not IDs

.. index:: pair: function; relOrderPrismBlock
.. _doxid-namespacepnt_to_pnt_1ad35ccbeea04f34625242accc1af6d6f8:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	int relOrderPrismBlock(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, std::vector<int>& outBasal1, std::vector<int>& outBasal2)

Get the relative ordering of a pair of basal rings for a deformed prism/perfect prism.

Outputs a vector of vectors of indices, such that the first vector is for the first basal ring, and the second vector is for the second basal ring.

.. index:: pair: function; fillPointSetPrismRing
.. _doxid-namespacepnt_to_pnt_1add7f31e0a4e17beae5c3ded8752e9259:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	Eigen::MatrixXd fillPointSetPrismRing(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basalRing, int startingIndex)

Fill up an Eigen Matrix of a prism basal ring from an input vector of atom indices.

.. index:: pair: function; fillPointSetPrismBlock
.. _doxid-namespacepnt_to_pnt_1ad9d450912979a4c05acb3e1f7829a55f:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	Eigen::MatrixXd fillPointSetPrismBlock(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, int startingIndex)

Fill up an Eigen matrix of a prism block (two basal rings) from input vectors for the basal rings.

.. index:: pair: function; getPointSetCage
.. _doxid-namespacepnt_to_pnt_1a332141ec965df89d231a1def4dc3f5d7:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	Eigen::MatrixXd getPointSetCage(:ref:`ring::strucType<doxid-group__ring_1ga301cfdc88452cfe51bd4f745d223a7e1>` type)

Fills up an eigen matrix point set a reference ring, which is a regular n-gonal polygon, constructed with radius 1 by default; where n is the number of nodes in the ring.

.. index:: pair: function; relOrderHC
.. _doxid-namespacepnt_to_pnt_1ae91f374f024840f0e75795a5b6c5f2ee:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	int relOrderHC(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, const std::vector<std::vector<int>>& nList, std::vector<int>& matchedBasal1, std::vector<int>& matchedBasal2)

Matches the order of the basal rings of an HC or a potential HC.

.. index:: pair: function; relOrderDDC
.. _doxid-namespacepnt_to_pnt_1afa4d01264e49ab06b2828332e961c8f4:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	std::vector<int> relOrderDDC(int index, const std::vector<std::vector<int>>& rings, const std::vector<:ref:`cage::Cage<doxid-structcage_1_1_cage>`>& cageList)

Matches the order of the basal rings of an DDC or a potential HC.

.. index:: pair: function; relOrderDDC
.. _doxid-namespacepnt_to_pnt_1a104a9978a1cec40aeb76f2dbb5afa277:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	std::vector<int> relOrderDDC(const std::vector<int>& equatorial, int index, const std::vector<std::vector<int>>& rings, const std::vector<:ref:`cage::Cage<doxid-structcage_1_1_cage>`>& cageList)

As relOrderDDC, but deriving the connectivity from an explicit equatorial traversal instead of the stored ring row; passing the reversed traversal yields the mirror correspondence for the shape-matching search.

.. index:: pair: function; changeHexCageOrder
.. _doxid-namespacepnt_to_pnt_1a640219c17f532aa11fe3269cd5d3a4e8:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	Eigen::MatrixXd changeHexCageOrder(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& basal1, const std::vector<int>& basal2, int startingIndex = 0)

Fills up an eigen matrix point set using the basal rings basal1 and basal2, changing the order of the point set by filling up from the startingIndex (starting from 0 to 5)

.. index:: pair: function; changeDiaCageOrder
.. _doxid-namespacepnt_to_pnt_1a76f40693a1710a7a2d065a211de8b033:

.. ref-code-block:: cpp
	:class: doxyrest-title-code-block

	Eigen::MatrixXd changeDiaCageOrder(const :ref:`molSys::PointCloud<doxid-structmol_sys_1_1_point_cloud>`<:ref:`molSys::Point<doxid-structmol_sys_1_1_point>`<double>, double>& yCloud, const std::vector<int>& ddcOrder, int startingIndex = 0)

Fills up an eigen matrix point set using information of the equatorial ring and peripheral rings, embedded in a vector, already filled in relOrderDDC.