Scine::Swoose
2.1.0
This is the SCINE module Swoose.
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This struct holds all objects used inside the MM parametrization algorithm. More...
#include <ParametrizationData.h>
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. | |
This struct holds all objects used inside the MM parametrization algorithm.