Scine::MMParametrization::ParametrizationData Struct Reference

This struct holds all objects used inside the MM parametrization algorithm. More...

#include <ParametrizationData.h>

Collaboration diagram for Scine::MMParametrization::ParametrizationData:

Public Attributes
Utils::AtomCollection	fullStructure
	The structure of the entire system to parametrize.
int	numberOfAtoms {0}
	Number of atoms in the full structure.
Eigen::SparseMatrix< double >	fullHessian
	Full Hessian matrix of the system that only contains the subblocks needed for the parametrization procedure.
std::vector< std::unique_ptr < Utils::HessianMatrix > >	vectorOfHessians
	Vector of unique pointers to dense Eigen matrices that represent the Hessians of the subsystems of the parametrization.
std::vector< std::unique_ptr < Utils::AtomCollection > >	vectorOfStructures
	Vector of unique pointers to molecular structures that represent the subsystems of the parametrization.
std::vector< std::unique_ptr < Utils::AtomCollection > >	vectorOfOptimizedStructures
	Vector of unique pointers to molecular structures that represent the optimized subsystems of the parametrization.
std::vector< std::pair< int, int > >	vectorOfChargesAndMultiplicities
	Vector of charge and spin multiplicity pairs for each molecular structure representing a subsystem of the parametrization.
std::vector< std::unique_ptr < Utils::BondOrderCollection > >	vectorOfBondOrderCollections
	Vector of unique pointers to bond order matrices for for each molecular structure representing a subsystem of the parametrization.
std::vector< double >	atomicCharges
	Atomic charges for the whole system calculated from fragments.
std::vector< std::vector < double > >	atomicChargesForEachFragment
	Vector that holds the atomic charges for each fragment of the system.
std::vector< std::list< int > >	listsOfNeighbors
	The connectivity of the system. It is a vector of a list of neighbor atom indices for each atom.
MolecularMechanics::IndexedStructuralTopology	topology
	Topology of the system.
MolecularMechanics::SfamParameters	parameters
	The SFAM molecular mechanics parameters.
MolecularMechanics::AtomTypesHolder	atomTypes
	The atom types.
std::vector< std::pair< int, int > >	vectorOfHessianSubmatrixIndices
	Vector that holds the pairs of atom indices corresponding to the partial Hessian blocks relevant for the current parameter's optimization.
std::vector< std::string >	vectorOfAtomTypesForParameter
	Vector that holds the atom types of the parameter currently optimized.
Utils::BondOrderCollection	bondOrders
	A bond order matrix of the full system.
std::map< int, int >	formalCharges
	A map containing the indices of atoms and their formal charge in the full system.
std::map< int, int >	unpairedElectrons
	A map containing the indices of atoms and the number of unpaired electrons that can be assigned to that atom.
std::map< int, std::string >	pHSensitiveSites
	A map containing the indices of atoms of which the protonation state can be changed and the corresponding type of amino acid.
std::vector< bool >	siteIspHSensitive
	A vector that indicates whether a fragment is pH sensitive.
std::vector< std::vector< int > >	atomIndexMapping
	Vector of all fragments containing a vector of indices that correspond to the indices of the atoms inside the fragment in the full system.
std::vector< std::vector< int > >	constrainedAtoms
	Contains the indices of the atoms to be constrained during a geometry optimization for each fragment.
std::vector< int >	superfluousFragments
	A vector of fragment indices which are superfluous and for which the reference data does not need to be calculated.

Detailed Description

This struct holds all objects used inside the MM parametrization algorithm.

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The documentation for this struct was generated from the following file:

• src/Swoose/Swoose/MMParametrization/ParametrizationData.h